data_mmcif_pdbx_vrpt.dic _datablock.id mmcif_pdbx_vrpt.dic _datablock.description "wwPDB Validation Report extension dictionary" # _dictionary.title mmcif_pdbx_vrpt.dic _dictionary.datablock_id mmcif_pdbx_vrpt.dic _dictionary.version 0.064 # loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.060 2021-04-09 "Preliminary translated version" 0.061 2021-04-20 ; Changes (ep): + Cleanup descriptions and types of many categories and attributes ; 0.062 2021-04-28 ; Changes (ep): + Extend enumerations for _pdbx_vrpt_dihedralangle_violation_model.ang_rest_type, _pdbx_vrpt_dihedralangle_ensemble_violation.ang_rest_type, _pdbx_vrpt_dihedralangle_violations_summary.restraint_type ; 0.063 2021-06-03 ; Changes (ep): + Add "DisulfideBond" and "HydrogenBond" to _pdbx_vrpt_distance_violation_summary enumeration ; 0.064 2022-07-20 ; Changes (ep): + Addition of Q-score data Add _pdbx_vrpt_summary_em.Q_score Add pdbx_vrpt_summary_entity_fit_to_map category Mark _pdbx_vrpt_summary_entity_geometry.average_residue_inclusion as deprecated and replaced by _pdbx_vrpt_summary_entity_fit_to_map.average_residue_inclusion Add pdbx_vrpt_model_instance_map_fitting category Mark pdbx_vrpt_model_instance_density as deprecated and replaced by pdbx_vrpt_model_instance_map_fitting Mark _pdbx_vrpt_model_instance_geometry.residue_inclusion deprecated and replaced by _pdbx_vrpt_model_instance_map_fitting.residue_inclusion ; # loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description inclusive_group . " The parent category group containing all of the data categories in the macromolecular dictionary." validation_report_group inclusive_group " Categories that reflect data from wwPDB validation calculation" audit_group inclusive_group ; Categories that describe dictionary maintenance and identification. ; # loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char ;[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words ..." ucode uchar ;[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* ; " code item types/single words (case insensitive) ..." line char ;[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " char item types / multi-word items ..." text char ;[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " text item types / multi-line text ..." float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? ; float item types are the subset of numbers that are the floating numbers. ; int numb "[+-]?[0-9]+" ; int item types are the subset of numbers that are the negative or positive integers. ; atcode char ;[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* ; " Character data type for atom names ..." yyyy-mm-dd:hh:mm char "[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9](-[0-9]?[0-9])?(:[0-9]?[0-9]:[0-9][0-9])?" ; Standard format for CIF dates with optional time stamp. ; yyyy-mm-dd char "[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]" ; Standard format for CIF dates. ; alphanum-csv char "[A-Za-z0-9]+(,[A-Za-z0-9]+){0,}" " comma separated alpha numeric codes (single words) (case sensitive) ..." # loop_ _item_units_list.code _item_units_list.detail angstroms "Angstroms (metres * 10^(-10)^)" degrees "degrees (of arc)" angstroms_squared "Angstroms squared (metres * 10^(-10)^)^2^" # loop_ _pdbx_item_linked_group.category_id _pdbx_item_linked_group.link_group_id _pdbx_item_linked_group.label _pdbx_item_linked_group.context _pdbx_item_linked_group.condition_id pdbx_vrpt_asym 1 pdbx_vrpt_asym:pdbx_vrpt_entity:1 . . pdbx_vrpt_instance_clashes 1 pdbx_vrpt_instance_clashes:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_intra_angle_outliers 1 pdbx_vrpt_instance_intra_angle_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_intra_bond_outliers 1 pdbx_vrpt_instance_intra_bond_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_intra_plane_outliers 1 pdbx_vrpt_instance_intra_plane_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_mogul_bond_outliers 1 pdbx_vrpt_instance_mogul_bond_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_mogul_angle_outliers 1 pdbx_vrpt_instance_mogul_angle_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_mogul_ring_outliers 1 pdbx_vrpt_instance_mogul_ring_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_mogul_torsion_outliers 1 pdbx_vrpt_instance_mogul_torsion_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_symm_clashes 1 pdbx_vrpt_instance_symm_clashes:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_instance_stereo_outliers 1 pdbx_vrpt_instance_stereo_outliers:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_model_instance 1 pdbx_vrpt_model_instance:pdbx_vrpt_asym:1 . . pdbx_vrpt_model_instance_geometry 1 pdbx_vrpt_model_instance_geometry:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_model_instance_density 1 pdbx_vrpt_model_instance_density:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_model_instance_map_fitting 1 pdbx_vrpt_model_instance_map_fitting:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_most_violated_dihedralangle_restraints 1 "_pdbx_vrpt_most_violated_dihedralangle_restraints:pdbx_vrpt_asym:1" . . pdbx_vrpt_most_violated_dihedralangle_restraints 2 "_pdbx_vrpt_most_violated_dihedralangle_restraints:pdbx_vrpt_asym:2" . . pdbx_vrpt_most_violated_dihedralangle_restraints 3 "_pdbx_vrpt_most_violated_dihedralangle_restraints:pdbx_vrpt_asym:3" . . pdbx_vrpt_most_violated_dihedralangle_restraints 4 "_pdbx_vrpt_most_violated_dihedralangle_restraints:pdbx_vrpt_asym:4" . . pdbx_vrpt_most_violated_distance_restraints 1 "_pdbx_vrpt_most_violated_distance_restraints:pdbx_vrpt_asym:1" . . pdbx_vrpt_most_violated_distance_restraints 2 "_pdbx_vrpt_most_violated_distance_restraints:pdbx_vrpt_asym:2" . . pdbx_vrpt_percentile_conditions 1 pdbx_vrpt_percentile_conditions:pdbx_vrpt_percentile_list:1 . . pdbx_vrpt_percentile_conditions 2 pdbx_vrpt_percentile_conditions:pdbx_vrpt_percentile_type:2 . . pdbx_vrpt_percentile_entity_view 1 pdbx_vrpt_percentile_entity_view:pdbx_vrpt_percentile_conditions:1 . . pdbx_vrpt_percentile_entity_view 2 pdbx_vrpt_percentile_entity_view:pdbx_vrpt_percentile_type:2 . . pdbx_vrpt_percentile_entity_view 3 pdbx_vrpt_percentile_entity_view:pdbx_vrpt_entity:3 . . pdbx_vrpt_em_2d_graph_data 1 pdbx_vrpt_em_2d_graph_data:pdbx_vrpt_em_2d_graph_info:1 . . pdbx_vrpt_em_graph_atom_inclusion 1 pdbx_vrpt_em_graph_atom_inclusion:pdbx_vrpt_em_2d_graph_info:1 . . pdbx_vrpt_em_graph_fsc_curve 1 pdbx_vrpt_em_graph_fsc_curve:pdbx_vrpt_em_2d_graph_info:1 . . pdbx_vrpt_em_graph_fsc_indicator_curve 1 pdbx_vrpt_em_graph_fsc_indicator_curve:pdbx_vrpt_em_2d_graph_info:1 . . pdbx_vrpt_summary_entity_geometry 1 pdbx_vrpt_summary_entity_geometry:pdbx_vrpt_asym:1 . . pdbx_vrpt_summary_entity_fit_to_map 1 pdbx_vrpt_summary_entity_fit_to_map:pdbx_vrpt_asym:1 . . pdbx_vrpt_violated_dihedralangle_restraints 1 pdbx_vrpt_violated_dihedralangle_restraints:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_violated_dihedralangle_restraints 2 pdbx_vrpt_violated_dihedralangle_restraints:pdbx_vrpt_model_instance:2 . . pdbx_vrpt_violated_dihedralangle_restraints 3 pdbx_vrpt_violated_dihedralangle_restraints:pdbx_vrpt_model_instance:3 . . pdbx_vrpt_violated_dihedralangle_restraints 4 pdbx_vrpt_violated_dihedralangle_restraints:pdbx_vrpt_model_instance:4 . . pdbx_vrpt_violated_distance_restraints 1 pdbx_vrpt_violated_distance_restraints:pdbx_vrpt_model_instance:1 . . pdbx_vrpt_violated_distance_restraints 2 pdbx_vrpt_violated_distance_restraints:pdbx_vrpt_model_instance:2 . . # loop_ _pdbx_item_linked_group_list.child_category_id _pdbx_item_linked_group_list.link_group_id _pdbx_item_linked_group_list.child_name _pdbx_item_linked_group_list.parent_name _pdbx_item_linked_group_list.parent_category_id pdbx_vrpt_asym 1 "_pdbx_vrpt_asym.entity_id" "_pdbx_vrpt_entity.id" pdbx_vrpt_entity pdbx_vrpt_instance_clashes 1 "_pdbx_vrpt_instance_clashes.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_mogul_bond_outliers 1 "_pdbx_vrpt_instance_mogul_bond_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_mogul_angle_outliers 1 "_pdbx_vrpt_instance_mogul_angle_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_mogul_ring_outliers 1 "_pdbx_vrpt_instance_mogul_ring_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_mogul_torsion_outliers 1 "_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_intra_angle_outliers 1 "_pdbx_vrpt_instance_intra_angle_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_intra_bond_outliers 1 "_pdbx_vrpt_instance_intra_bond_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_intra_plane_outliers 1 "_pdbx_vrpt_instance_intra_plane_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_stereo_outliers 1 "_pdbx_vrpt_instance_stereo_outliers.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_instance_symm_clashes 1 "_pdbx_vrpt_instance_symm_clashes.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_model_instance 1 "_pdbx_vrpt_model_instance.entity_id" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_model_instance 1 "_pdbx_vrpt_model_instance.label_asym_id" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_model_instance_geometry 1 "_pdbx_vrpt_model_instance_geometry.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_model_instance_density 1 "_pdbx_vrpt_model_instance_density.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_model_instance_map_fitting 1 "_pdbx_vrpt_model_instance_map_fitting.instance_id" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_most_violated_dihedralangle_restraints 1 "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_1" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 1 "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_1" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 2 "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_2" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 2 "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_2" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 3 "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_3" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 3 "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_3" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 4 "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_4" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_dihedralangle_restraints 4 "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_4" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_distance_restraints 1 "_pdbx_vrpt_most_violated_distance_restraints.said_1" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_distance_restraints 1 "_pdbx_vrpt_most_violated_distance_restraints.ent_1" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_distance_restraints 2 "_pdbx_vrpt_most_violated_distance_restraints.said_2" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_most_violated_distance_restraints 2 "_pdbx_vrpt_most_violated_distance_restraints.ent_2" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_percentile_conditions 1 "_pdbx_vrpt_percentile_conditions.percentile_list_id" "_pdbx_vrpt_percentile_list.id" pdbx_vrpt_percentile_list pdbx_vrpt_percentile_conditions 2 "_pdbx_vrpt_percentile_conditions.type_id" "_pdbx_vrpt_percentile_type.id" pdbx_vrpt_percentile_type pdbx_vrpt_percentile_entity_view 1 "_pdbx_vrpt_percentile_entity_view.conditions_id" "_pdbx_vrpt_percentile_conditions.id" pdbx_vrpt_percentile_conditions pdbx_vrpt_percentile_entity_view 2 "_pdbx_vrpt_percentile_entity_view.type_id" "_pdbx_vrpt_percentile_type.id" pdbx_vrpt_percentile_type pdbx_vrpt_percentile_entity_view 3 "_pdbx_vrpt_percentile_entity_view.entity_id" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_percentile_entity_view 3 "_pdbx_vrpt_percentile_entity_view.label_asym_id" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_em_2d_graph_data 1 "_pdbx_vrpt_em_2d_graph_data.graph_data_id" "_pdbx_vrpt_em_2d_graph_info.graph_data_id" pdbx_vrpt_em_2d_graph_info pdbx_vrpt_em_graph_atom_inclusion 1 "_pdbx_vrpt_em_graph_atom_inclusion.graph_id" "_pdbx_vrpt_em_2d_graph_info.graph_id" pdbx_vrpt_em_2d_graph_info pdbx_vrpt_em_graph_fsc_curve 1 "_pdbx_vrpt_em_graph_fsc_curve.graph_id" "_pdbx_vrpt_em_2d_graph_info.graph_id" pdbx_vrpt_em_2d_graph_info pdbx_vrpt_em_graph_fsc_indicator_curve 1 "_pdbx_vrpt_em_graph_fsc_indicator_curve.graph_id" "_pdbx_vrpt_em_2d_graph_info.graph_id" pdbx_vrpt_em_2d_graph_info pdbx_vrpt_summary_entity_geometry 1 "_pdbx_vrpt_summary_entity_geometry.entity_id" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_summary_entity_geometry 1 "_pdbx_vrpt_summary_entity_geometry.label_asym_id" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_summary_entity_fit_to_map 1 "_pdbx_vrpt_summary_entity_fit_to_map.entity_id" "_pdbx_vrpt_asym.entity_id" pdbx_vrpt_asym pdbx_vrpt_summary_entity_fit_to_map 1 "_pdbx_vrpt_summary_entity_fit_to_map.label_asym_id" "_pdbx_vrpt_asym.label_asym_id" pdbx_vrpt_asym pdbx_vrpt_violated_dihedralangle_restraints 1 "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_1" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_violated_dihedralangle_restraints 2 "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_2" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_violated_dihedralangle_restraints 3 "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_3" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_violated_dihedralangle_restraints 4 "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_4" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_violated_distance_restraints 1 "_pdbx_vrpt_violated_distance_restraints.instance_id_1" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance pdbx_vrpt_violated_distance_restraints 2 "_pdbx_vrpt_violated_distance_restraints.instance_id_2" "_pdbx_vrpt_model_instance.id" pdbx_vrpt_model_instance ## save_pdbx_vrpt_summary _category.id pdbx_vrpt_summary _category.description ; pdbx_vrpt_summary contains most information that has a single value for the structure analyzed and in the run. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary.entry_id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary.entry_id _item_description.description "pdbx_vrpt_summary accesion code (PDB, EMDB or BMRB)" # _item.name "_pdbx_vrpt_summary.entry_id" _item.category_id pdbx_vrpt_summary _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_summary.PDB_deposition_date _item_description.description ; Date in yyyy-mm-dd format when structure was deposited to the PDB. Obtained from model file _pdbx_database_status.recvd_initial_deposition_date. ; # _item.name "_pdbx_vrpt_summary.PDB_deposition_date" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code yyyy-mm-dd # _item_aliases.alias_name "_Entry.PDB-deposition-date" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.PDB_revision_number _item_description.description ; The highest number that appears in mmCIF model item _pdbx_audit_revision_history.ordinal. ; # _item.name "_pdbx_vrpt_summary.PDB_revision_number" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.PDB-revision-number" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.PDB_revision_date _item_description.description ; Date in yyyy-mm-dd format when the structure was last revised by PDB. Obtained from the mmCIF model file _pdbx_audit_revision_history.revision_date ; # _item.name "_pdbx_vrpt_summary.PDB_revision_date" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code yyyy-mm-dd # _item_aliases.alias_name "_Entry.PDB-revision-date" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.EMDB_deposition_date _item_description.description ; Date in yyyy-mm-dd format when map was deposited to the EMDB. ; # _item.name "_pdbx_vrpt_summary.EMDB_deposition_date" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code yyyy-mm-dd # _item_aliases.alias_name "_Entry.EMDB-deposition-date" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.report_creation_date _item_description.description ; The date, time and time-zone that the validation report was created. The string will be formatted like yyyy-mm-dd:hh:mm in GMT time. ; # _item.name "_pdbx_vrpt_summary.report_creation_date" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code yyyy-mm-dd:hh:mm # _item_aliases.alias_name "_Entry.XMLcreationDate" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.attempted_validation_steps _item_description.description ; The steps that were attempted by the validation pipeline software. A step typically involves running a 3rd party validation tool, for instance "mogul" Each step will be enumerated in _pdbx_vrpt_software category. ; # _item.name "_pdbx_vrpt_summary.attempted_validation_steps" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_Entry.attemptedValidationSteps" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.ligands_for_buster_report _item_description.description ; A flag indicating if there are ligands in the model used for detailed Buster analysis. ; # _item.name "_pdbx_vrpt_summary.ligands_for_buster_report" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_Entry.ligands-for-buster-report" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save__pdbx_vrpt_summary.restypes_notchecked_for_bond_angle_geometry _item_description.description ; This is a comma separated list of the residue types whose bond lengths and bond angles have not been checked against "standard geometry" using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996) ; # _item.name "_pdbx_vrpt_summary.restypes_notchecked_for_bond_angle_geometry" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code alphanum-csv # _item_aliases.alias_name "_Entry.RestypesNotcheckedForBondAngleGeometry" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary.RNA_suiteness _item_description.description ; The MolProbity conformer-match quality parameter for RNA structures. Low values are worse. Specific to structures that contain RNA polymers. ; # _item.name "_pdbx_vrpt_summary.RNA_suiteness" _item.category_id pdbx_vrpt_summary _item.mandatory_code no # _item_type.code float # _item_examples.case 0.89 # _item_aliases.alias_name "_Entry.RNAsuiteness" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_model_list _category.id pdbx_vrpt_model_list _category.description ; A "pdbx_vrpt_model_list" is one of the structures that are described by a PDB entry. Most NMR entries as well as some entries determined by other experimental techniques, contain an ensemble of models (structures). For most NMR entries, the models should be chemically identical - i.e., contain the exact same atoms, and will only differ in the cartesian coordinates of constituent atoms. For older NMR entries, and for non-NMR entries, this is not enforced. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_model_list.PDB_model_num" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_model_list.PDB_model_num _item_description.description ; The integer identifier of a Model. ; # _item.name "_pdbx_vrpt_model_list.PDB_model_num" _item.category_id pdbx_vrpt_model_list _item.mandatory_code yes # _item_type.code int # _item_aliases.alias_name "_Model.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_list.nmrclust_cluster_id _item_description.description ; NMRClust software is used to compare models in NMR entries. It clusters similar models. Each model in an NMR entry, therefore, can have an "nmrclust_cluster_id" indicating to which cluster the given model belongs. This value is either an integer or the string "outlier" if the model is sufficiently different from other models in the ensemble. ; # _item.name "_pdbx_vrpt_model_list.nmrclust_cluster_id" _item.category_id pdbx_vrpt_model_list _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_Model.nmrclust_cluster_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_list.nmrclust_representative _item_description.description ; A flag indicating if the given model is also the representative model of the cluster to which it belongs. ; # _item.name "_pdbx_vrpt_model_list.nmrclust_representative" _item.category_id pdbx_vrpt_model_list _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail True . False . # _item_aliases.alias_name "_Model.nmrclust_representative" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_model_instance _category.id pdbx_vrpt_model_instance _category.description ; This category contains both an id that identifies an individual occurrence of a residue as well as providing counting summaries about the residue. This id is used other categories. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_model_instance.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_model_instance.id _item_description.description "Uniquely identifies each instance of the model." # _item.name "_pdbx_vrpt_model_instance.id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_model_instance.auth_asym_id _item_description.description ; The auth_asym_id identifier for the residue is the same as in the model mmCIF item _atom_site.auth_asym_id. ; # _item.name "_pdbx_vrpt_model_instance.auth_asym_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code code # _item_examples.case A # _item_aliases.alias_name "_ModelledSubgroup.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.auth_seq_id _item_description.description ; The authors residue number for a residue. This is obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_model_instance.auth_seq_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # _item_examples.case 8 # _item_aliases.alias_name "_ModelledSubgroup.resnum" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.label_comp_id _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. This is the same and the model mmCIF _atom_site.auth_comp_id. ; # _item.name "_pdbx_vrpt_model_instance.label_comp_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code ucode # _item_examples.case GLY # _item_aliases.alias_name "_ModelledSubgroup.resname" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.PDB_model_num _item_description.description ; The number corresponding to _atom_site.pdbx_PDB_model_num. If the structure does not have multiple models then PDB_model_num will be "1". ; # _item.name "_pdbx_vrpt_model_instance.PDB_model_num" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # _item_examples.case 1 # _item_aliases.alias_name "_ModelledSubgroup.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.label_alt_id _item_description.description ; This attribute will be set if the pdbx_vrpt_model_instance has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example label_alt_id="A" Obtained from _atom_site.label_alt_id ; # _item.name "_pdbx_vrpt_model_instance.label_alt_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledSubgroup.altcode" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.PDB_ins_code _item_description.description ; Insertion code for residue from _atom_site.pdbx_PDB_ins_code ; # _item.name "_pdbx_vrpt_model_instance.PDB_ins_code" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledSubgroup.icode" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.entity_id _item_description.description ; The entity id for the residue or chain. This is a pointer to _pdbx_vrpt_entity.id ; # _item.name "_pdbx_vrpt_model_instance.entity_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledSubgroup.ent" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_linked.child_name "_pdbx_vrpt_model_instance.entity_id" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # save_ # save__pdbx_vrpt_model_instance.label_asym_id _item_description.description ; The _atom_site.label_asym_id label for the residue. Normally this is the same as the author chain name. ; # _item.name "_pdbx_vrpt_model_instance.label_asym_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_model_instance.label_asym_id" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_ModelledSubgroup.said" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.label_seq_id _item_description.description ; From the modell mmCIF item _atom_site.label_seq_id. This is an internal sequence number within a polymer chain or "." for non-polymeric residue. ; # _item.name "_pdbx_vrpt_model_instance.label_seq_id" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.seq" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance.count_angle_outliers _item_description.description " Count of number of atoms with angle outliers for this instance" # _item.name "_pdbx_vrpt_model_instance.count_angle_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_bond_outliers _item_description.description " Count of number of atoms with bond outliers in this instance" # _item.name "_pdbx_vrpt_model_instance.count_bond_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_symm_clashes _item_description.description " Count of number of symmetry related clashes for this instance." # _item.name "_pdbx_vrpt_model_instance.count_symm_clashes" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_chiral_outliers _item_description.description " Count of number of chiral outliers for instance." # _item.name "_pdbx_vrpt_model_instance.count_chiral_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_plane_outliers _item_description.description " Count of number of planar outliers for this instance." # _item.name "_pdbx_vrpt_model_instance.count_plane_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_mogul_angle_outliers _item_description.description " Count of number of angle outliers as reported by MOGUL for this instance." # _item.name "_pdbx_vrpt_model_instance.count_mogul_angle_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_mogul_bond_outliers _item_description.description " Count of number of bond outliers as reported by MOGUL for this residue." # _item.name "_pdbx_vrpt_model_instance.count_mogul_bond_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_mogul_torsion_outliers _item_description.description " Count of number torsion angle outliers as reported by MOGUL for this instance." # _item.name "_pdbx_vrpt_model_instance.count_mogul_torsion_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_mogul_ring_outliers _item_description.description " Count of number of atoms with ring outliers as reported by MOGUL for this instance." # _item.name "_pdbx_vrpt_model_instance.count_mogul_ring_outliers" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.count_clashes _item_description.description " Count of number of atoms a with a pdbx_vrpt_instance_clashes for this instance." # _item.name "_pdbx_vrpt_model_instance.count_clashes" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_model_instance.ligand_of_interest _item_description.description " A flag to indicate if this instance is a ligand of interest." # _item.name "_pdbx_vrpt_model_instance.ligand_of_interest" _item.category_id pdbx_vrpt_model_instance _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save_pdbx_vrpt_cyrange_domain _category.id pdbx_vrpt_cyrange_domain _category.description ; Cyrange software is used to identify well-defined regions of protein structures in NMR ensembles. The well-defined region may contain more than one well-defined core or domain, which are not well defined with respect to each other. Each of these individual cores/domains is described as a "cyrange_domain". ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_cyrange_domain.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_cyrange_domain.ordinal _item_description.description " Uniquely identifies each domain." # _item.name "_pdbx_vrpt_cyrange_domain.ordinal" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_cyrange_domain.domain _item_description.description ; Identifier of the well-defined core ; # _item.name "_pdbx_vrpt_cyrange_domain.domain" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_cyrange_domain.domain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.number_of_gaps _item_description.description ; Number of omissions from the contiguous protein _atom_site.auth_asym_id within the individual well-defined core (domain). ; # _item.name "_pdbx_vrpt_cyrange_domain.number_of_gaps" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_cyrange_domain.number_of_gaps" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.number_of_residues _item_description.description ; Number of residues composing the individual well-defined core (domain). ; # _item.name "_pdbx_vrpt_cyrange_domain.number_of_residues" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_cyrange_domain.number_of_residues" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.percentage_of_core _item_description.description ; What fraction the individual core contributes to the total well-defined portion of the protein. ; # _item.name "_pdbx_vrpt_cyrange_domain.percentage_of_core" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_cyrange_domain.percentage_of_core" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.rmsd _item_description.description ; Average pairwise backbone RMSD of the individual well-defined core (domain) over the ensemble. ; # _item.name "_pdbx_vrpt_cyrange_domain.rmsd" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_cyrange_domain.rmsd" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.medoid_model _item_description.description ; For each Cyrange well-defined core ("cyrange_domain") the id of the model which is most similar to other models as measured by pairwise RMSDs over the domain. For the whole entry, the medoid model of the largest core is taken as an overall representative of the structure. ; # _item.name "_pdbx_vrpt_cyrange_domain.medoid_model" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_cyrange_domain.medoid_model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.medoid_rmsd _item_description.description ; Average RMSD between the medoid model and other members of the ensemble. ; # _item.name "_pdbx_vrpt_cyrange_domain.medoid_rmsd" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_cyrange_domain.medoid_rmsd" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_cyrange_domain.residue_string _item_description.description ; Simplified description of the residue composition of the individual well-defined core (domain). ; # _item.name "_pdbx_vrpt_cyrange_domain.residue_string" _item.category_id pdbx_vrpt_cyrange_domain _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_cyrange_domain.residue_string" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_summary_entity_fit_to_map _category.id pdbx_vrpt_summary_entity_fit_to_map _category.description ; This category provides summary of the fit of each entity within each auth_asym_id and each model to a map ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary_entity_fit_to_map.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.ordinal _item_description.description "Uniquely identifies each instance of this summary." # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.ordinal" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.PDB_model_num _item_description.description ; The unique model number from _atom_site.pdbx_PDB_model_num. ; # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.PDB_model_num" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.entity_id _item_description.description ; The entity id for the residue or chain. ; # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.entity_id" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_summary_entity_fit_to_map.entity_id" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.label_asym_id _item_description.description ; The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.label_asym_id" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_summary_entity_fit_to_map.label_asym_id" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.auth_asym_id _item_description.description ; The _atom_site.auth_asym_id identifier for the instance. ; # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.auth_asym_id" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code no # _item_type.code code # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.Q_score _item_description.description ; The calculated average Q-score. ; # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.Q_score" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_summary_entity_fit_to_map.average_residue_inclusion _item_description.description ; The average of the residue inclusions for all residues in this instance ; # _item.name "_pdbx_vrpt_summary_entity_fit_to_map.average_residue_inclusion" _item.category_id pdbx_vrpt_summary_entity_fit_to_map _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledEntityInstance.average_residue_inclusion" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_related.related_name "_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion" _item_related.function_code replaces # save_ # save_pdbx_vrpt_summary_entity_geometry _category.id pdbx_vrpt_summary_entity_geometry _category.description ; This category provides summary geometry information of each entity within each auth_asym_id and each model. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary_entity_geometry.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary_entity_geometry.ordinal _item_description.description "Uniquely identifies each instance of this summary." # _item.name "_pdbx_vrpt_summary_entity_geometry.ordinal" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_summary_entity_geometry.PDB_model_num _item_description.description ; The unique model number from _atom_site.pdbx_PDB_model_num. ; # _item.name "_pdbx_vrpt_summary_entity_geometry.PDB_model_num" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledEntityInstance.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.entity_id _item_description.description ; The entity id for the residue or chain. ; # _item.name "_pdbx_vrpt_summary_entity_geometry.entity_id" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledEntityInstance.ent" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_linked.child_name "_pdbx_vrpt_summary_entity_geometry.entity_id" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # save_ # save__pdbx_vrpt_summary_entity_geometry.label_asym_id _item_description.description ; The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_summary_entity_geometry.label_asym_id" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_summary_entity_geometry.label_asym_id" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_ModelledEntityInstance.said" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.auth_asym_id _item_description.description ; The _atom_site.auth_asym_id identifier for the instance. ; # _item.name "_pdbx_vrpt_summary_entity_geometry.auth_asym_id" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledEntityInstance.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.angles_RMSZ _item_description.description ; The overall root mean square of the Z-score for deviations of bond angles in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_summary_entity_geometry.angles_RMSZ" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledEntityInstance.angles_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.bonds_RMSZ _item_description.description ; The overall root mean square of the Z-score for deviations of bond lengths in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledEntityInstance.bonds_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ _item_description.description ; The number of bond lengths compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledEntityInstance.num_bonds_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ _item_description.description ; The number of bond angles compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledEntityInstance.num_angles_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_entity_geometry.average_residue_inclusion _item_description.description ; The average of the residue inclusions for all residues in this instance ; # _item.name "_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion" _item.category_id pdbx_vrpt_summary_entity_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledEntityInstance.average_residue_inclusion" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _pdbx_item_context.type WWPDB_DEPRECATED _pdbx_item_context.item_name "_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion" # save_ # save_pdbx_vrpt_chemical_shift_list _category.id pdbx_vrpt_chemical_shift_list _category.description ; NMR entries are normally linked to one or more assigned chemical shift lists. A typical reason for containing multiple chemical shift lists would be differing experimental conditions or samples. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_chemical_shift_list.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_chemical_shift_list.ordinal _item_description.description "Uniquely identifies each chemical shift." # _item.name "_pdbx_vrpt_chemical_shift_list.ordinal" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_chemical_shift_list.file_id _item_description.description ; An identifier of a chemical shifts file. ; # _item.name "_pdbx_vrpt_chemical_shift_list.file_id" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.file_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.file_name _item_description.description ; The name of the chemical shifts file supplied to the validation pipeline. ; # _item.name "_pdbx_vrpt_chemical_shift_list.file_name" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_chemical_shift_list.file_name" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.block_name _item_description.description ; Label of the section that contains chemical shifts. ; # _item.name "_pdbx_vrpt_chemical_shift_list.block_name" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_chemical_shift_list.block_name" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.list_id _item_description.description ; Identifier of the chemical shift list in the file. ; # _item.name "_pdbx_vrpt_chemical_shift_list.list_id" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_chemical_shift_list.list_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.type _item_description.description ; A flag indicating if the chemical shift list contains all the required data items i.e., NMR-STAR 3.1 tags ("full") or if any data items are missing ("partial"). ; # _item.name "_pdbx_vrpt_chemical_shift_list.type" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_chemical_shift_list.type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.number_of_errors_while_mapping _item_description.description ; Number of chemical shifts that could not be mapped to structure. ; # _item.name "_pdbx_vrpt_chemical_shift_list.number_of_errors_while_mapping" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.number_of_errors_while_mapping" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.number_of_warnings_while_mapping _item_description.description ; Currently not used. Reserved for ambiguous mappings. ; # _item.name "_pdbx_vrpt_chemical_shift_list.number_of_warnings_while_mapping" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.number_of_warnings_while_mapping" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.number_of_mapped_shifts _item_description.description ; Number of chemical shifts successfully mapped to the structure. ; # _item.name "_pdbx_vrpt_chemical_shift_list.number_of_mapped_shifts" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.number_of_mapped_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.number_of_parsed_shifts _item_description.description ; Number of chemical shifts successfully parsed. ; # _item.name "_pdbx_vrpt_chemical_shift_list.number_of_parsed_shifts" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.number_of_parsed_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.total_number_of_shifts _item_description.description ; Total number of records in the chemical shift list. ; # _item.name "_pdbx_vrpt_chemical_shift_list.total_number_of_shifts" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.total_number_of_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_list.number_of_unparsed_shifts _item_description.description ; Number of chemical shifts that could not be parsed. ; # _item.name "_pdbx_vrpt_chemical_shift_list.number_of_unparsed_shifts" _item.category_id pdbx_vrpt_chemical_shift_list _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_list.number_of_unparsed_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_unmapped_chemical_shift _category.id pdbx_vrpt_unmapped_chemical_shift _category.description ; Each assigned chemical shift should map to one or more nuclei of the studied biological macromolecule or complex. In preliminary reports and for some older entries, this mapping is not always accurate and some chemical shifts can therefore be "unmapped". It implies, that the chemical shift was parsed, but not mapped to any nucleus expected from the molecular description. It may result for instance from typos or from an incomplete molecular description. Details are given in the free text "diagnostic" attribute. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_unmapped_chemical_shift.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_unmapped_chemical_shift.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_unmapped_chemical_shift.ordinal" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_unmapped_chemical_shift.auth_asym_id _item_description.description ; The auth_asym_id identifier for the residue or auth_asym_id obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: auth_asym_id="A" ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.auth_asym_id" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_unmapped_chemical_shift.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.rescode _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.rescode" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code ucode # _item_examples.case GLY # _item_aliases.alias_name "_unmapped_chemical_shift.rescode" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.auth_seq_id _item_description.description ; The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.auth_seq_id" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_unmapped_chemical_shift.resnum" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.label_atom_id" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_unmapped_chemical_shift.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.value _item_description.description ; Value in ppm of a chemical shift ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.value" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_unmapped_chemical_shift.value" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.error _item_description.description ; Uncertainty on a chemical shift value, if known. ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.error" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_unmapped_chemical_shift.error" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.ambiguity _item_description.description ; Ambiguity of the chemical shift assignment as per NMR-STAR V3.1 dictionary. ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.ambiguity" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_unmapped_chemical_shift.ambiguity" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unmapped_chemical_shift.diagnostic _item_description.description ; Diagnostic text message when a chemical shift was not parsed or not mapped to structure. ; # _item.name "_pdbx_vrpt_unmapped_chemical_shift.diagnostic" _item.category_id pdbx_vrpt_unmapped_chemical_shift _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_unmapped_chemical_shift.diagnostic" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_unparsed_chemical_shift _category.id pdbx_vrpt_unparsed_chemical_shift _category.description ; An unparsed chemical shift implies that some expected values were missing or did not conform to expected format: e.g., non-numeric value of a shift measurement or missing chain/entity identifier. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_unparsed_chemical_shift.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_unparsed_chemical_shift.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_unparsed_chemical_shift.ordinal" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_unparsed_chemical_shift.id _item_description.description ; ID of the chemical shift as parsed in the chemical shifts file. ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.id" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_unparsed_chemical_shift.id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.auth_asym_id _item_description.description ; The auth_asym_id identifier for the residue obtained from mmCIF item _atom_site.auth_asym_id. ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.auth_asym_id" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_unparsed_chemical_shift.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.rescode _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.rescode" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code ucode # _item_examples.case GLY # _item_aliases.alias_name "_unparsed_chemical_shift.rescode" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.auth_seq_id _item_description.description ; The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.auth_seq_id" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_unparsed_chemical_shift.resnum" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.label_atom_id" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_unparsed_chemical_shift.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.value _item_description.description ; Value in ppm of a chemical shift ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.value" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_unparsed_chemical_shift.value" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.error _item_description.description ; Uncertainty on a chemical shift value - usually not available ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.error" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_unparsed_chemical_shift.error" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.ambiguity _item_description.description ; Ambiguity of the chemical shift assignment as per NMR-STAR V3.1 dictionary. ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.ambiguity" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_unparsed_chemical_shift.ambiguity" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_unparsed_chemical_shift.diagnostic _item_description.description ; Diagnostic text message when a chemical shift was not parsed or not mapped to structure. ; # _item.name "_pdbx_vrpt_unparsed_chemical_shift.diagnostic" _item.category_id pdbx_vrpt_unparsed_chemical_shift _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_unparsed_chemical_shift.diagnostic" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_missing_nmrstar_tags _category.id pdbx_vrpt_missing_nmrstar_tags _category.description ; The chemical shifts must be supplied in NMR-STAR 3.1 format. In order for the shifts to be mapped to the molecular structure, certain values (data items or tags) must be provided. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_missing_nmrstar_tags.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_missing_nmrstar_tags.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_missing_nmrstar_tags.ordinal" _item.category_id pdbx_vrpt_missing_nmrstar_tags _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_missing_nmrstar_tags.nmrstar_tag_description _item_description.description ; Description of the missing but required data item (tag). ; # _item.name "_pdbx_vrpt_missing_nmrstar_tags.nmrstar_tag_description" _item.category_id pdbx_vrpt_missing_nmrstar_tags _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_missing_nmrstar_tag.nmrstar_tag_description" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_missing_nmrstar_tags.nmrstar_tag _item_description.description ; The name of the missing data item (tag). ; # _item.name "_pdbx_vrpt_missing_nmrstar_tags.nmrstar_tag" _item.category_id pdbx_vrpt_missing_nmrstar_tags _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_missing_nmrstar_tag.nmrstar_tag" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_random_coil_index _category.id pdbx_vrpt_random_coil_index _category.description ; The Random Coil Index (RCI) is calculated for each residue from the protein sequence and assigned chemical shifts. Via an empirical formula the RCI correlates with disorder propensity of the residue. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_random_coil_index.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_random_coil_index.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_random_coil_index.ordinal" _item.category_id pdbx_vrpt_random_coil_index _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_random_coil_index.auth_asym_id _item_description.description ; The auth_asym_id identifier for the residue or auth_asym_id obtained from cif item _atom_site.auth_asym_id. ; # _item.name "_pdbx_vrpt_random_coil_index.auth_asym_id" _item.category_id pdbx_vrpt_random_coil_index _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_random_coil_index.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_random_coil_index.rescode _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_random_coil_index.rescode" _item.category_id pdbx_vrpt_random_coil_index _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_random_coil_index.rescode" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_random_coil_index.auth_seq_id _item_description.description ; The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_random_coil_index.auth_seq_id" _item.category_id pdbx_vrpt_random_coil_index _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_random_coil_index.resnum" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_random_coil_index.value _item_description.description ; Value in ppm of a chemical shift ; # _item.name "_pdbx_vrpt_random_coil_index.value" _item.category_id pdbx_vrpt_random_coil_index _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_random_coil_index.value" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_chemical_shift_outlier _category.id pdbx_vrpt_chemical_shift_outlier _category.description ; BMRB compiled statistics of assigned chemical shifts, against which a given value is checked. A value is deemed an outlier if it is 5 standard deviation away from the expected mean. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_chemical_shift_outlier.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_chemical_shift_outlier.ordinal _item_description.description "Uniquely identifies each outlier." # _item.name "_pdbx_vrpt_chemical_shift_outlier.ordinal" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_chemical_shift_outlier.auth_asym_id _item_description.description ; The auth_asym_id identifier for the residue or auth_asym_id obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: auth_asym_id="A" ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.auth_asym_id" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_chemical_shift_outlier.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.rescode _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.rescode" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_chemical_shift_outlier.rescode" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.auth_seq_id _item_description.description ; The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.auth_seq_id" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_chemical_shift_outlier.resnum" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.label_atom_id" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_chemical_shift_outlier.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.value _item_description.description ; Value in ppm of a chemical shift ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.value" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_chemical_shift_outlier.value" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.zscore _item_description.description ; The Zscore of the deviation of the bond length or bond angle in the model compared to Mogul expected values and standard deviation. A Z score is generally defined as the difference between an observed value an expected or average value, divided by the standard deviations of the latter. Units depend on the parameter being analyzed. ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.zscore" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code float # _item_examples.case -2.40 # _item_aliases.alias_name "_chemical_shift_outlier.zscore" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.prediction _item_description.description ; The mean value of the chemical shift expected from the BMRB statistics. ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.prediction" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_chemical_shift_outlier.prediction" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_chemical_shift_outlier.method _item_description.description ; Method to determine the expected value and standard deviation. At present this is limited to BMRB statistics. ; # _item.name "_pdbx_vrpt_chemical_shift_outlier.method" _item.category_id pdbx_vrpt_chemical_shift_outlier _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_chemical_shift_outlier.method" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_referencing_offset _category.id pdbx_vrpt_referencing_offset _category.description ; PANAV software is used to calculate suggested referencing correction for each chemical shift list. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_referencing_offset.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_referencing_offset.ordinal _item_description.description "Uniquely identifies each referencing_offset." # _item.name "_pdbx_vrpt_referencing_offset.ordinal" _item.category_id pdbx_vrpt_referencing_offset _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_referencing_offset.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_referencing_offset.label_atom_id" _item.category_id pdbx_vrpt_referencing_offset _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_referencing_offset.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_referencing_offset.uncertainty _item_description.description ; Default uncertainty of the prediction, set to 0.05 ppm for protons and 0.5 ppm for 13C and 15N nuclei. ; # _item.name "_pdbx_vrpt_referencing_offset.uncertainty" _item.category_id pdbx_vrpt_referencing_offset _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_referencing_offset.uncertainty" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_referencing_offset.precision _item_description.description ; Precision of the suggested correction, as estimated by jack-knifing algorithm. ; # _item.name "_pdbx_vrpt_referencing_offset.precision" _item.category_id pdbx_vrpt_referencing_offset _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_referencing_offset.precision" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_referencing_offset.value _item_description.description ; Value in ppm of a chemical shift ; # _item.name "_pdbx_vrpt_referencing_offset.value" _item.category_id pdbx_vrpt_referencing_offset _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_referencing_offset.value" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_referencing_offset.number_of_measurements _item_description.description ; How many chemical shift values for this kind of nucleus are reported in the chemical shift list. ; # _item.name "_pdbx_vrpt_referencing_offset.number_of_measurements" _item.category_id pdbx_vrpt_referencing_offset _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_referencing_offset.number_of_measurements" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_assign_completeness_well_defined _category.id pdbx_vrpt_assign_completeness_well_defined _category.description ; For the well-defined regions of the structure, what is the completeness of chemical shift assignments for the typically assigned nuclei. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_assign_completeness_well_defined.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_assign_completeness_well_defined.ordinal _item_description.description "Uniquely identifies each well defined region." # _item.name "_pdbx_vrpt_assign_completeness_well_defined.ordinal" _item.category_id pdbx_vrpt_assign_completeness_well_defined _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_assign_completeness_well_defined.number_of_assigned_shifts _item_description.description ; Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that have a chemical shift assignment. ; # _item.name "_pdbx_vrpt_assign_completeness_well_defined.number_of_assigned_shifts" _item.category_id pdbx_vrpt_assign_completeness_well_defined _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_assignment_completeness_well_defined.number_of_assigned_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_well_defined.number_of_unassigned_shifts _item_description.description ; Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that lack a chemical shift assignment ; # _item.name "_pdbx_vrpt_assign_completeness_well_defined.number_of_unassigned_shifts" _item.category_id pdbx_vrpt_assign_completeness_well_defined _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_assignment_completeness_well_defined.number_of_unassigned_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_well_defined.number_of_shifts _item_description.description ; Total number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C)in the structure irrespective of assignment. It should be a sum of "number_of_unassigned_shifts" and "number_of_assigned_shifts" for the same type and element. ; # _item.name "_pdbx_vrpt_assign_completeness_well_defined.number_of_shifts" _item.category_id pdbx_vrpt_assign_completeness_well_defined _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_assignment_completeness_well_defined.number_of_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_well_defined.type _item_description.description ; "Type" refers to a subset of assignments: overall, backbone, aliphatic sidechain, aromatic protein rings, nucleic acid base and ribose or deoxyribose ring. ; # _item.name "_pdbx_vrpt_assign_completeness_well_defined.type" _item.category_id pdbx_vrpt_assign_completeness_well_defined _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_assignment_completeness_well_defined.type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_well_defined.element _item_description.description ; The chemical element (isotope) for which the assignment completeness is calculated. ; # _item.name "_pdbx_vrpt_assign_completeness_well_defined.element" _item.category_id pdbx_vrpt_assign_completeness_well_defined _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_assignment_completeness_well_defined.element" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_assign_completeness_full_length _category.id pdbx_vrpt_assign_completeness_full_length _category.description ; For the complete structure, what is the completeness of chemical shift assignments for the typically assigned nuclei. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_assign_completeness_full_length.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_assign_completeness_full_length.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_assign_completeness_full_length.ordinal" _item.category_id pdbx_vrpt_assign_completeness_full_length _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_assign_completeness_full_length.number_of_assigned_shifts _item_description.description ; Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that have a chemical shift assignment. ; # _item.name "_pdbx_vrpt_assign_completeness_full_length.number_of_assigned_shifts" _item.category_id pdbx_vrpt_assign_completeness_full_length _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_assignment_completeness_full_length.number_of_assigned_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_full_length.number_of_unassigned_shifts _item_description.description ; Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that lack a chemical shift assignment ; # _item.name "_pdbx_vrpt_assign_completeness_full_length.number_of_unassigned_shifts" _item.category_id pdbx_vrpt_assign_completeness_full_length _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_assignment_completeness_full_length.number_of_unassigned_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_full_length.number_of_shifts _item_description.description ; Total number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure irrespective of assignment. It should be a sum of "number_of_unassigned_shifts" and "number_of_assigned_shifts" for the same type and element. ; # _item.name "_pdbx_vrpt_assign_completeness_full_length.number_of_shifts" _item.category_id pdbx_vrpt_assign_completeness_full_length _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_assignment_completeness_full_length.number_of_shifts" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_full_length.type _item_description.description ; "Type" refers to a subset of assignments: overall, backbone, aliphatic sidechain, aromatic protein rings, nucleic acid base and ribose or deoxyribose ring. ; # _item.name "_pdbx_vrpt_assign_completeness_full_length.type" _item.category_id pdbx_vrpt_assign_completeness_full_length _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_assignment_completeness_full_length.type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_assign_completeness_full_length.element _item_description.description ; The chemical element (isotope) for which the assignment completeness is calculated. ; # _item.name "_pdbx_vrpt_assign_completeness_full_length.element" _item.category_id pdbx_vrpt_assign_completeness_full_length _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_assignment_completeness_full_length.element" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save_pdbx_vrpt_software _category.id pdbx_vrpt_software _category.description ; An individual pdbx_vrpt_software used by the validation pipeline. Normally this corresponds to a "step" but not always. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_software.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_software.ordinal _item_description.description "Uniquely identifies each software used." # _item.name "_pdbx_vrpt_software.ordinal" _item.category_id pdbx_vrpt_software _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_software.name _item_description.description ; The name of the program. ; # _item.name "_pdbx_vrpt_software.name" _item.category_id pdbx_vrpt_software _item.mandatory_code no # _item_examples.case mogul # _item_type.code text # _item_aliases.alias_name "_program.name" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_software.classification _item_description.description ; This aims to provide a comma seperate list of the attributes/elements that pdbx_vrpt_software supplied. The list is in an arbitrary order that can vary. Example: classification="mogul_rmsz_numangles,mogul_angles_rmsz,mogul-torsion-outlier,mogul-angle-outlier,mogul-bond-outlier,mogul_bonds_rmsz,mogul-ring-outlier,mogul_rmsz_numbonds". Note that the cross-referencing is not currently consistent as names can vary for instance classification list includes "mogul-angle-outlier" but the attribute is "mog-angle-outlier". ; # _item.name "_pdbx_vrpt_software.classification" _item.category_id pdbx_vrpt_software _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_program.properties" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_software.version _item_description.description ; Version string for the program. The format is software dependent. ; # _item.name "_pdbx_vrpt_software.version" _item.category_id pdbx_vrpt_software _item.mandatory_code no # _item_type.code text # _item_examples.case "1.7.2 (RC1), CSD as538be (2017)" # _item_aliases.alias_name "_program.version" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_software.details _item_description.description "Details about pdbx_vrpt_software used in calculations" # _item.name "_pdbx_vrpt_software.details" _item.category_id pdbx_vrpt_software _item.mandatory_code no # _item_type.code line # save_ # save__pdbx_vrpt_software.success_y_or_n _item_description.description "Indicates if pdbx_vrpt_software for step ran successfully" # _item.name "_pdbx_vrpt_software.success_y_or_n" _item.category_id pdbx_vrpt_software _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save_pdbx_vrpt_instance_intra_bond_outliers _category.id pdbx_vrpt_instance_intra_bond_outliers _category.description ; Bond outlier for standard amino acid or nucleic acid in comparison to the Engh and Huber EH99 parameters, Parkinson et al. parameter set. It involves two atoms. The obs, mean, stdev will all be in Angstroms units. Example: ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_intra_bond_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _category_examples.detail ; Example 1 - based on PDB entry 1ivs ; _category_examples.case ; loop_ _pdbx_vrpt_instance_intra_bond_outliers.ordinal _pdbx_vrpt_instance_intra_bond_outliers.instance_id _pdbx_vrpt_instance_intra_bond_outliers.atom_1 _pdbx_vrpt_instance_intra_bond_outliers.atom_2 _pdbx_vrpt_instance_intra_bond_outliers.obs _pdbx_vrpt_instance_intra_bond_outliers.mean _pdbx_vrpt_instance_intra_bond_outliers.stdev _pdbx_vrpt_instance_intra_bond_outliers.Z 1 1 OP3 P 1.523 1.607 0.012 -7.03 2 76 OP3 P 1.521 1.607 0.012 -7.20 ; # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.ordinal _item_description.description "Uniquely identifies each outlier." # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.ordinal" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.instance_id" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_intra_bond_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.atom_1 _item_description.description ; A label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.atom_1" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.atom_2 _item_description.description ; A label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.atom_2" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.mean _item_description.description ; The "ideal" value of the bond length. Source is mean value from Engh and Huber EH99 parameters, Parkinson et al. parameter set or Mogul analysis of CSD structures that have a similar local chemistry. Units depend on the parameter being analyzed in Angstroms. ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.mean" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code float # _item_examples.case 1.607 # _item_units.code angstroms # _item_aliases.alias_name "_bond-outlier.mean" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.stdev _item_description.description ; The standard deviation for the bond length. Source is standard deviation found from Engh and Huber EH99 parameters, Parkinson et al. parameter set or Mogul analysis of CSD structures that have a similar local chemistry. Units depend on the parameter being analyzed. ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.stdev" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_examples.case 0.012 # _item_aliases.alias_name "_bond-outlier.stdev" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.obs _item_description.description ; The observed value for the bond length. that is the value found in the structure being analyzed for the atoms involved. ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.obs" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_bond-outlier.obs" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.Z _item_description.description ; The Zscore of the deviation of the bond length compared to ideal values. A Z score is generally defined as the difference between an observed value an expected or average value, divided by the standard deviations of the latter. ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.Z" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_bond-outlier.z" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_bond_outliers.link _item_description.description ; Flag indicating that the bond involves an atom that is in another residue ; # _item.name "_pdbx_vrpt_instance_intra_bond_outliers.link" _item.category_id pdbx_vrpt_instance_intra_bond_outliers _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_bond-outlier.link" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save_pdbx_vrpt_instance_intra_angle_outliers _category.id pdbx_vrpt_instance_intra_angle_outliers _category.description ; Bond angle outlier for standard amino acid or nucleic acid in comparison to the Engh and Huber EH99 parameters, Parkinson et al. parameter set. It involves three atoms. The obsval, mean, mindiff, stdev will all be in degrees. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_intra_angle_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _category_examples.detail ; Example 1 - based on PDB entry 1ivs ; _category_examples.case ; loop_ _pdbx_vrpt_instance_intra_angle_outliers.ordinal _pdbx_vrpt_instance_intra_angle_outliers.instance_id _pdbx_vrpt_instance_intra_angle_outliers.atom_1 _pdbx_vrpt_instance_intra_angle_outliers.atom_2 _pdbx_vrpt_instance_intra_angle_outliers.atom_3 _pdbx_vrpt_instance_intra_angle_outliers.obs _pdbx_vrpt_instance_intra_angle_outliers.mean _pdbx_vrpt_instance_intra_angle_outliers.stdev _pdbx_vrpt_instance_intra_angle_outliers.Z _pdbx_vrpt_instance_intra_angle_outliers.link 1 20 N9 "C1'" "C2'" 120.758 114.000 1.300 5.20 ? 2 37 "C2'" "C3'" "O3'" 121.832 113.700 1.600 5.08 ? ; # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.ordinal _item_description.description "Uniquely identifies each angle outlier." # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.ordinal" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.mean _item_description.description ; The "ideal" value of the bond angle. Source is mean value from Engh and Huber EH99 parameters, Parkinson et al. parameter set or Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.mean" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_angle-outlier.mean" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.stdev _item_description.description ; The standard deviation for the bond bond angle. Source is standard deviation found from Engh and Huber EH99 parameters, Parkinson et al. parameter set or Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.stdev" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_angle-outlier.stdev" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.obs _item_description.description ; The observed value for bond angle, that is the value fouund for the atoms involved. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.obs" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_angle-outlier.obs" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.Z _item_description.description ; The Zscore of the deviation of the bond angle compared to ideal values. A Z score is generally defined as the difference between an observed value an expected or average value, divided by the standard deviations of the latter. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.Z" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_angle-outlier.z" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.link _item_description.description ; Flag indicating that the bond involves an atom that is in another residue. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.link" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # _item_aliases.alias_name "_angle-outlier.link" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.atom_1" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.atom_2" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.atom_3 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.atom_3" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_intra_angle_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_intra_angle_outliers.instance_id" _item.category_id pdbx_vrpt_instance_intra_angle_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_intra_angle_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save_pdbx_vrpt_instance_stereo_outliers _category.id pdbx_vrpt_instance_stereo_outliers _category.description ; Indicates there is a problem in the chirality compared to that expected with an atom in the residue. Chiral centres for all compounds occurring in the PDB are described in the chemical component dictionary. Chirality can be assessed in a number of ways, including calculation of the chiral volume, e.g. for the Calpha of amino acids this is 2.6 or -2.6 Angstrom cubed for L or D configurations, respectively. If the sign of the computed volume is incorrect, the handedness is wrong. If the absolute volume is less than 0.7Å3 , the chiral centre has been modelled as a planar moiety which is very likely to be erroneous. Chirality deviations are summarised per chain. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_stereo_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_instance_stereo_outliers.ordinal _item_description.description "Uniquely identifies each stereo outlier." # _item.name "_pdbx_vrpt_instance_stereo_outliers.ordinal" _item.category_id pdbx_vrpt_instance_stereo_outliers _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_instance_stereo_outliers.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_stereo_outliers.label_atom_id" _item.category_id pdbx_vrpt_instance_stereo_outliers _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_chiral-outlier.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_stereo_outliers.problem _item_description.description ; The type of chiral problem that the label_atom_id has. either "WRONG HAND" or "PLANAR" ; # _item.name "_pdbx_vrpt_instance_stereo_outliers.problem" _item.category_id pdbx_vrpt_instance_stereo_outliers _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_chiral-outlier.problem" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail "WRONG HAND" . PLANAR . # save_ # save__pdbx_vrpt_instance_stereo_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_stereo_outliers.instance_id" _item.category_id pdbx_vrpt_instance_stereo_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_stereo_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save_pdbx_vrpt_instance_intra_plane_outliers _category.id pdbx_vrpt_instance_intra_plane_outliers _category.description ; Indicates that there is a problem with planarity of group defined in the standard_geometry.cif for amino acids/proteins or nucleic acid. Calculated by the Validation-pack program. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_intra_plane_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _category_examples.detail ; Example 1 - based on PDB entry 1o08 ; _category_examples.case ; loop_ _pdbx_vrpt_instance_intra_plane_outliers.ordinal _pdbx_vrpt_instance_intra_plane_outliers.instance_id _pdbx_vrpt_instance_intra_plane_outliers.type _pdbx_vrpt_instance_intra_plane_outliers.improper _pdbx_vrpt_instance_intra_plane_outliers.omega 1 225 mainchain -16.25 ? 2 225 peptide ? -36.57 ; # save_ # save__pdbx_vrpt_instance_intra_plane_outliers.ordinal _item_description.description "Uniquely identifies each planar outlier." # _item.name "_pdbx_vrpt_instance_intra_plane_outliers.ordinal" _item.category_id pdbx_vrpt_instance_intra_plane_outliers _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_instance_intra_plane_outliers.type _item_description.description ; The type of chiral problem that the label_atom_id has. One of: (A) "mainchain": The N label_atom_id of an amino acid residue is expected to be in the same plane as the Calpha, C, and O atoms of the previous residue. If the improper torsion angle of these atoms is more than 10 degrees, this is flagged as a planarity deviation. From mmcif item "_pdbx_validate_main_chain_plane". (B) "peptide": A deviation is flagged if the omega torsion angle of a peptide group differs by more than 30 degrees from the values expected for a proper cis or trans conformation (0 degrees and 180 degrees, respectively). For mmcif item: "_pdbx_validate_peptide_omega". (C) "sidechain": Certain groups of atoms in protein sidechains and nucleotide bases are expected to be in the same plane. An atom's deviation from planarity is calculated by fitting a plane through these atoms and then calculating distance of individual label_atom_id from the plane. Expected value of such distances have been pre-calculated from data analysis (wwPDB, 2012). If an label_atom_id is modelled to be more than six times farther than the pre-calculated value, the residue is flagged to have a sidechain planarity deviation. From mmcif item "_pdbx_validate_planes". ; # _item.name "_pdbx_vrpt_instance_intra_plane_outliers.type" _item.category_id pdbx_vrpt_instance_intra_plane_outliers _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_plane-outlier.type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail mainchain . peptide . sidechain . # save_ # save__pdbx_vrpt_instance_intra_plane_outliers.improper _item_description.description ; For a type="mainchain" outlier, the improper torsion angle in degrees. ; # _item.name "_pdbx_vrpt_instance_intra_plane_outliers.improper" _item.category_id pdbx_vrpt_instance_intra_plane_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_plane-outlier.improper" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_plane_outliers.omega _item_description.description ; For a type="peptide" outlier, the omega torsion angle in degrees. ; # _item.name "_pdbx_vrpt_instance_intra_plane_outliers.omega" _item.category_id pdbx_vrpt_instance_intra_plane_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_plane-outlier.omega" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd _item_description.description ; For a type="sidechain" outlier, the root mean squared deviation from the mean plane in Angstroms. ; # _item.name "_pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd" _item.category_id pdbx_vrpt_instance_intra_plane_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_plane-outlier.planeRMSD" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_intra_plane_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_intra_plane_outliers.instance_id" _item.category_id pdbx_vrpt_instance_intra_plane_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_intra_plane_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save_pdbx_vrpt_instance_clashes _category.id pdbx_vrpt_instance_clashes _category.description ; A MolProbity all-atom pdbx_vrpt_instance_clashes outlier within the residue. Note that hydrogen atoms are added to the model and optimized by the reduce program. Outliers often involve these added hydrogen atoms. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_clashes.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _category_examples.detail ; Example 1 - based on PDB entry 1o08 ; _category_examples.case ; loop_ _pdbx_vrpt_instance_clashes.ordinal _pdbx_vrpt_instance_clashes.instance_id _pdbx_vrpt_instance_clashes.label_atom_id _pdbx_vrpt_instance_clashes.cid _pdbx_vrpt_instance_clashes.clashmag _pdbx_vrpt_instance_clashes.dist 1 1 HG3 1 0.83 1.42 2 1 HG3 2 0.61 2.13 ; # save_ # save__pdbx_vrpt_instance_clashes.ordinal _item_description.description "Uniquely identifies each clash instance." # _item.name "_pdbx_vrpt_instance_clashes.ordinal" _item.category_id pdbx_vrpt_instance_clashes _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_instance_clashes.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_clashes.label_atom_id" _item.category_id pdbx_vrpt_instance_clashes _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_clash.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_clashes.cid _item_description.description ; An identifier that cross references the other label_atom_id in the clash. The two atoms in the clash will have the same unique cid. ; # _item.name "_pdbx_vrpt_instance_clashes.cid" _item.category_id pdbx_vrpt_instance_clashes _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_clash.cid" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_clashes.clashmag _item_description.description ; The "magnitude" of the pdbx_vrpt_instance_clashes in Angstroms assessed by MolProbity. The MolProbity "magnitude" of a pdbx_vrpt_instance_clashes is defined as the difference between the observed interatomic distance and the sum of the van der Waals radii of the atoms involved. ; # _item.name "_pdbx_vrpt_instance_clashes.clashmag" _item.category_id pdbx_vrpt_instance_clashes _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_clash.clashmag" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_clashes.dist _item_description.description ; The distance in Angstroms between two atoms involved a clash. ; # _item.name "_pdbx_vrpt_instance_clashes.dist" _item.category_id pdbx_vrpt_instance_clashes _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_clash.dist" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_clashes.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_clashes.instance_id" _item.category_id pdbx_vrpt_instance_clashes _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_clashes.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save_pdbx_vrpt_instance_symm_clashes _category.id pdbx_vrpt_instance_symm_clashes _category.description ; A symmetry-related pdbx_vrpt_instance_clashes identified by Validation-pack. Symmetry related clashes are too-close contacts between two atoms across a crystallographic symmetry contact. Only relevant to crystallographic structures. From mmcif item "_pdbx_validate_symm_contact". ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_symm_clashes.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_instance_symm_clashes.ordinal _item_description.description "Uniquely identifies each symmetry clash." # _item.name "_pdbx_vrpt_instance_symm_clashes.ordinal" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_instance_symm_clashes.label_atom_id _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_symm_clashes.label_atom_id" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_symm-clash.atom" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_symm_clashes.symop _item_description.description ; The symmetry operator for the label_atom_id in the contact. The 1_555 notation is crystallographic shorthand to describe a particular symmetry operator (the number before the underscore) and any required translation (the three numbers following the underscore). Symmetry operators are defined by the space group and the translations are given for the three-unit cell axis (a, b, and c) where 5 indicates no translation and numbers higher or lower signify the number of unit cell translations in the positive or negative direction. For example, 4_565 indicates the use of symmetry operator 4 followed by a one-unit cell translation in the positive b direction. One of the atoms in the contact will have symop="1_555" that indicates the identity operator. ; # _item.name "_pdbx_vrpt_instance_symm_clashes.symop" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_symm-clash.symop" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_symm_clashes.scid _item_description.description ; An identifier that cross references the other label_atom_id in the clash. The two atoms in the clash will have the same unique scid. ; # _item.name "_pdbx_vrpt_instance_symm_clashes.scid" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_symm-clash.scid" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_symm_clashes.clashmag _item_description.description ; The "magnitude" of the pdbx_vrpt_instance_clashes in Angstroms assessed by the validation package. In this case, the "magnitude" of a pdbx_vrpt_instance_clashes is defined as 2.2 Angstrom (or 1.6 Angstrom if either label_atom_id is a hydrogen atom) minus the interatomic distance. ; # _item.name "_pdbx_vrpt_instance_symm_clashes.clashmag" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_symm-clash.clashmag" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_symm_clashes.dist _item_description.description ; The distance in Angstroms between two atoms involved a clash. ; # _item.name "_pdbx_vrpt_instance_symm_clashes.dist" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_symm-clash.dist" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_symm_clashes.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_symm_clashes.instance_id" _item.category_id pdbx_vrpt_instance_symm_clashes _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_symm_clashes.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save_pdbx_vrpt_instance_mogul_bond_outliers _category.id pdbx_vrpt_instance_mogul_bond_outliers _category.description ; Bond outlier for ligand or modified amino acid/nucleic acid identified by the Mogul program. It will involve two atoms. The Mogul software (Bruno et al., 2004) works by comparing the ligand geometry with preferred molecular geometries derived from high-quality, small-molecule structures in the Cambridge Structural pdbx_vrpt_database (CSD) ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_mogul_bond_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _category_examples.detail ; Example 1 - based on PDB entry 1o08 ; _category_examples.case ; loop_ _pdbx_vrpt_instance_mogul_bond_outliers.ordinal _pdbx_vrpt_instance_mogul_bond_outliers.instance_id _pdbx_vrpt_instance_mogul_bond_outliers.atom_1 _pdbx_vrpt_instance_mogul_bond_outliers.atom_2 _pdbx_vrpt_instance_mogul_bond_outliers.obsval _pdbx_vrpt_instance_mogul_bond_outliers.mean _pdbx_vrpt_instance_mogul_bond_outliers.numobs _pdbx_vrpt_instance_mogul_bond_outliers.stdev _pdbx_vrpt_instance_mogul_bond_outliers.Zscore _pdbx_vrpt_instance_mogul_bond_outliers.mindiff 1 227 O5 C1 1.47 1.41 9866 0.03 2.04 0.00 2 227 "P'" O1 1.96 1.59 23 0.02 19.44 0.34 ; # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.obsval _item_description.description ; The observed value for the bond length that is the value found in the structure being analyzed for the atoms involved. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.obsval" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_mog-bond-outlier.obsval" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.mean _item_description.description ; The "ideal" value of the bond length. Source is mean value from Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.mean" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_mog-bond-outlier.mean" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.stdev _item_description.description ; The standard deviation for the bond length. Source is standard deviation found from Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.stdev" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_mog-bond-outlier.stdev" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.numobs _item_description.description ; The number of observations found for bond length or bond angle or torsion angle in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.numobs" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_mog-bond-outlier.numobs" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.Zscore _item_description.description ; The Zscore of the deviation of the bond length compared to the Mogul expected values and standard deviation. A Z score is generally defined as the difference between an observed value an expected or average value, divided by the standard deviations of the latter. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.Zscore" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_mog-bond-outlier.Zscore" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.mindiff _item_description.description ; The difference to the nearest value of the bond length found in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.mindiff" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_mog-bond-outlier.mindiff" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.atom_1" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.atom_2" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.instance_id" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_mogul_bond_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_instance_mogul_bond_outliers.ordinal _item_description.description "Uniquely identifies each bond outlier." # _item.name "_pdbx_vrpt_instance_mogul_bond_outliers.ordinal" _item.category_id pdbx_vrpt_instance_mogul_bond_outliers _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_instance_mogul_angle_outliers _category.id pdbx_vrpt_instance_mogul_angle_outliers _category.description ; Bond angle outlier for ligand or modified amino acid/nucleic acid identified by the Mogul program. It involves three atoms. The Mogul software (Bruno et al., 2004) works by comparing the ligand geometry with preferred molecular geometries derived from high-quality, small-molecule structures in the Cambridge Structural pdbx_vrpt_database (CSD). ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_mogul_angle_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.obsval _item_description.description ; The observed value for the bond angle that is the value found in the structure being analyzed for the atoms involved. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.obsval" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-angle-outlier.obsval" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.mean _item_description.description ; The "ideal" value of the bond length or bond angle or torsion angle. Source is mean value Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.mean" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-angle-outlier.mean" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.stdev _item_description.description ; The standard deviation for the bond angle. Source is standard deviation found Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.stdev" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-angle-outlier.stdev" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.numobs _item_description.description ; The number of observations found for bond length in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.numobs" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_mog-angle-outlier.numobs" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.Zscore _item_description.description ; The Zscore of the deviation of the bond angle in the model compared to Mogul expected values and standard deviation. A Z score is generally defined as the difference between an observed value an expected or average value, divided by the standard deviations of the latter. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.Zscore" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_mog-angle-outlier.Zscore" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.mindiff _item_description.description ; The difference to the nearest value of the bond angle found in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.mindiff" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_mog-angle-outlier.mindiff" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.atom_1" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.atom_2" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.atom_3 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.atom_3" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.instance_id" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_mogul_angle_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_instance_mogul_angle_outliers.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_instance_mogul_angle_outliers.ordinal" _item.category_id pdbx_vrpt_instance_mogul_angle_outliers _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_instance_mogul_torsion_outliers _category.id pdbx_vrpt_instance_mogul_torsion_outliers _category.description ; Torsion angle outlier for ligand or modified amino acid/nucleic acid identified by the Mogul program. It will involve four atoms. The Mogul pdbx_vrpt_software (Bruno et al., 2004) works by comparing the ligand geometry with preferred molecular geometries derived from high-quality, small-molecule structures in the Cambridge Structural database (CSD). ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.obsval _item_description.description ; The observed value for the torsion angle, that is the value found in the structure being analyzed for the atoms involved. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.obsval" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-torsion-outlier.obsval" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.mean _item_description.description ; The "ideal" value of the torsion angle. Source is mean value from Mogul analysis of CSD structures that have a similar local chemistry. Units depend on the parameter being analyzed. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.mean" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-torsion-outlier.mean" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.mindiff _item_description.description ; The difference to the nearest value of the torsion angle found in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-torsion-outlier.mindiff" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.numobs _item_description.description ; The number of observations found for torsion angle in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.numobs" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_mog-torsion-outlier.numobs" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.stdev _item_description.description ; The standard deviation for the torsion angle. Source is standard deviation found from Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.stdev" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-torsion-outlier.stdev" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.local_density _item_description.description ; The local density is the percentage of observed Mogul torsion angles within certain units of the query torsion angle. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.local_density" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_mog-torsion-outlier.local_density" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.atom_3 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.atom_4 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code no # _item_type.code atcode # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_instance_mogul_torsion_outliers.ordinal _item_description.description "Uniquely identifies each torsion outlier." # _item.name "_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal" _item.category_id pdbx_vrpt_instance_mogul_torsion_outliers _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_instance_mogul_ring_outliers _category.id pdbx_vrpt_instance_mogul_ring_outliers _category.description ; Unusual ring conformation identified by Mogul. Mogul finds similar ring and works out the rmsd deviation of the ring torsion angles compared to the CSD similar rings. Each ring involves five or six atoms. The Mogul software (Bruno et al., 2004) works by comparing the ligand geometry with preferred molecular geometries derived from high-quality, small-molecule structures in the Cambridge Structural pdbx_vrpt_database (CSD). ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_instance_mogul_ring_outliers.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.atoms _item_description.description ; A comma separated list of label_atom_id names. ; # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.atoms" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code no # _item_type.code alphanum-csv # _item_examples.case O5,C1,C2 # _item_aliases.alias_name "_mog-ring-outlier.atoms" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.mean _item_description.description ; The "ideal" value of the bond length or bond angle or torsion angle. Source is mean value from Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.mean" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-ring-outlier.mean" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.mindiff _item_description.description ; The difference to the nearest value thetorsion angle found in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.mindiff" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code no # _item_units.code degrees # _item_type.code float # _item_aliases.alias_name "_mog-ring-outlier.mindiff" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.stdev _item_description.description ; The standard deviation of the torsion angles. Source is standard deviation found in Mogul analysis of CSD structures that have a similar local chemistry. ; # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.stdev" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_mog-ring-outlier.stdev" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.numobs _item_description.description ; The number of observations found for torsion angles in the Mogul analysis. ; # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.numobs" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_mog-ring-outlier.numobs" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.instance_id" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_instance_mogul_ring_outliers.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_instance_mogul_ring_outliers.ordinal _item_description.description "Uniquely identifies each ring outlier." # _item.name "_pdbx_vrpt_instance_mogul_ring_outliers.ordinal" _item.category_id pdbx_vrpt_instance_mogul_ring_outliers _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_restraint_summary _category.id pdbx_vrpt_restraint_summary _category.description "Provides summaries on hte number of restraints used in the analysis" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_restraint_summary.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _category_examples.detail ; Example 1 - based on PDB entry 1o08 ; _category_examples.case ; loop_ _pdbx_vrpt_restraint_summary.ordinal _pdbx_vrpt_restraint_summary.description _pdbx_vrpt_restraint_summary.value 1 "Total distance restraints" 1484 2 "Intra-residue (|i-j|=0)" 0 3 "Sequential (|i-j|=1)" 204 ; # save_ # save__pdbx_vrpt_restraint_summary.description _item_description.description "The description of the restraint type." # _item.name "_pdbx_vrpt_restraint_summary.description" _item.category_id pdbx_vrpt_restraint_summary _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_restraint_summary.description" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_restraint_summary.value _item_description.description ; The number of restraints or the value associated with the description. ; # _item.name "_pdbx_vrpt_restraint_summary.value" _item.category_id pdbx_vrpt_restraint_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_restraint_summary.value" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_restraint_summary.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_restraint_summary.ordinal" _item.category_id pdbx_vrpt_restraint_summary _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_residual_angle_violations _category.id pdbx_vrpt_residual_angle_violations _category.description "Dihedral-angle violation statistics within the bin" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_residual_angle_violations.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_residual_angle_violations.max_violation _item_description.description " The maximum value of the dihedral-angle violation within the bin" # _item.name "_pdbx_vrpt_residual_angle_violations.max_violation" _item.category_id pdbx_vrpt_residual_angle_violations _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_residual_angle_violation.max_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_residual_angle_violations.bins _item_description.description "The violations are binned as small, medium and large violations based on its absolute value." # _item.name "_pdbx_vrpt_residual_angle_violations.bins" _item.category_id pdbx_vrpt_residual_angle_violations _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_residual_angle_violation.bins" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_residual_angle_violations.violations_per_model _item_description.description "Average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble." # _item.name "_pdbx_vrpt_residual_angle_violations.violations_per_model" _item.category_id pdbx_vrpt_residual_angle_violations _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_residual_angle_violation.violations_per_model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_residual_angle_violations.ordinal _item_description.description "Uniquely identifies each residual angle violation." # _item.name "_pdbx_vrpt_residual_angle_violations.ordinal" _item.category_id pdbx_vrpt_residual_angle_violations _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_distance_violation_summary _category.id pdbx_vrpt_distance_violation_summary _category.description "Violated and consistently violated statistics in different restraints type" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_distance_violation_summary.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_distance_violation_summary.restraint_type _item_description.description "The restraint type (Intra-residue, Sequential, MediumRange, LongRange, InterChain, Total)" # _item.name "_pdbx_vrpt_distance_violation_summary.restraint_type" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail DisulfideBond . HydrogenBond . InterChain . Intra-residue . MediumRange . LongRange . Sequential . Total . # _item_aliases.alias_name "_distance_violation_summary.restraint_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_summary.restraint_sub_type _item_description.description "The restraint sub type (BackboneBackbone, BackboneSidechain, SidechainSidechain, all)" # _item.name "_pdbx_vrpt_distance_violation_summary.restraint_sub_type" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail all . BackboneBackbone . BackboneSidechain . SidechainSidechain . # _item_aliases.alias_name "_distance_violation_summary.restraint_sub_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_summary.consistently_violated_count _item_description.description " Number of restraints that are violated in all models" # _item.name "_pdbx_vrpt_distance_violation_summary.consistently_violated_count" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_distance_violation_summary.consistently_violated_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_summary.consistently_violated_percent_total _item_description.description " Percentage of restraints that are violated in all models against total number of restraints" # _item.name "_pdbx_vrpt_distance_violation_summary.consistently_violated_percent_total" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violation_summary.consistently_violated_percent_total" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # save_ # save__pdbx_vrpt_distance_violation_summary.consistently_violated_percent_type _item_description.description " Percentage of restraints that are violated in all models against number of restraints in a given restraint type." # _item.name "_pdbx_vrpt_distance_violation_summary.consistently_violated_percent_type" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violation_summary.consistently_violated_percent_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # save_ # save__pdbx_vrpt_distance_violation_summary.restraints_count _item_description.description "Number of restraints in a given restraint type." # _item.name "_pdbx_vrpt_distance_violation_summary.restraints_count" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_distance_violation_summary.restraints_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_summary.violated_count _item_description.description "Number of restraints that are violated at least in one model" # _item.name "_pdbx_vrpt_distance_violation_summary.violated_count" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_distance_violation_summary.violated_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_summary.percent_total _item_description.description "Percentage of restraints in a given restraint type" # _item.name "_pdbx_vrpt_distance_violation_summary.percent_total" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violation_summary.percent_total" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # save_ # save__pdbx_vrpt_distance_violation_summary.violated_percent_total _item_description.description "Percentage of restraints that are violated at least in one model in given restraint type against the total restraints." # _item.name "_pdbx_vrpt_distance_violation_summary.violated_percent_total" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violation_summary.violated_percent_total" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # save_ # save__pdbx_vrpt_distance_violation_summary.violated_percent_type _item_description.description "Percentage of restraints that are violated at least in one model against the total number of restraints in a given restraints type." # _item.name "_pdbx_vrpt_distance_violation_summary.violated_percent_type" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violation_summary.violated_percent_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # save_ # save__pdbx_vrpt_distance_violation_summary.ordinal _item_description.description "Uniquely identifies each violation summary." # _item.name "_pdbx_vrpt_distance_violation_summary.ordinal" _item.category_id pdbx_vrpt_distance_violation_summary _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_distance_violation_model_summary _category.id pdbx_vrpt_distance_violation_model_summary _category.description " List of number of violated distance restraints in each model" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_distance_violation_model_summary.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_distance_violation_model_summary.max_violation _item_description.description " The maximum value of violation of a particular restraint in an ensemble." # _item.name "_pdbx_vrpt_distance_violation_model_summary.max_violation" _item.category_id pdbx_vrpt_distance_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violations_in_model.max_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_summary.mean_violation _item_description.description " The mean value of the violation of a given restraint in an ensemble." # _item.name "_pdbx_vrpt_distance_violation_model_summary.mean_violation" _item.category_id pdbx_vrpt_distance_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violations_in_model.mean_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_summary.PDB_model_num _item_description.description ; Model identifier. If the structure does not have multiple models then PDB_model_num will be "1". ; # _item.name "_pdbx_vrpt_distance_violation_model_summary.PDB_model_num" _item.category_id pdbx_vrpt_distance_violation_model_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_distance_violations_in_model.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_summary.standard_deviation _item_description.description " The standard deviation of the value of the violations of a given restraint in an ensemble." # _item.name "_pdbx_vrpt_distance_violation_model_summary.standard_deviation" _item.category_id pdbx_vrpt_distance_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violations_in_model.standard_deviation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_summary.median_violation _item_description.description " The median value of the violation of a given restraint in an ensemble" # _item.name "_pdbx_vrpt_distance_violation_model_summary.median_violation" _item.category_id pdbx_vrpt_distance_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violations_in_model.median_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_summary.ordinal _item_description.description "Uniquely identifies each distance violation." # _item.name "_pdbx_vrpt_distance_violation_model_summary.ordinal" _item.category_id pdbx_vrpt_distance_violation_model_summary _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_distance_violation_model_restraints _category.id pdbx_vrpt_distance_violation_model_restraints _category.description ">List of number of violated distance restraints in each model" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_distance_violation_model_restraints.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_distance_violation_model_restraints.dist_rest_type _item_description.description "The type of distance restraint (intraresidue, sequential, etc.)." # _item.name "_pdbx_vrpt_distance_violation_model_restraints.dist_rest_type" _item.category_id pdbx_vrpt_distance_violation_model_restraints _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail intraresidue . sequential . medium . long . interchain . total . # _item_aliases.alias_name "_dist_rest_types.dist_rest_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_restraints.violations_count _item_description.description "Number of violated restraints." # _item.name "_pdbx_vrpt_distance_violation_model_restraints.violations_count" _item.category_id pdbx_vrpt_distance_violation_model_restraints _item.mandatory_code yes # _item_type.code int # _item_aliases.alias_name "_dist_rest_types.violations_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_restraints.PDB_model_num _item_description.description ; The model number. ; # _item.name "_pdbx_vrpt_distance_violation_model_restraints.PDB_model_num" _item.category_id pdbx_vrpt_distance_violation_model_restraints _item.mandatory_code yes # _item_type.code text # _item_aliases.alias_name "_dist_rest_types.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_model_restraints.ordinal _item_description.description "Uniquely identifies each model restraint." # _item.name "_pdbx_vrpt_distance_violation_model_restraints.ordinal" _item.category_id pdbx_vrpt_distance_violation_model_restraints _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_violated_dihedralangle_restraints _category.id pdbx_vrpt_violated_dihedralangle_restraints _category.description " Enumerated all dihedral-angle violations." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_violated_dihedralangle_restraints.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.atom_1" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_violated_dihedralangle_restraint.atom_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.atom_2" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_violated_dihedralangle_restraint.atom_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.violation _item_description.description ; The measureed violation. ; # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.violation" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code float # _item_units.code degrees # _item_aliases.alias_name "_violated_dihedralangle_restraint.violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.atom_3 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.atom_3" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_violated_dihedralangle_restraint.atom_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.atom_4 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.atom_4" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_violated_dihedralangle_restraint.atom_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.rlist_id _item_description.description "An identifier used to uniquely identify a particular restraints loop." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.rlist_id" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_violated_dihedralangle_restraint.rlist_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.rest_id _item_description.description "An identifier used to uniquely identify a restraint with in a particular restraint loop." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.rest_id" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_violated_dihedralangle_restraint.rest_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.instance_id_1 _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_1" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_1" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.instance_id_2 _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_2" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_2" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.instance_id_3 _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_3" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_3" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.instance_id_4 _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_4" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_violated_dihedralangle_restraints.instance_id_4" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_violated_dihedralangle_restraints.ordinal _item_description.description "Uniquely identifies each dihedral angle restraint." # _item.name "_pdbx_vrpt_violated_dihedralangle_restraints.ordinal" _item.category_id pdbx_vrpt_violated_dihedralangle_restraints _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_distance_violations_ensemble_summary _category.id pdbx_vrpt_distance_violations_ensemble_summary _category.description " Distance violation statistics in an ensemble." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_distance_violations_ensemble_summary.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_distance_violations_ensemble_summary.fraction_of_ensemble_count _item_description.description "Number of violated models for given set of violated restraints." # _item.name "_pdbx_vrpt_distance_violations_ensemble_summary.fraction_of_ensemble_count" _item.category_id pdbx_vrpt_distance_violations_ensemble_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_distance_violation_in_ensemble.fraction_of_ensemble_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violations_ensemble_summary.fraction_of_ensemble_percent _item_description.description "Percentage of violated models for given set of violated restraints" # _item.name "_pdbx_vrpt_distance_violations_ensemble_summary.fraction_of_ensemble_percent" _item.category_id pdbx_vrpt_distance_violations_ensemble_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_distance_violation_in_ensemble.fraction_of_ensemble_percent" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violations_ensemble_summary.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_distance_violations_ensemble_summary.id" _item.category_id pdbx_vrpt_distance_violations_ensemble_summary _item.mandatory_code yes # _item_type.code code # save_ # save_pdbx_vrpt_distance_violation_ensemble _category.id pdbx_vrpt_distance_violation_ensemble _category.description " This category enumerates the number of violated models for a given set of restraints." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_distance_violation_ensemble.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_distance_violation_ensemble.dist_rest_type _item_description.description "The type of distance restraint (intraresidue, sequential, etc.)" # _item.name "_pdbx_vrpt_distance_violation_ensemble.dist_rest_type" _item.category_id pdbx_vrpt_distance_violation_ensemble _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail intraresidue . sequential . medium . long . interchain . total . # _item_aliases.alias_name "_dist_rest_types2.dist_rest_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_ensemble.violations_count _item_description.description "Number of violated restraints in ensemble." # _item.name "_pdbx_vrpt_distance_violation_ensemble.violations_count" _item.category_id pdbx_vrpt_distance_violation_ensemble _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_dist_rest_types2.violations_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_distance_violation_ensemble.ensemble_distance_count _item_description.description "Number of violated models for given set of violated restraint" # _item.name "_pdbx_vrpt_distance_violation_ensemble.ensemble_distance_count" _item.category_id pdbx_vrpt_distance_violation_ensemble _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_distance_violation_ensemble.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_distance_violation_ensemble.ordinal" _item.category_id pdbx_vrpt_distance_violation_ensemble _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_dihedralangle_violations_summary _category.id pdbx_vrpt_dihedralangle_violations_summary _category.description ; Statistics about violated and consistently violated restraints. Restraints that are violated in all models are called consistently violated restraints. ; _category.mandatory_code no # _category_key.name "_pdbx_vrpt_dihedralangle_violations_summary.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.restraint_type _item_description.description "The dihedral-angle restraint type (PHI,PSI,etc)" # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.restraint_type" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail PHI . PSI . CHI1 . CHI2 . CHI21 . Total . # _item_aliases.alias_name "_dihedralangle_violation_summary.restraint_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.consistently_violated_count _item_description.description " Number of restraints that are violated in all models" # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.consistently_violated_count" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_dihedralangle_violation_summary.consistently_violated_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.consistently_violated_percent_total _item_description.description " Percentage of restraints that are violated in all models against total number of restraints." # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.consistently_violated_percent_total" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # _item_aliases.alias_name "_dihedralangle_violation_summary.consistently_violated_percent_total" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.consistently_violated_percent_type _item_description.description ; Percentage of restraints that are violated in all models against number of restraints in a given restraint type. ; # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.consistently_violated_percent_type" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # _item_aliases.alias_name "_dihedralangle_violation_summary.consistently_violated_percent_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.restraints_count _item_description.description "Number of restraints in a given restraint type." # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.restraints_count" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_dihedralangle_violation_summary.restraints_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.violated_count _item_description.description "Number of restraints that are violated that are violated at least in one model." # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.violated_count" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_dihedralangle_violation_summary.violated_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.percent_total _item_description.description "Percentage of restraints in a given restraint type." # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.percent_total" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # _item_aliases.alias_name "_dihedralangle_violation_summary.percent_total" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.violated_percent_total _item_description.description ; Percentage of restraints that are violated at least in one model in given restraint type against the total restraints ; # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.violated_percent_total" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # _item_aliases.alias_name "_dihedralangle_violation_summary.violated_percent_total" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.violated_percent_type _item_description.description "Percentage of restraints that are violated at least in one model against the total number of restraints in a given restraints type" # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.violated_percent_type" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code no # _item_type.code float # loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 # _item_aliases.alias_name "_dihedralangle_violation_summary.violated_percent_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violations_summary.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_dihedralangle_violations_summary.ordinal" _item.category_id pdbx_vrpt_dihedralangle_violations_summary _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_dihedralangle_violation_model_summary _category.id pdbx_vrpt_dihedralangle_violation_model_summary _category.description "Number of violated restraints in a given model" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_dihedralangle_violation_model_summary.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_dihedralangle_violation_model_summary.PDB_model_num _item_description.description ; Model number in summary. ; # _item.name "_pdbx_vrpt_dihedralangle_violation_model_summary.PDB_model_num" _item.category_id pdbx_vrpt_dihedralangle_violation_model_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_dihedralangle_violations_in_model.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model_summary.max_violation _item_description.description " The maximum value of violation of a particular restraint in an ensemble" # _item.name "_pdbx_vrpt_dihedralangle_violation_model_summary.max_violation" _item.category_id pdbx_vrpt_dihedralangle_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_dihedralangle_violations_in_model.max_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model_summary.mean_violation _item_description.description " The mean value of the violation of a given restraint in an ensemble." # _item.name "_pdbx_vrpt_dihedralangle_violation_model_summary.mean_violation" _item.category_id pdbx_vrpt_dihedralangle_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_dihedralangle_violations_in_model.mean_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model_summary.standard_deviation _item_description.description " The standard deviation of the value of the violations of a given restraint in an ensemble." # _item.name "_pdbx_vrpt_dihedralangle_violation_model_summary.standard_deviation" _item.category_id pdbx_vrpt_dihedralangle_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_dihedralangle_violations_in_model.standard_deviation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model_summary.median_violation _item_description.description " The median value of the violation of a given restraint in an ensemble" # _item.name "_pdbx_vrpt_dihedralangle_violation_model_summary.median_violation" _item.category_id pdbx_vrpt_dihedralangle_violation_model_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_dihedralangle_violations_in_model.median_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model_summary.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_dihedralangle_violation_model_summary.ordinal" _item.category_id pdbx_vrpt_dihedralangle_violation_model_summary _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_dihedralangle_violation_model _category.id pdbx_vrpt_dihedralangle_violation_model _category.description " Number of violated restraints ina given model." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_dihedralangle_violation_model.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_dihedralangle_violation_model.ang_rest_type _item_description.description "The type of dihedral-angle restraint" # _item.name "_pdbx_vrpt_dihedralangle_violation_model.ang_rest_type" _item.category_id pdbx_vrpt_dihedralangle_violation_model _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail PHI . PSI . CHI1 . CHI2 . CHI21 . Total . # _item_aliases.alias_name "_ang_rest_types.ang_rest_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model.violations_count _item_description.description "Number of violated restraints." # _item.name "_pdbx_vrpt_dihedralangle_violation_model.violations_count" _item.category_id pdbx_vrpt_dihedralangle_violation_model _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ang_rest_types.violations_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model.PDB_model_num _item_description.description ; Model number. ; # _item.name "_pdbx_vrpt_dihedralangle_violation_model.PDB_model_num" _item.category_id pdbx_vrpt_dihedralangle_violation_model _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ang_rest_types.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_model.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_dihedralangle_violation_model.ordinal" _item.category_id pdbx_vrpt_dihedralangle_violation_model _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_dihedralangle_violation_ensemble_summary _category.id pdbx_vrpt_dihedralangle_violation_ensemble_summary _category.description " Dihedral-angle violation statistics in the ensemble" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_dihedralangle_violation_ensemble_summary.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_dihedralangle_violation_ensemble_summary.fraction_of_ensemble_count _item_description.description "Number of violated models for given set of violated restraints" # _item.name "_pdbx_vrpt_dihedralangle_violation_ensemble_summary.fraction_of_ensemble_count" _item.category_id pdbx_vrpt_dihedralangle_violation_ensemble_summary _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_dihedralangle_violation_in_ensemble.fraction_of_ensemble_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_ensemble_summary.fraction_of_ensemble_percent _item_description.description "Percentage of violated models for given set of violated restraints" # _item.name "_pdbx_vrpt_dihedralangle_violation_ensemble_summary.fraction_of_ensemble_percent" _item.category_id pdbx_vrpt_dihedralangle_violation_ensemble_summary _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_dihedralangle_violation_in_ensemble.fraction_of_ensemble_percent" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_violation_ensemble_summary.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_dihedralangle_violation_ensemble_summary.id" _item.category_id pdbx_vrpt_dihedralangle_violation_ensemble_summary _item.mandatory_code yes # _item_type.code code # save_ # save_pdbx_vrpt_dihedralangle_ensemble_violation _category.id pdbx_vrpt_dihedralangle_ensemble_violation _category.description " Dihedral-angle violation statistics in the ensemble." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_dihedralangle_ensemble_violation.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_dihedralangle_ensemble_violation.ang_rest_type _item_description.description "The type of dihedral-angle restraint." # _item.name "_pdbx_vrpt_dihedralangle_ensemble_violation.ang_rest_type" _item.category_id pdbx_vrpt_dihedralangle_ensemble_violation _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail PHI . PSI . CHI1 . CHI2 . CHI21 . Total . # _item_aliases.alias_name "_ang_rest_types.ang_rest_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_ensemble_violation.violations_count _item_description.description "Number of violated restraints " # _item.name "_pdbx_vrpt_dihedralangle_ensemble_violation.violations_count" _item.category_id pdbx_vrpt_dihedralangle_ensemble_violation _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ang_rest_types.violations_count" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_dihedralangle_ensemble_violation.ensemble_dihedral_count _item_description.description "Indicates the count of the ensemble" # _item.name "_pdbx_vrpt_dihedralangle_ensemble_violation.ensemble_dihedral_count" _item.category_id pdbx_vrpt_dihedralangle_ensemble_violation _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_dihedralangle_ensemble_violation.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_dihedralangle_ensemble_violation.ordinal" _item.category_id pdbx_vrpt_dihedralangle_ensemble_violation _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_residual_distance_violations _category.id pdbx_vrpt_residual_distance_violations _category.description "Summary of distance violations in different bins based on its magnitude of violation" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_residual_distance_violations.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_residual_distance_violations.max_violation _item_description.description ;The maximum value of distance violation with in the given bin ; # _item.name "_pdbx_vrpt_residual_distance_violations.max_violation" _item.category_id pdbx_vrpt_residual_distance_violations _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_residual_distance_violation.max_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_residual_distance_violations.bins _item_description.description "The violations are binned as small, medium and large violations based on its absolute value." # _item.name "_pdbx_vrpt_residual_distance_violations.bins" _item.category_id pdbx_vrpt_residual_distance_violations _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_residual_distance_violation.bins" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_residual_distance_violations.violations_per_model _item_description.description "Average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble." # _item.name "_pdbx_vrpt_residual_distance_violations.violations_per_model" _item.category_id pdbx_vrpt_residual_distance_violations _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_residual_distance_violation.violations_per_model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_residual_distance_violations.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_residual_distance_violations.ordinal" _item.category_id pdbx_vrpt_residual_distance_violations _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_most_violated_distance_restraints _category.id pdbx_vrpt_most_violated_distance_restraints _category.description " Restraints that are violated in more than one models" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_most_violated_distance_restraints.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_most_violated_distance_restraints.altcode_1 _item_description.description ; This attribute will be set if the model has atoms with the alternate position indicator set. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.altcode_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_distance_restraint.altcode_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.chain_1 _item_description.description ; The auth_asym_id obtained from cif item _atom_site.auth_asym_id. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.chain_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_distance_restraint.chain_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.resnum_1 _item_description.description ; The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.resnum_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.resnum_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.resname_1 _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.resname_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_most_violated_distance_restraint.resname_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.icode_1 _item_description.description ; Insertion code for residue from _atom_site.pdbx_PDB_ins_code ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.icode_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_distance_restraint.icode_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.ent_1 _item_description.description ; The entity id for the residue or chain. This is from item _atom_site.label_entity_id. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.ent_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_distance_restraints.ent_1" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_most_violated_distance_restraint.ent_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.said_1 _item_description.description ; The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.said_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_distance_restraints.said_1" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_most_violated_distance_restraint.said_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.seq_1 _item_description.description ; From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.seq_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.seq_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.chain_2 _item_description.description ; The auth_asym_id identifier for the residue. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.chain_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_distance_restraint.chain_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.altcode_2 _item_description.description ; This attribute will be set if the pdbx_vrpt_model_instance has atoms with the alternate position indicator set. Obtained from _atom_site.label_alt_id ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.altcode_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_distance_restraint.altcode_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.atom_1" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_most_violated_distance_restraint.atom_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.resnum_2 _item_description.description ; The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.resnum_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.resnum_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.resname_2 _item_description.description ; The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.resname_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_most_violated_distance_restraint.resname_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.seq_2 _item_description.description ; From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.seq_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.seq_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.said_2 _item_description.description ; The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.said_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_distance_restraints.said_2" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_most_violated_distance_restraint.said_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.ent_2 _item_description.description ; The entity id for the residue or chain. This is from item _atom_site.label_entity_id that is a pointer to _entity.id. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.ent_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_distance_restraints.ent_2" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_most_violated_distance_restraint.ent_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.icode_2 _item_description.description ; Insertion code for residue from _atom_site.pdbx_PDB_ins_code ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.icode_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_distance_restraint.icode_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_most_violated_distance_restraints.atom_2" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_most_violated_distance_restraint.atom_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.mean_distance_violation _item_description.description "Mean distance violation over the violated models" # _item.name "_pdbx_vrpt_most_violated_distance_restraints.mean_distance_violation" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_most_violated_distance_restraint.mean_distance_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.median_violation _item_description.description "The median value of the violation of a given restraint in an ensemble" # _item.name "_pdbx_vrpt_most_violated_distance_restraints.median_violation" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_most_violated_distance_restraint.median_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.standard_deviation _item_description.description " The standard deviation of the value of the violations of a given restraint in an ensemble" # _item.name "_pdbx_vrpt_most_violated_distance_restraints.standard_deviation" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_most_violated_distance_restraint.standard_deviation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.violated_models _item_description.description " Number of violated models for a given restraint or set of restraints" # _item.name "_pdbx_vrpt_most_violated_distance_restraints.violated_models" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.violated_models" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.rlist_id _item_description.description "An identifier used to uniquely identify a particular restraints loop." # _item.name "_pdbx_vrpt_most_violated_distance_restraints.rlist_id" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.rlist_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.rest_id _item_description.description "An identifier used to uniquely identify a restraint with in a particular restraint loop" # _item.name "_pdbx_vrpt_most_violated_distance_restraints.rest_id" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_distance_restraint.rest_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_distance_restraints.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_most_violated_distance_restraints.ordinal" _item.category_id pdbx_vrpt_most_violated_distance_restraints _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_violated_distance_restraints _category.id pdbx_vrpt_violated_distance_restraints _category.description " List of all violated distance restraints" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_violated_distance_restraints.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_violated_distance_restraints.atom_1 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. The first atom in the pair. ; # _item.name "_pdbx_vrpt_violated_distance_restraints.atom_1" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_violated_distance_restraint.atom_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_distance_restraints.atom_2 _item_description.description ; An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. The second atom in the pair. ; # _item.name "_pdbx_vrpt_violated_distance_restraints.atom_2" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_violated_distance_restraint.atom_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_distance_restraints.violation _item_description.description " Absolute value of the violation" # _item.name "_pdbx_vrpt_violated_distance_restraints.violation" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_violated_distance_restraint.violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_distance_restraints.rlist_id _item_description.description "An identifier used to uniquely identify a particular restraints loop" # _item.name "_pdbx_vrpt_violated_distance_restraints.rlist_id" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_violated_distance_restraint.rlist_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_distance_restraints.rest_id _item_description.description "An identifier used to uniquely identify a restraint with in a particular restraint loop" # _item.name "_pdbx_vrpt_violated_distance_restraints.rest_id" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_violated_distance_restraint.rest_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_violated_distance_restraints.instance_id_1 _item_description.description "A pointer to the first atom fro pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_violated_distance_restraints.instance_id_1" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_violated_distance_restraints.instance_id_1" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_violated_distance_restraints.instance_id_2 _item_description.description "A pointer to pdbx_vrpt_model_instance.id for second atom" # _item.name "_pdbx_vrpt_violated_distance_restraints.instance_id_2" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_violated_distance_restraints.instance_id_2" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_violated_distance_restraints.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_violated_distance_restraints.ordinal" _item.category_id pdbx_vrpt_violated_distance_restraints _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_most_violated_dihedralangle_restraints _category.id pdbx_vrpt_most_violated_dihedralangle_restraints _category.description "Dihedral-angle restraints that are violated in more than one model" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_1 _item_description.description ; This attribute will be set if the first pdb x_vrpt_model_instance has atoms with the alternate position indicator set. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.altcode_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.chain_1 _item_description.description ; The auth_asym_id identifier for the first residue or from cif item _atom_site.auth_asym_id. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.chain_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.chain_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_1 _item_description.description ; The residue number aka sequence id for the first residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resnum_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resname_1 _item_description.description ; The firs "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resname_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resname_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.icode_1 _item_description.description ; Insertion code for first residue from _atom_site.pdbx_PDB_ins_code ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.icode_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.icode_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.ent_1 _item_description.description ; The entity id for the first residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_1" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.ent_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.said_1 _item_description.description ; The _atom_site.label_asym_id label for the first residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_1" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.said_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.seq_1 _item_description.description ; From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.seq_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.seq_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.atom_1 _item_description.description ; The first atom label from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.atom_1" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.atom_1" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.chain_2 _item_description.description ; The auth_asym_id identifier for the second residue or auth_asym_id obtained from cif item _atom_site.auth_asym_id. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.chain_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.chain_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_2 _item_description.description ; This attribute will be set if the second atom has the alternate position indicator set. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.altcode_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_2 _item_description.description ; The residue number aka sequence id for the second residue. Obtained from _atom_site.auth_seq_id ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resnum_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resname_2 _item_description.description ; The "residue type" of the second atom, this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resname_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resname_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.seq_2 _item_description.description ; The sequence number for the second atom mrom cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.seq_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.seq_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.said_2 _item_description.description ; The _atom_site.label_asym_id label for the second residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_2" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.said_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.ent_2 _item_description.description ; The entity id for the second residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_2" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.ent_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.icode_2 _item_description.description ; Insertion code for second residue from _atom_site.pdbx_PDB_ins_code ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.icode_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.icode_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.atom_2 _item_description.description ; An label_atom_id name for the second item from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.atom_2" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.atom_2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.mean_angle_violation _item_description.description " Mean value of dihedral-angle violation over all violated models" # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.mean_angle_violation" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.mean_angle_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.standard_deviation _item_description.description " The standard deviation of the value of the violations of a given restraint in an ensemble" # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.standard_deviation" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.standard_deviation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.median_violation _item_description.description "The median value of the violation of a given restraint in an ensemble" # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.median_violation" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.median_violation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_3 _item_description.description ; Alternate position setting for the third atom. Obtained from _atom_site.label_alt_id ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.altcode_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.chain_3 _item_description.description ; The auth_asym_id identifier for the third residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.chain_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.chain_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_3 _item_description.description ; The residue number aka sequence id for the third residue. Obtained from _atom_site.auth_seq_id. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resnum_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resname_3 _item_description.description ; The "residue type", of the third residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resname_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resname_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.icode_3 _item_description.description ; Insertion code for third residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.icode_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.icode_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.ent_3 _item_description.description ; The entity id for the third residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_3" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.ent_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.said_3 _item_description.description ; The _atom_site.label_asym_id label for the third residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_3" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.said_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.seq_3 _item_description.description ; From cif item _atom_site.label_seq_id for the third residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.seq_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.seq_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.atom_3 _item_description.description ; The label_atom_id name for the third atom. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.atom_3" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.atom_3" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_4 _item_description.description ; This attribute will be set if the alternate position is set for the fourth atom. Obtained from _atom_site.label_alt_id ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.altcode_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.altcode_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.chain_4 _item_description.description ; The auth_asym_id identifier for the fourth residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.chain_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.chain_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_4 _item_description.description ; The residue number aka sequence id for the fourth residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resnum_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resnum_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.resname_4 _item_description.description ; The "residue type", of the fourth atom. Obtained from _atom_site.auth_comp_id ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.resname_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code ucode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.resname_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.icode_4 _item_description.description ; Insertion code for fourth residue. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.icode_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.icode_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.ent_4 _item_description.description ; The entity id for the fourth atom. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ent_4" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.ent_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.said_4 _item_description.description ; The _atom_site.label_asym_id label for the fourth atom. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_most_violated_dihedralangle_restraints.said_4" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.said_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.seq_4 _item_description.description ; From cif item _atom_site.label_seq_id of fourth atom. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.seq_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.seq_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.atom_4 _item_description.description ; The label_atom_id name for the fourth atom. ; # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.atom_4" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code atcode # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.atom_4" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.rlist_id _item_description.description "An identifier used to uniquely identify a particular restraints loop." # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.rlist_id" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.rlist_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.rest_id _item_description.description "An identifier used to uniquely identify a restraint with in a particular restraint loop." # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.rest_id" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.rest_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.violated_models _item_description.description "number of violated models for a given restraint or set of restraints" # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.violated_models" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_most_violated_dihedralangle_restraint.violated_models" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_most_violated_dihedralangle_restraints.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_most_violated_dihedralangle_restraints.ordinal" _item.category_id pdbx_vrpt_most_violated_dihedralangle_restraints _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_model_instance_geometry _category.id pdbx_vrpt_model_instance_geometry _category.description " This category formation on the geometry of all residues" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_model_instance_geometry.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_model_instance_geometry.OWAB _item_description.description ; The Occupancy-Weighted Average B (OWAB) value per residue (in units Angstroms squared). This value is calculated by multiplying the B factor for each label_atom_id in the residue by its occupancy and then averaging this value over all atoms in the residue. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.OWAB" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_units.code angstroms_squared # _item_aliases.alias_name "_ModelledSubgroup.owab" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.residue_inclusion _item_description.description ; The proportion of all atoms of the residue in density ; # _item.name "_pdbx_vrpt_model_instance_geometry.residue_inclusion" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.residue_inclusion" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _pdbx_item_context.type WWPDB_DEPRECATED _pdbx_item_context.item_name "_pdbx_vrpt_model_instance_geometry.residue_inclusion" # save_ # save__pdbx_vrpt_model_instance_geometry.num_H_reduce _item_description.description ; This is the number of hydrogen atoms added and optimized by the MolProbity reduce software as part of the all-atom clashscore. ; # _item.name "_pdbx_vrpt_model_instance_geometry.num_H_reduce" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.num-H-reduce" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ _item_description.description ; The number of bond lengths compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.num_bonds_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.bonds_RMSZ _item_description.description ; The overall root mean square of the Z-score for deviations of bond lengths in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_model_instance_geometry.bonds_RMSZ" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.bonds_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.num_angles_RMSZ _item_description.description ; The number of bond angles compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.num_angles_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.angles_RMSZ _item_description.description ; The overall root mean square of the Z-score for deviations of bond angles in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). ; # _item.name "_pdbx_vrpt_model_instance_geometry.angles_RMSZ" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.angles_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry _item_description.description ; The software used to calculate the bond and angle RMSZ statistics. ; # _item.name "_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail molprobity . mogul . # save_ # save__pdbx_vrpt_model_instance_geometry.average_occupancy _item_description.description ; The average occupancy for the residue. Hydrogen atoms are excluded from consideration. X-ray specific produce by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.average_occupancy" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.avgoccu" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.ligand_chirality_outlier _item_description.description ; A flag indicating of a ligand has a chirality outlier. ; # _item.name "_pdbx_vrpt_model_instance_geometry.ligand_chirality_outlier" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_ModelledSubgroup.ligand_chirality_outlier" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save__pdbx_vrpt_model_instance_geometry.validate _item_description.description ; A flag for NMR entries to indicate if a residue should be included in calculating the overall entry scores ("True") or if it should be excluded from such calculations ("False"). ; # _item.name "_pdbx_vrpt_model_instance_geometry.validate" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail True . False . # _item_aliases.alias_name "_ModelledSubgroup.validate" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.cyrange_domain_id _item_description.description ; Identifier of the well-defined core (domain) to which the residue belongs, as determined by Cyrange. ; # _item.name "_pdbx_vrpt_model_instance_geometry.cyrange_domain_id" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.cyrange_domain_id" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.cis_peptide _item_description.description ; A flag to indicate that the residue is a cis-peptide. ; # _item.name "_pdbx_vrpt_model_instance_geometry.cis_peptide" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_ModelledSubgroup.cis_peptide" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save__pdbx_vrpt_model_instance_geometry.RNA_score _item_description.description ; MolProbity RNA match quality parameter "suiteness". The suiteness is a measure of how well the detailed local backbone conformation fits one of the most commonly observed (and thus presumably most favorable) conformational clusters. Varies between 1.0 meaning a good match to a commonly observed cluster to 0.0 meaning an outlier. ; # _item.name "_pdbx_vrpt_model_instance_geometry.RNA_score" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.RNAscore" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.RNA_suite _item_description.description ; MolProbity RNA_suite conformation analysis. RNA specific produced by the molprobity step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.RNA_suite" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_ModelledSubgroup.RNAsuite" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail NonRotameric . NotAvailable . Rotameric . Triaged/NotBinned . # save_ # save__pdbx_vrpt_model_instance_geometry.RNA_pucker _item_description.description ; Placeholder for reporting RNA pucker problem from MolProbity. ; # _item.name "_pdbx_vrpt_model_instance_geometry.RNA_pucker" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_ModelledSubgroup.RNApucker" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.flippable_sidechain _item_description.description ; MolProbity identifies side chains of asparagine, glutamine and histidine that can be be rotated ("flipped") to make optimal hydrogen bonds, improving its contacts with its neighbours, without affecting their fit to the experimental electron density. These residues will have flippable_sidechain="1". Protein and polypeptide specific produced by the molprobity step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.flippable_sidechain" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_ModelledSubgroup.flippable-sidechain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_enumeration.value 1 _item_enumeration.detail . # save_ # save__pdbx_vrpt_model_instance_geometry.ramachandran_class _item_description.description ; MolProbity Ramachandran plot classification for this residue one of "Favored", "Allowed" or "OUTLIER". Example: ramachandran_class="Favored" Protein and polypeptide specific produced by the molprobity step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.ramachandran_class" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_ModelledSubgroup.rama" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Favored . Allowed . OUTLIER . # save_ # save__pdbx_vrpt_model_instance_geometry.rotamer_class _item_description.description ; For proteins the MolProbity classification of the side conformation from the chi dihedral angles. For proline the ring pucker is classified as "Cg_endo", "Cg_exo" or "OUTLIER" Examples of common observed classifications: Protein and polypeptide specific produced by the molprobity step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.rotamer_class" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code line # loop_ _item_examples.case mt t OUTLIER m p m-20 m-85 tp t80 mt-10 Cg_endo Cg_exo # _item_aliases.alias_name "_ModelledSubgroup.rota" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.phi _item_description.description ; The phi torsion angle for the residue in degrees. Protein and polypeptide specific produced by the molprobity step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.phi" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.phi" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.psi _item_description.description ; The psi torsion angle for the residue in degrees. Protein and polypeptide specific produced by the molprobity step. ; # _item.name "_pdbx_vrpt_model_instance_geometry.psi" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.psi" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_geometry.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_model_instance_geometry.instance_id" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_model_instance_geometry.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_model_instance_geometry.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_model_instance_geometry.ordinal" _item.category_id pdbx_vrpt_model_instance_geometry _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_model_instance_density _category.id pdbx_vrpt_model_instance_density _category.description " This category provides information on X-ray density analysis of a residue. It is not DEPRECATED" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_model_instance_density.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # _pdbx_category_context.type WWPDB_DEPRECATED _pdbx_category_context.category_id pdbx_vrpt_model_instance_density # save_ # save__pdbx_vrpt_model_instance_density.natoms_eds _item_description.description ; The number of atoms in the residue returned by the EDS software. ; # _item.name "_pdbx_vrpt_model_instance_density.natoms_eds" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.NatomsEDS" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_density.RSRCC _item_description.description ; The real space correlation coefficient for the instance. This is an alternative to RSR for assessing how well the residue's calculated electron density map matches the EDS electron density map calculated from the experimental diffraction data. A value above 0.95 normally indicates a very good fit. RSCC around 0.90 are generally OK. A poor fit results in a value around or below 0.80. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_density.RSRCC" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.rscc" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_density.RSR _item_description.description ; Real Space R-value (RSR) for the residue from the EDS generated map. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_density.RSR" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.rsr" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_density.RSRZ _item_description.description ; RSR Z-score (RSRZ) is a normalisation of RSR specific to a residue type and a resolution bin. RSRZ is calculated only for standard amino acids and nucleotides in protein, DNA and RNA chains. A residue is considered an RSRZ outlier if its RSRZ value is greater than 2. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_density.RSRZ" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.rsrz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_model_instance_density.ligand_density_outlier _item_description.description ; A flag indicating an outlier in the electron density map for a ligand. ; # _item.name "_pdbx_vrpt_model_instance_density.ligand_density_outlier" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledSubgroup.ligand_density_outlier" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # save_ # save__pdbx_vrpt_model_instance_density.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_model_instance_density.instance_id" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_model_instance_density.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_model_instance_density.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_model_instance_density.ordinal" _item.category_id pdbx_vrpt_model_instance_density _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_model_instance_map_fitting _category.id pdbx_vrpt_model_instance_map_fitting _category.description " This category provides information on per residue map fitting analysis" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_model_instance_map_fitting.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_model_instance_map_fitting.natoms_eds _item_description.description ; The number of atoms in the residue returned by the EDS software. ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.natoms_eds" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_ModelledSubgroup.NatomsEDS" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_related.related_name "_pdbx_vrpt_model_instance_density.natoms_eds" _item_related.function_code replaces # save_ # save__pdbx_vrpt_model_instance_map_fitting.RSRCC _item_description.description ; The real space correlation coefficient for the instance. This is an alternative to RSR for assessing how well the residue's calculated electron density map matches the EDS electron density map calculated from the experimental diffraction data. A value above 0.95 normally indicates a very good fit. RSCC around 0.90 are generally OK. A poor fit results in a value around or below 0.80. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.RSRCC" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.rscc" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_related.related_name "_pdbx_vrpt_model_instance_density.RSRCC" _item_related.function_code replaces # save_ # save__pdbx_vrpt_model_instance_map_fitting.RSR _item_description.description ; Real Space R-value (RSR) for the residue from the EDS generated map. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.RSR" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.rsr" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_related.related_name "_pdbx_vrpt_model_instance_density.RSR" _item_related.function_code replaces # save_ # save__pdbx_vrpt_model_instance_map_fitting.RSRZ _item_description.description ; RSR Z-score (RSRZ) is a normalisation of RSR specific to a residue type and a resolution bin. RSRZ is calculated only for standard amino acids and nucleotides in protein, DNA and RNA chains. A residue is considered an RSRZ outlier if its RSRZ value is greater than 2. X-ray specific produced by the EDS step. ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.RSRZ" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.rsrz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_related.related_name "_pdbx_vrpt_model_instance_density.RSRZ" _item_related.function_code replaces # save_ # save__pdbx_vrpt_model_instance_map_fitting.ligand_density_outlier _item_description.description ; A flag indicating an outlier in the electron density map for a ligand. ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.ligand_density_outlier" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_ModelledSubgroup.ligand_density_outlier" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail Y . N . # _item_related.related_name "_pdbx_vrpt_model_instance_density.ligand_density_outlier" _item_related.function_code replaces # save_ # save__pdbx_vrpt_model_instance_map_fitting.residue_inclusion _item_description.description ; The proportion of all atoms of the residue in density ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.residue_inclusion" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_ModelledSubgroup.residue_inclusion" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # _item_related.related_name "_pdbx_vrpt_model_instance_geometry.residue_inclusion" _item_related.function_code replaces # save_ # save__pdbx_vrpt_model_instance_map_fitting.Q_score _item_description.description ; The Q-score for the residue in the map ; # _item.name "_pdbx_vrpt_model_instance_map_fitting.Q_score" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_model_instance_map_fitting.instance_id _item_description.description "A pointer to pdbx_vrpt_model_instance.id." # _item.name "_pdbx_vrpt_model_instance_map_fitting.instance_id" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_model_instance_map_fitting.instance_id" _item_linked.parent_name "_pdbx_vrpt_model_instance.id" # save_ # save__pdbx_vrpt_model_instance_map_fitting.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_model_instance_map_fitting.ordinal" _item.category_id pdbx_vrpt_model_instance_map_fitting _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_summary_diffraction _category.id pdbx_vrpt_summary_diffraction _category.description " This category provides summary information on the analysis of of the structure factor file for X-ray/Neutron entries." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary_diffraction.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary_diffraction.exp_method _item_description.description "Experimental method for statistics" # _item.name "_pdbx_vrpt_summary_diffraction.exp_method" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_summary_diffraction.Babinet_b _item_description.description ; REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. X-ray entry specific, obtained in the EDS step from REFMAC calculation. ; # _item.name "_pdbx_vrpt_summary_diffraction.Babinet_b" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.babinet_b" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.bulk_solvent_b _item_description.description ; REFMAC scaling parameter as reported in log output file. X-ray entry specific, obtained in the EDS step from REFMAC calculation. ; # _item.name "_pdbx_vrpt_summary_diffraction.bulk_solvent_b" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.bulk_solvent_b" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.Wilson_B_estimate _item_description.description ; An estimate of the overall B-value of the structure, calculated from the diffraction data. Units Angstroms squared. It serves as an indicator of the degree of order in the crystal and the value is usually not hugely different from the average B-value calculated from the model. X-ray entry specific, calculated by Phenix Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.Wilson_B_estimate" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_units.code angstroms_squared # _item_aliases.alias_name "_Entry.WilsonBestimate" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.I_over_sigma _item_description.description ; Each reflection has an intensity (I) and an uncertainty in measurement (sigma(I)), so I/sigma(I) is the signal-to-noise ratio. This ratio decreases at higher resolution. is the mean of individual I/sigma(I) values. Value for outer resolution shell is given in parentheses. In case structure factor amplitudes are deposited, Xtriage estimates the intensities first and then calculates this metric. When intensities are available in the deposited file, these are converted to amplitudes and then back to intensity estimate before calculating the metric. X-ray entry specific, calculated by Phenix Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.I_over_sigma" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_Entry.IoverSigma" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.num_miller_indices _item_description.description ; The number of Miller Indices reported by the Xtriage program. This should be the same as the number of _refln in the input structure factor file. X-ray entry specific, calculated by Phenix Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.num_miller_indices" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.numMillerIndices" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.Babinet_k _item_description.description ; REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. X-ray entry specific, obtained in the EDS step from REFMAC calculation. ; # _item.name "_pdbx_vrpt_summary_diffraction.Babinet_k" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.babinet_k" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.bulk_solvent_k _item_description.description ; REFMAC reported scaling parameter. X-ray entry specific, obtained in the EDS step from REFMAC calculation. ; # _item.name "_pdbx_vrpt_summary_diffraction.bulk_solvent_k" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.bulk_solvent_k" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean _item_description.description ; Padilla and Yeates twinning parameter <|L|>. Theoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case. X-ray entry specific, obtained from the Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.TwinL" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean _item_description.description ; Padilla and Yeates twinning parameter <|L**2|>. Theoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case. X-ray entry specific, obtained from the Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.TwinL2" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.DCC_R _item_description.description ; The overall R-factor from a DCC recalculation of an electron density map. Currently value is rounded to 2 decimal places. X-ray entry specific, obtained from the DCC program. ; # _item.name "_pdbx_vrpt_summary_diffraction.DCC_R" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.DCC_R" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.DCC_Rfree _item_description.description ; Rfree as calculated by DCC. ; # _item.name "_pdbx_vrpt_summary_diffraction.DCC_Rfree" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.DCC_Rfree" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.EDS_R _item_description.description ; The overall R factor from the EDS REFMAC calculation (no free set is used in this). Currently value is rounded to 2 decimal places. X-ray entry specific, obtained in the eds step from REFMAC calculation. ; # _item.name "_pdbx_vrpt_summary_diffraction.EDS_R" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.EDS_R" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.EDS_res_high _item_description.description ; The data high resolution diffraction limit, in Angstroms, found in the input structure factor file. X-ray entry specific, obtained in the EDS step. ; # _item.name "_pdbx_vrpt_summary_diffraction.EDS_res_high" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_Entry.EDS_resolution" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.EDS_res_low _item_description.description ; The data low resolution diffraction limit, in Angstroms, found in the input structure factor file. X-ray entry specific, obtained in the EDS step. ; # _item.name "_pdbx_vrpt_summary_diffraction.EDS_res_low" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_units.code angstroms # _item_aliases.alias_name "_Entry.EDS_resolution_low" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.Wilson_B_aniso _item_description.description ; Result of absolute likelihood based Wilson scaling, The anisotropic B value of the data is determined using a likelihood based approach. The resulting B tensor is reported, the 3 diagonal values are given first, followed by the 3 off diagonal values. A large spread in (especially the diagonal) values indicates anisotropy. X-ray entry specific, calculated by Phenix Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.Wilson_B_aniso" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code line # _item_aliases.alias_name "_Entry.WilsonBaniso" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.data_anisotropy _item_description.description ; The ratio (Bmax - Bmin) / Bmean where Bmax, Bmin and Bmean are computed from the B-values associated with the principal axes of the anisotropic thermal ellipsoid. This ratio is usually less than 0.5; for only 1% of PDB entries it is more than 1.0 (Read et al., 2011). X-ray entry specific, obtained from the Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.data_anisotropy" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.DataAnisotropy" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.trans_NCS_details _item_description.description ; A sentence giving the result of Xtriage's analysis on translational NCS. X-ray entry specific, obtained from the Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.trans_NCS_details" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code text # _item_examples.case "The largest off-origin peak in the Patterson function is 8.82% of the height of the origin peak. No significant pseudotranslation is detected." # _item_aliases.alias_name "_Entry.TransNCS" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.B_factor_type _item_description.description ; An indicator if isotropic B factors are partial or full values. ; # _item.name "_pdbx_vrpt_summary_diffraction.B_factor_type" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_Entry.B_factor_type" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_enumeration.value _item_enumeration.detail PARTIAL . FULL . # save_ # save__pdbx_vrpt_summary_diffraction.acentric_outliers _item_description.description ; The number of acentric reflections that Xtriage identifies as outliers on the basis of Wilson statistics. Note that if pseudo translational symmetry is present, a large number of 'outliers' will be present. X-ray entry specific, calculated by Phenix Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.acentric_outliers" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.acentric_outliers" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.centric_outliers _item_description.description ; The number of centric reflections that Xtriage identifies as outliers. X-ray entry specific, calculated by Phenix Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.centric_outliers" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.centric_outliers" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.data_completeness _item_description.description ; The percent completeness of diffraction data. ; # _item.name "_pdbx_vrpt_summary_diffraction.data_completeness" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.DataCompleteness" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_diffraction.number_reflns_R_free _item_description.description ; The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. X-ray entry specific, obtained from the DCC program. ; # _item.name "_pdbx_vrpt_summary_diffraction.number_reflns_R_free" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.num-free-reflections" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.percent_free_reflections _item_description.description ; A percentage, Normally percent proportion of the total number. Between 0% and 100%. ; # _item.name "_pdbx_vrpt_summary_diffraction.percent_free_reflections" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.percent-free-reflections" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers _item_description.description ; The percent of RSRZ outliers. ; # _item.name "_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.percent-RSRZ-outliers" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_diffraction.PDB_resolution_high _item_description.description ; The high resolution limit of the data. ; # _item.name "_pdbx_vrpt_summary_diffraction.PDB_resolution_high" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.PDB-resolution" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.PDB_resolution_low _item_description.description ; The low resolution limit of the diffraction data. ; # _item.name "_pdbx_vrpt_summary_diffraction.PDB_resolution_low" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.PDB-resolution-low" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.PDB_R _item_description.description ; The reported R in the model file. ; # _item.name "_pdbx_vrpt_summary_diffraction.PDB_R" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.PDB-R" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.PDB_Rfree _item_description.description ; The reported Rfree. ; # _item.name "_pdbx_vrpt_summary_diffraction.PDB_Rfree" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.PDB-Rfree" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.twin_fraction _item_description.description ; Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated list of operators with fractions is givens X-ray entry specific, obtained from the Xtriage program. ; # _item.name "_pdbx_vrpt_summary_diffraction.twin_fraction" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code text # _item_examples.case h,h-k,h-l:0.477;-h,-h+k,-l:0.020;-h,-k,-h+l:0.017 # _item_aliases.alias_name "_Entry.TwinFraction" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.Fo_Fc_correlation _item_description.description ; Fo,Fc correlation: The difference between the observed structure factors (Fo) and the calculated structure factors (Fc) measures the correlation between the model and the experimental data. X-ray entry specific, obtained in the eds step from REFMAC calculation. ; # _item.name "_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.Fo_Fc_correlation" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_diffraction.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_summary_diffraction.ordinal" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_summary_diffraction.Q_score _item_description.description ; The overall Q-score of the fit of coordinates to the electron map. The Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020) ; # _item.name "_pdbx_vrpt_summary_diffraction.Q_score" _item.category_id pdbx_vrpt_summary_diffraction _item.mandatory_code no # _item_type.code float # save_ # save_pdbx_vrpt_summary_geometry _category.id pdbx_vrpt_summary_geometry _category.description " This category provides a summary of geometrical issue information on the entry" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary_geometry.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary_geometry.percent_ramachandran_outliers _item_description.description ; The percentage of residues with Ramachandran outliers. ; # _item.name "_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.percent-rama-outliers" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_geometry.clashscore _item_description.description ; This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other. It is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms. For structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the well-defined (core) residues from ensemble analysis. ; # _item.name "_pdbx_vrpt_summary_geometry.clashscore" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.clashscore" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.angles_RMSZ _item_description.description ; The overall root mean square of the Z-score for deviations of bond angles in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. ; # _item.name "_pdbx_vrpt_summary_geometry.angles_RMSZ" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.angles_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.bonds_RMSZ _item_description.description ; The overall root mean square of the Z-score for deviations of bond lengths in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. ; # _item.name "_pdbx_vrpt_summary_geometry.bonds_RMSZ" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.bonds_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.num_angles_RMSZ _item_description.description ; The number of bond angles compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. ; # _item.name "_pdbx_vrpt_summary_geometry.num_angles_RMSZ" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.num_angles_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.num_bonds_RMSZ _item_description.description ; The number of bond lengths compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. ; # _item.name "_pdbx_vrpt_summary_geometry.num_bonds_RMSZ" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.num_bonds_rmsz" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.percent_rotamer_outliers _item_description.description ; The MolProbity sidechain outlier score (a percentage). Protein sidechains mostly adopt certain (combinations of) preferred torsion angle values (called rotamers or rotameric conformers), much like their backbone torsion angles (as assessed in the Ramachandran analysis). MolProbity considers the sidechain conformation of a residue to be an outlier if its set of torsion angles is not similar to any preferred combination. The sidechain outlier score is calculated as the percentage of residues with an unusual sidechain conformation with respect to the total number of residues for which the assessment is available. Example: percent-rota-outliers="2.44". Specific to structure that contain protein chains and have sidechains modelled. For NMR structures only the well-defined (core) residues from ensemble analysis will be considered. The percentage of residues with rotamer outliers. ; # _item.name "_pdbx_vrpt_summary_geometry.percent_rotamer_outliers" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.percent-rota-outliers" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_geometry.percent_ramachandran_outliers_full_length _item_description.description ; Only given for structures determined by NMR. The MolProbity Ramachandran outlier score for all atoms in the structure rather than just the well-defined (core) residues. ; # _item.name "_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers_full_length" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.percent-rama-outliers-full-length" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_geometry.percent_rotamer_outliers_full_length _item_description.description ; Only given for structures determined by NMR. The MolProbity sidechain outlier score for all atoms in the structure rather than just the well-defined (core) residues. ; # _item.name "_pdbx_vrpt_summary_geometry.percent_rotamer_outliers_full_length" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.percent-rota-outliers-full-length" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # loop_ _item_range.minimum _item_range.maximum 0. 0. 0. 100. 100. 100. # save_ # save__pdbx_vrpt_summary_geometry.clashscore_full_length _item_description.description ; Only given for structures determined by NMR. The MolProbity pdbx_vrpt_instance_clashes score for all label_atom_id pairs. ; # _item.name "_pdbx_vrpt_summary_geometry.clashscore_full_length" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.clashscore-full-length" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.num_H_reduce _item_description.description ; This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the all-atom clashscore. ; # _item.name "_pdbx_vrpt_summary_geometry.num_H_reduce" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.num-H-reduce" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_geometry.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_summary_geometry.ordinal" _item.category_id pdbx_vrpt_summary_geometry _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_summary_nmr _category.id pdbx_vrpt_summary_nmr _category.description " This category provides a summary of NMR report information" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary_nmr.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary_nmr.exp_method _item_description.description "Experimental method for statistics" # _item.name "_pdbx_vrpt_summary_nmr.exp_method" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_summary_nmr.nmr_models_consistency_flag _item_description.description ; A flag indicating if all models in the NMR ensemble contain the exact same atoms ("True") or if the models differ in this respect ("False"). ; # _item.name "_pdbx_vrpt_summary_nmr.nmr_models_consistency_flag" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code code # _item_aliases.alias_name "_Entry.nmr_models_consistency_flag" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.nmrclust_representative_model _item_description.description ; Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust. ; # _item.name "_pdbx_vrpt_summary_nmr.nmrclust_representative_model" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.nmrclust_representative_model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.medoid_model _item_description.description ; For each Cyrange well-defined core ("cyrange_domain") the id of the PDB_model_num which is most similar to other models as measured by pairwise RMSDs over the domain. For the whole entry ("Entry"), the medoid PDB_model_num of the largest core is taken as an overall representative of the structure. ; # _item.name "_pdbx_vrpt_summary_nmr.medoid_model" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.medoid_model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.nmrclust_number_of_outliers _item_description.description ; Number of models that do not belong to any cluster as deemed by NMRClust. ; # _item.name "_pdbx_vrpt_summary_nmr.nmrclust_number_of_outliers" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.nmrclust_number_of_outliers" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.nmrclust_number_of_models _item_description.description ; Number of models analysed by NMRClust - should in almost all cases be the same as the number of models in the NMR ensemble. ; # _item.name "_pdbx_vrpt_summary_nmr.nmrclust_number_of_models" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.nmrclust_number_of_models" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.nmrclust_number_of_clusters _item_description.description ; Total number of clusters in the NMR ensemble identified by NMRClust. ; # _item.name "_pdbx_vrpt_summary_nmr.nmrclust_number_of_clusters" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.nmrclust_number_of_clusters" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.cyrange_number_of_domains _item_description.description ; Total number of well-defined cores (domains) identified by Cyrange ; # _item.name "_pdbx_vrpt_summary_nmr.cyrange_number_of_domains" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code int # _item_aliases.alias_name "_Entry.cyrange_number_of_domains" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.chemical_shift_completeness _item_description.description ; Overall completeness of the chemical shift assignments for the well-defined regions of the structure. ; # _item.name "_pdbx_vrpt_summary_nmr.chemical_shift_completeness" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.chemical_shift_completeness" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.chemical_shift_completeness_full_length _item_description.description ; Overall completeness of the chemical shift assignments for the full macromolecule or complex as suggested by the molecular description of an entry (whether some portion of it is modelled or not). ; # _item.name "_pdbx_vrpt_summary_nmr.chemical_shift_completeness_full_length" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.chemical_shift_completeness_full_length" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.cyrange_error _item_description.description ; Diagnostic message from the wrapper of Cyrange software which identifies the well-defined cores (domains) of NMR protein structures. ; # _item.name "_pdbx_vrpt_summary_nmr.cyrange_error" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_Entry.cyrange_error" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.nmrclust_error _item_description.description ; Diagnostic message from the wrapper of NMRClust software which clusters NMR models. ; # _item.name "_pdbx_vrpt_summary_nmr.nmrclust_error" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_Entry.nmrclust_error" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_nmr.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_summary_nmr.ordinal" _item.category_id pdbx_vrpt_summary_nmr _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_summary_em _category.id pdbx_vrpt_summary_em _category.description " This category provides a summary of EM report information" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_summary_em.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_summary_em.exp_method _item_description.description "Experimental method for statistics" # _item.name "_pdbx_vrpt_summary_em.exp_method" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_summary_em.contour_level_primary_map _item_description.description ; The recommended contour level for the primary map of this deposition. ; # _item.name "_pdbx_vrpt_summary_em.contour_level_primary_map" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.contour_level_primary_map" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.atom_inclusion_all_atoms _item_description.description ; The proportion of all non hydrogen atoms within density. ; # _item.name "_pdbx_vrpt_summary_em.atom_inclusion_all_atoms" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.atom_inclusion_all_atoms" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.atom_inclusion_backbone _item_description.description ; The proportion of backbone atoms within density. ; # _item.name "_pdbx_vrpt_summary_em.atom_inclusion_backbone" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.atom_inclusion_backbone" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_pt_143 _item_description.description ; The resolution from the intersection of the author provided fsc and the indicator curve 0.143. ; # _item.name "_pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_pt_143" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.author_provided_fsc_resolution_by_cutoff_0.143" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_pt_333 _item_description.description ; The resolution from the intersection of the author provided fsc and the indicator curve 0.333. ; # _item.name "_pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_pt_333" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.author_provided_fsc_resolution_by_cutoff_0.333" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_pt_5 _item_description.description ; The resolution from the intersection of the author provided fsc and the indicator curve 0.5. ; # _item.name "_pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_pt_5" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.author_provided_fsc_resolution_by_cutoff_0.5" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_halfbit _item_description.description ; The resolution from the intersection of the author provided fsc and the indicator curve halfbit. ; # _item.name "_pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_halfbit" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.author_provided_fsc_resolution_by_cutoff_halfbit" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_onebit _item_description.description ; The resolution from the intersection of the author provided fsc and the indicator curve onebit. ; # _item.name "_pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_onebit" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.author_provided_fsc_resolution_by_cutoff_onebit" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_threesigma _item_description.description ; The resolution from the intersection of the author provided fsc and the indicator curve threesigma. ; # _item.name "_pdbx_vrpt_summary_em.author_provided_fsc_resolution_by_cutoff_threesigma" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.author_provided_fsc_resolution_by_cutoff_threesigma" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_pt_143 _item_description.description ; The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143. ; # _item.name "_pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_pt_143" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.calculated_fsc_resolution_by_cutoff_0.143" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_pt_333 _item_description.description ; The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333. ; # _item.name "_pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_pt_333" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.calculated_fsc_resolution_by_cutoff_0.333" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_pt_5 _item_description.description ; The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5. ; # _item.name "_pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_pt_5" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.calculated_fsc_resolution_by_cutoff_0.5" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_halfbit _item_description.description ; The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit. ; # _item.name "_pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_halfbit" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.calculated_fsc_resolution_by_cutoff_halfbit" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_onebit _item_description.description ; The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit. ; # _item.name "_pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_onebit" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.calculated_fsc_resolution_by_cutoff_onebit" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_threesigma _item_description.description ; The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma. ; # _item.name "_pdbx_vrpt_summary_em.calculated_fsc_resolution_by_cutoff_threesigma" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.calculated_fsc_resolution_by_cutoff_threesigma" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.EMDB_resolution _item_description.description ; The resolution reported in the entry. ; # _item.name "_pdbx_vrpt_summary_em.EMDB_resolution" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # _item_aliases.alias_name "_Entry.EMDB-resolution" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_summary_em.Q_score _item_description.description ; The overall Q-score of the fit of coordinates to the electron map. The Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020) ; # _item.name "_pdbx_vrpt_summary_em.Q_score" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_summary_em.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_summary_em.ordinal" _item.category_id pdbx_vrpt_summary_em _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_percentile_list _category.id pdbx_vrpt_percentile_list _category.description ' A "pdbx_vrpt_percentile_list" provides a summary of which structures are used for comparisons' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_percentile_list.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_percentile_list.exp_method _item_description.description "Experimental method for statistics" # _item.name "_pdbx_vrpt_percentile_list.exp_method" _item.category_id pdbx_vrpt_percentile_list _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_percentile_list.range _item_description.description "High resolution relative range of percentiles or 'all' to indicate all resolutions" # _item.name "_pdbx_vrpt_percentile_list.range" _item.category_id pdbx_vrpt_percentile_list _item.mandatory_code no # _item_type.code line # save_ # save__pdbx_vrpt_percentile_list.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_percentile_list.id" _item.category_id pdbx_vrpt_percentile_list _item.mandatory_code yes # _item_type.code code # save_ # save_pdbx_vrpt_percentile_type _category.id pdbx_vrpt_percentile_type _category.description ' A "pdbx_vrpt_percentile_type" provides a mapping of a type id to the percentile type' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_percentile_type.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_percentile_type.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_percentile_type.id" _item.category_id pdbx_vrpt_percentile_type _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_percentile_type.type _item_description.description "Describes the percentile type being reported" # _item.name "_pdbx_vrpt_percentile_type.type" _item.category_id pdbx_vrpt_percentile_type _item.mandatory_code yes # _item_type.code text # loop_ _item_enumeration.value _item_enumeration.detail all_atom_clashscore . Ramachandran_outlier_percent . rotamer_outliers_percent . R_value_R_free . RSRZ_outliers_percent . RNAsuiteness_percent . # save_ # save_pdbx_vrpt_percentile_conditions _category.id pdbx_vrpt_percentile_conditions _category.description ' A "pdbx_vrpt_percentile_conditions" provides a summary of various scores by resolution include number of structues comparing to' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_percentile_conditions.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_percentile_conditions.percentile_list_id _item_description.description "A pointer to pdbx_vrpt_percentile_list.id." # _item.name "_pdbx_vrpt_percentile_conditions.percentile_list_id" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_percentile_conditions.percentile_list_id" _item_linked.parent_name "_pdbx_vrpt_percentile_list.id" # save_ # save__pdbx_vrpt_percentile_conditions.type_id _item_description.description "A pointer to _pdbx_vrpt_percentile_type.id indicating the type" # _item.name "_pdbx_vrpt_percentile_conditions.type_id" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_percentile_conditions.type_id" _item_linked.parent_name "_pdbx_vrpt_percentile_type.id" # save_ # save__pdbx_vrpt_percentile_conditions.rank _item_description.description "The score or percentile" # _item.name "_pdbx_vrpt_percentile_conditions.rank" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_percentile_conditions.res_high _item_description.description "The high resolution limit of relative entries or '?' if all entries" # _item.name "_pdbx_vrpt_percentile_conditions.res_high" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_percentile_conditions.res_low _item_description.description "The low resolution limit of relative entries or '?' if all entries" # _item.name "_pdbx_vrpt_percentile_conditions.res_low" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_percentile_conditions.number_entries_total _item_description.description "The number of entries is this set of entries" # _item.name "_pdbx_vrpt_percentile_conditions.number_entries_total" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code no # _item_type.code int # save_ # save__pdbx_vrpt_percentile_conditions.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_percentile_conditions.id" _item.category_id pdbx_vrpt_percentile_conditions _item.mandatory_code yes # _item_type.code code # save_ # save_pdbx_vrpt_percentile_entity_view _category.id pdbx_vrpt_percentile_entity_view _category.description ' A "pdbx_vrpt_percentile_entity_view" provides various statistics on a per entity basis for relative and global structure comparisons' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_percentile_entity_view.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_percentile_entity_view.conditions_id _item_description.description "Points to a specific condition." # _item.name "_pdbx_vrpt_percentile_entity_view.conditions_id" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_percentile_entity_view.conditions_id" _item_linked.parent_name "_pdbx_vrpt_percentile_conditions.id" # save_ # save__pdbx_vrpt_percentile_entity_view.type_id _item_description.description "A pointer to _pdbx_vrpt_percentile_type.id indicating the type" # _item.name "_pdbx_vrpt_percentile_entity_view.type_id" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_percentile_entity_view.type_id" _item_linked.parent_name "_pdbx_vrpt_percentile_type.id" # save_ # save__pdbx_vrpt_percentile_entity_view.label_asym_id _item_description.description ; The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain. ; # _item.name "_pdbx_vrpt_percentile_entity_view.label_asym_id" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_percentile_entity_view.label_asym_id" _item_linked.parent_name "_pdbx_vrpt_asym.label_asym_id" # _item_aliases.alias_name "_PercentileEntityView.said" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_percentile_entity_view.PDB_model_num _item_description.description ; Model identifier. If the structure does not have multiple models then PDB_model_num will be "1". ; # _item.name "_pdbx_vrpt_percentile_entity_view.PDB_model_num" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_PercentileEntityView.model" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_percentile_entity_view.entity_id _item_description.description ; The entity id for the residue or chain. This is from item _atom_site.label_entity_id that is a pointer to _entity.id in the ENTITY category. ; # _item.name "_pdbx_vrpt_percentile_entity_view.entity_id" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code no # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_percentile_entity_view.entity_id" _item_linked.parent_name "_pdbx_vrpt_asym.entity_id" # _item_aliases.alias_name "_PercentileEntityView.ent" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_percentile_entity_view.auth_asym_id _item_description.description ; The auth_asym_id identifier for the polymer. ; # _item.name "_pdbx_vrpt_percentile_entity_view.auth_asym_id" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_PercentileEntityView.chain" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd _item_aliases.version V6.00 # save_ # save__pdbx_vrpt_percentile_entity_view.rank _item_description.description "The score or percentile" # _item.name "_pdbx_vrpt_percentile_entity_view.rank" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_percentile_entity_view.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_percentile_entity_view.ordinal" _item.category_id pdbx_vrpt_percentile_entity_view _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_database _category.id pdbx_vrpt_database _category.description ' A "pdbx_vrpt_database" provides the accession codes used in this entry' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_database.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_database.code _item_description.description "Accession code" # _item.name "_pdbx_vrpt_database.code" _item.category_id pdbx_vrpt_database _item.mandatory_code no # _item_type.code line # save_ # save__pdbx_vrpt_database.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_database.id" _item.category_id pdbx_vrpt_database _item.mandatory_code yes # _item_type.code code # save_ # save_pdbx_vrpt_exptl _category.id pdbx_vrpt_exptl _category.description ' A "pdbx_vrpt_exptl" list the types of experiments used in this entry' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_exptl.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_exptl.method _item_description.description "Experimental methods used in structure determination" # _item.name "_pdbx_vrpt_exptl.method" _item.category_id pdbx_vrpt_exptl _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_exptl.ordinal _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_exptl.ordinal" _item.category_id pdbx_vrpt_exptl _item.mandatory_code yes # _item_type.code int # save_ # save_pdbx_vrpt_entity _category.id pdbx_vrpt_entity _category.description ' A "pdbx_vrpt_entity" lists the entity and type in the model' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_entity.id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_entity.id _item_description.description "Uniquely identifies each instance of this category." # _item.name "_pdbx_vrpt_entity.id" _item.category_id pdbx_vrpt_entity _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_entity.type _item_description.description "Describes the percentile type being reported" # _item.name "_pdbx_vrpt_entity.type" _item.category_id pdbx_vrpt_entity _item.mandatory_code yes # _item_type.code code # loop_ _item_enumeration.value _item_enumeration.detail macrolide . non-polymer . polymer . branched . water . # save_ # save__pdbx_vrpt_entity.description _item_description.description "The name of the entity" # _item.name "_pdbx_vrpt_entity.description" _item.category_id pdbx_vrpt_entity _item.mandatory_code no # _item_type.code line # save_ # save_pdbx_vrpt_asym _category.id pdbx_vrpt_asym _category.description ' A "pdbx_vrpt_asym" provides a mapping between the label_asym_id and entity in the model' _category.mandatory_code no # _category_key.name "_pdbx_vrpt_asym.label_asym_id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_asym.label_asym_id _item_description.description "The _struct_asym.label_asym_id in the PDB_model_num" # _item.name "_pdbx_vrpt_asym.label_asym_id" _item.category_id pdbx_vrpt_asym _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_asym.entity_id _item_description.description ; The entity id corresponding to the label_asym_id. ; # _item.name "_pdbx_vrpt_asym.entity_id" _item.category_id pdbx_vrpt_asym _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_asym.entity_id" _item_linked.parent_name "_pdbx_vrpt_entity.id" # save_ # save_pdbx_vrpt_em_graph_fsc_indicator_curve _category.id pdbx_vrpt_em_graph_fsc_indicator_curve _category.description " EM validation report 2D plot of Fourier Shell Correlation (fsc) indicator curve" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_graph_fsc_indicator_curve.graph_id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_graph_fsc_indicator_curve.graph_id _item_description.description " A unique identifier for a EM validation report 2D graph." # _item.name "_pdbx_vrpt_em_graph_fsc_indicator_curve.graph_id" _item.category_id pdbx_vrpt_em_graph_fsc_indicator_curve _item.mandatory_code yes # _item_type.code line # _item_linked.child_name "_pdbx_vrpt_em_graph_fsc_indicator_curve.graph_id" _item_linked.parent_name "_pdbx_vrpt_em_2d_graph_info.graph_id" # save_ # save__pdbx_vrpt_em_graph_fsc_indicator_curve.type _item_description.description " The fsc indicator curve type (e.g. threshold)." # _item.name "_pdbx_vrpt_em_graph_fsc_indicator_curve.type" _item.category_id pdbx_vrpt_em_graph_fsc_indicator_curve _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_em_graph_fsc_indicator_curve.curve_name _item_description.description " The fsc indicator curve name." # _item.name "_pdbx_vrpt_em_graph_fsc_indicator_curve.curve_name" _item.category_id pdbx_vrpt_em_graph_fsc_indicator_curve _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_em_graph_fsc_indicator_curve.data_curve_name _item_description.description " The fsc data (curve_name) used to calculate this fsc indicator curve." # _item.name "_pdbx_vrpt_em_graph_fsc_indicator_curve.data_curve_name" _item.category_id pdbx_vrpt_em_graph_fsc_indicator_curve _item.mandatory_code yes # _item_type.code line # save_ # save_pdbx_vrpt_em_graph_fsc_curve _category.id pdbx_vrpt_em_graph_fsc_curve _category.description " EM validation report 2D plot of Fourier Shell Correlation (fsc) curve" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_graph_fsc_curve.graph_id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_graph_fsc_curve.graph_id _item_description.description " A unique identifier for a EM validation report 2D graph." # _item.name "_pdbx_vrpt_em_graph_fsc_curve.graph_id" _item.category_id pdbx_vrpt_em_graph_fsc_curve _item.mandatory_code yes # _item_type.code line # _item_linked.child_name "_pdbx_vrpt_em_graph_fsc_curve.graph_id" _item_linked.parent_name "_pdbx_vrpt_em_2d_graph_info.graph_id" # save_ # save__pdbx_vrpt_em_graph_fsc_curve.type _item_description.description " The fsc curve type (e.g. half_map to half_map fsc)." # _item.name "_pdbx_vrpt_em_graph_fsc_curve.type" _item.category_id pdbx_vrpt_em_graph_fsc_curve _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_em_graph_fsc_curve.curve_name _item_description.description " The fsc curve name." # _item.name "_pdbx_vrpt_em_graph_fsc_curve.curve_name" _item.category_id pdbx_vrpt_em_graph_fsc_curve _item.mandatory_code yes # _item_type.code line # save_ # save_pdbx_vrpt_em_resolution_intersections _category.id pdbx_vrpt_em_resolution_intersections _category.description " EM validation report intersections between fsc_curves and their corresponding fsc_indicator_curves" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_resolution_intersections.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_resolution_intersections.ordinal _item_description.description "Uniquely identifies each instance of data in this category." # _item.name "_pdbx_vrpt_em_resolution_intersections.ordinal" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_em_resolution_intersections.resolution_units _item_description.description "Units of resolution." # _item.name "_pdbx_vrpt_em_resolution_intersections.resolution_units" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code no # _item_type.code code # _item_default.value A # save_ # save__pdbx_vrpt_em_resolution_intersections.spatial_frequency_units _item_description.description "Units of spatial frequency." # _item.name "_pdbx_vrpt_em_resolution_intersections.spatial_frequency_units" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code no # _item_type.code code # _item_default.value 1/A # save_ # save__pdbx_vrpt_em_resolution_intersections.correlation _item_description.description "fsc intersection correlation." # _item.name "_pdbx_vrpt_em_resolution_intersections.correlation" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_em_resolution_intersections.resolution _item_description.description "fsc intersection resolution." # _item.name "_pdbx_vrpt_em_resolution_intersections.resolution" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code no # _item_type.code float # save_ # save__pdbx_vrpt_em_resolution_intersections.spatial_frequency _item_description.description "fsc intersection spatial frequency." # _item.name "_pdbx_vrpt_em_resolution_intersections.spatial_frequency" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code yes # _item_type.code float # save_ # save__pdbx_vrpt_em_resolution_intersections.curve _item_description.description "fsc curve name." # _item.name "_pdbx_vrpt_em_resolution_intersections.curve" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_em_resolution_intersections.type _item_description.description "fsc curve type." # _item.name "_pdbx_vrpt_em_resolution_intersections.type" _item.category_id pdbx_vrpt_em_resolution_intersections _item.mandatory_code yes # _item_type.code line # save_ # save_pdbx_vrpt_em_graph_atom_inclusion _category.id pdbx_vrpt_em_graph_atom_inclusion _category.description " EM validation report 2D plot of atom inclusion for the primary map" _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_graph_atom_inclusion.graph_id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_graph_atom_inclusion.graph_id _item_description.description " A unique identifier for a EM validation report 2D graph." # _item.name "_pdbx_vrpt_em_graph_atom_inclusion.graph_id" _item.category_id pdbx_vrpt_em_graph_atom_inclusion _item.mandatory_code yes # _item_type.code line # _item_linked.child_name "_pdbx_vrpt_em_graph_atom_inclusion.graph_id" _item_linked.parent_name "_pdbx_vrpt_em_2d_graph_info.graph_id" # save_ # save__pdbx_vrpt_em_graph_atom_inclusion.type _item_description.description " The atom type subset for this graph" # _item.name "_pdbx_vrpt_em_graph_atom_inclusion.type" _item.category_id pdbx_vrpt_em_graph_atom_inclusion _item.mandatory_code yes # _item_type.code line # loop_ _item_enumeration.value _item_enumeration.detail all_atoms "Containing the data required to plot the atom inclusion for for all atoms." backbone "Containing the data required to plot the atom inclusion for the backbone." # save_ # save_pdbx_vrpt_em_details _category.id pdbx_vrpt_em_details _category.description " This category provides details specific to EM." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_details.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_details.ordinal _item_description.description "Uniquely identifies each instance of data in this category." # _item.name "_pdbx_vrpt_em_details.ordinal" _item.category_id pdbx_vrpt_em_details _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_em_details.recommended_contour_level _item_description.description "Recommended contour level for the primary map of this entry." # _item.name "_pdbx_vrpt_em_details.recommended_contour_level" _item.category_id pdbx_vrpt_em_details _item.mandatory_code yes # _item_type.code float # _item_aliases.alias_name "_Entry.RecommendedContourLevel" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save_pdbx_vrpt_em_2d_graph_data _category.id pdbx_vrpt_em_2d_graph_data _category.description " pdbx_vrpt_em_2d_graph_data contains the data contents for EM validation report 2D graphs." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_2d_graph_data.ordinal" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_2d_graph_data.ordinal _item_description.description "Uniquely identifies each instance of data in this category." # _item.name "_pdbx_vrpt_em_2d_graph_data.ordinal" _item.category_id pdbx_vrpt_em_2d_graph_data _item.mandatory_code yes # _item_type.code int # save_ # save__pdbx_vrpt_em_2d_graph_data.graph_data_id _item_description.description "A reference to the 2D graph containing this item of data." # _item.name "_pdbx_vrpt_em_2d_graph_data.graph_data_id" _item.category_id pdbx_vrpt_em_2d_graph_data _item.mandatory_code yes # _item_type.code code # _item_linked.child_name "_pdbx_vrpt_em_2d_graph_data.graph_data_id" _item_linked.parent_name "_pdbx_vrpt_em_2d_graph_info.graph_data_id" # save_ # save__pdbx_vrpt_em_2d_graph_data.x_value _item_description.description "Data X-value." # _item.name "_pdbx_vrpt_em_2d_graph_data.x_value" _item.category_id pdbx_vrpt_em_2d_graph_data _item.mandatory_code yes # _item_type.code float # save_ # save__pdbx_vrpt_em_2d_graph_data.y_value _item_description.description "Data Y-value." # _item.name "_pdbx_vrpt_em_2d_graph_data.y_value" _item.category_id pdbx_vrpt_em_2d_graph_data _item.mandatory_code yes # _item_type.code float # save_ # save_pdbx_vrpt_em_2d_graph_info _category.id pdbx_vrpt_em_2d_graph_info _category.description " pdbx_vrpt_em_2d_graph_info contains common details for representation of EM validation report 2D graphs." _category.mandatory_code no # _category_key.name "_pdbx_vrpt_em_2d_graph_info.graph_id" # loop_ _category_group.id inclusive_group validation_report_group # save_ # save__pdbx_vrpt_em_2d_graph_info.graph_data_id _item_description.description " An identifier for the data set associated with this 2D graph." # _item.name "_pdbx_vrpt_em_2d_graph_info.graph_data_id" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code yes # _item_type.code code # save_ # save__pdbx_vrpt_em_2d_graph_info.graph_id _item_description.description " A unique identifier for a EM validation report 2D graph." # _item.name "_pdbx_vrpt_em_2d_graph_info.graph_id" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code yes # _item_type.code line # save_ # save__pdbx_vrpt_em_2d_graph_info.title _item_description.description " 2D graph title." # _item.name "_pdbx_vrpt_em_2d_graph_info.title" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.Title" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save__pdbx_vrpt_em_2d_graph_info.x_axis_title _item_description.description " 2D graph X-axis title." # _item.name "_pdbx_vrpt_em_2d_graph_info.x_axis_title" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code yes # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.xTitle" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save__pdbx_vrpt_em_2d_graph_info.x_axis_scale _item_description.description " 2D graph X-axis scale. (linear if not provided)" # _item.name "_pdbx_vrpt_em_2d_graph_info.x_axis_scale" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.xScale" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save__pdbx_vrpt_em_2d_graph_info.x_axis_units _item_description.description " 2D graph X-axis units. (arbitrary if not provided)" # _item.name "_pdbx_vrpt_em_2d_graph_info.x_axis_units" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.xUnit" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save__pdbx_vrpt_em_2d_graph_info.y_axis_title _item_description.description " 2D graph Y-axis title." # _item.name "_pdbx_vrpt_em_2d_graph_info.y_axis_title" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code yes # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.xTitle" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save__pdbx_vrpt_em_2d_graph_info.y_axis_scale _item_description.description " 2D graph Y-axis scale. (linear if not provided)" # _item.name "_pdbx_vrpt_em_2d_graph_info.y_axis_scale" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.xScale" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save__pdbx_vrpt_em_2d_graph_info.y_axis_units _item_description.description " 2D graph X-axis units. (arbitrary if not provided)" # _item.name "_pdbx_vrpt_em_2d_graph_info.y_axis_units" _item.category_id pdbx_vrpt_em_2d_graph_info _item.mandatory_code no # _item_type.code text # _item_aliases.alias_name "_EM_validation.graph.xUnit" _item_aliases.dictionary http://wwpdb.org/validation/schema/wwpdb_validation_v006.xsd _item_aliases.version V006 # save_ # save_audit_conform _category.description ; Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. ; _category.id audit_conform _category.mandatory_code no # loop_ _category_key.name "_audit_conform.dict_name" "_audit_conform.dict_version" # loop_ _category_group.id inclusive_group audit_group # _category_examples.detail ; Example 1 - any file conforming to the current CIF core dictionary. ; _category_examples.case ; _audit_conform.dict_name cif_core.dic _audit_conform.dict_version 2.3.1 _audit_conform.dict_location ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic ; # save_ # save__audit_conform.dict_location _item_description.description ; A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. ; # _item.name "_audit_conform.dict_location" _item.category_id audit_conform _item.mandatory_code no # _item_aliases.alias_name "_audit_conform_dict_location" _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_type.code text # save_ # save__audit_conform.dict_name _item_description.description ; The string identifying the highest-level dictionary defining data names used in this file. ; # _item.name "_audit_conform.dict_name" _item.category_id audit_conform _item.mandatory_code yes # _item_aliases.alias_name "_audit_conform_dict_name" _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_type.code text # save_ # save__audit_conform.dict_version _item_description.description ; The version number of the dictionary to which the current data block conforms. ; # _item.name "_audit_conform.dict_version" _item.category_id audit_conform _item.mandatory_code yes # _item_aliases.alias_name "_audit_conform_dict_version" _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_type.code text # save_ #