vrpt Schema

• Primary Key: pdbid
• Tables: 69

brief_summary

Column	Type	Description
pdbid	text
docid	bigint
update_date	timestamp without time zone	Entry update date (within the RDB).
keywords	text[]	Array of keywords.

audit_conform

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
dict_location	text	A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms.
dict_name	text	The string identifying the highest-level dictionary defining data names used in this file.
dict_version	text	The version number of the dictionary to which the current data block conforms.

entity

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
id	text	The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier.
type	text	Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category.
src_method	text	The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category.
pdbx_description	text	A description of the entity. Corresponds to the compound name in the PDB format.
formula_weight	double precision	Formula mass in daltons of the entity.
pdbx_number_of_molecules	integer	A place holder for the number of molecules of the entity in the entry.
pdbx_ec	text	Enzyme Commission (EC) number(s)
pdbx_mutation	text	Details about any entity mutation(s).
pdbx_fragment	text	Entity fragment description(s).
details	text	A description of special aspects of the entity.

entry

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
id	text	The value of _entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier.

pdbx_vrpt_assign_completeness_full_length

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of this category.
number_of_assigned_shifts	integer	Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that have a chemical shift assignment.
number_of_unassigned_shifts	integer	Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that lack a chemical shift assignment
number_of_shifts	integer	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.
type	text	"Type" refers to a subset of assignments: overall, backbone, aliphatic sidechain, aromatic protein rings, nucleic acid base and ribose or deoxyribose ring.
element	text	The chemical element (isotope) for which the assignment completeness is calculated.

pdbx_vrpt_assign_completeness_well_defined

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each well defined region.
number_of_assigned_shifts	integer	Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that have a chemical shift assignment.
number_of_unassigned_shifts	integer	Number of typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C) in the structure that lack a chemical shift assignment
number_of_shifts	integer	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.
type	text	"Type" refers to a subset of assignments: overall, backbone, aliphatic sidechain, aromatic protein rings, nucleic acid base and ribose or deoxyribose ring.
element	text	The chemical element (isotope) for which the assignment completeness is calculated.

pdbx_vrpt_asym

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
label_asym_id	text	The _struct_asym.label_asym_id in the PDB_model_num
entity_id	text	The entity id corresponding to the label_asym_id.

pdbx_vrpt_chemical_shift_list

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each chemical shift.
file_id	integer	An identifier of a chemical shifts file.
file_name	text	The name of the chemical shifts file supplied to the validation pipeline.
block_name	text	Label of the section that contains chemical shifts.
list_id	text	Identifier of the chemical shift list in the file.
type	text	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").
number_of_errors_while_mapping	integer	Number of chemical shifts that could not be mapped to structure.
number_of_warnings_while_mapping	integer	Currently not used. Reserved for ambiguous mappings.
number_of_mapped_shifts	integer	Number of chemical shifts successfully mapped to the structure.
number_of_parsed_shifts	integer	Number of chemical shifts successfully parsed.
total_number_of_shifts	integer	Total number of records in the chemical shift list.
number_of_unparsed_shifts	integer	Number of chemical shifts that could not be parsed.

pdbx_vrpt_chemical_shift_outlier

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each outlier.
auth_asym_id	text	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"
rescode	text	The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id
auth_seq_id	integer	The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
value	double precision	Value in ppm of a chemical shift
zscore	double precision	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.
prediction	text	The mean value of the chemical shift expected from the BMRB statistics.
method	text	Method to determine the expected value and standard deviation. At present this is limited to BMRB statistics.

pdbx_vrpt_cyrange_domain

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each domain.
domain	integer	Identifier of the well-defined core
number_of_gaps	integer	Number of omissions from the contiguous protein _atom_site.auth_asym_id within the individual well-defined core (domain).
number_of_residues	integer	Number of residues composing the individual well-defined core (domain).
percentage_of_core	double precision	What fraction the individual core contributes to the total well-defined portion of the protein.
rmsd	double precision	Average pairwise backbone RMSD of the individual well-defined core (domain) over the ensemble.
medoid_model	integer	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.
medoid_rmsd	double precision	Average RMSD between the medoid model and other members of the ensemble.
residue_string	text	Simplified description of the residue composition of the individual well-defined core (domain).

pdbx_vrpt_database

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
code	text	Accession code
id	text	Uniquely identifies each instance of this category.
extended_code	text	Extended accession code

pdbx_vrpt_dihedralangle_ensemble_violation

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ang_rest_type	text	The type of dihedral-angle restraint.
violations_count	integer	Number of violated restraints
ensemble_dihedral_count	text	Indicates the count of the ensemble
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_dihedralangle_violation_ensemble_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
fraction_of_ensemble_count	integer	Number of violated models for given set of violated restraints
fraction_of_ensemble_percent	double precision	Percentage of violated models for given set of violated restraints
id	text	Uniquely identifies each instance of this category.

pdbx_vrpt_dihedralangle_violation_model

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ang_rest_type	text	The type of dihedral-angle restraint
violations_count	integer	Number of violated restraints.
PDB_model_num	integer	Model number.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_dihedralangle_violation_model_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
PDB_model_num	integer	Model number in summary.
max_violation	double precision	The maximum value of violation of a particular restraint in an ensemble
mean_violation	double precision	The mean value of the violation of a given restraint in an ensemble.
standard_deviation	double precision	The standard deviation of the value of the violations of a given restraint in an ensemble.
median_violation	double precision	The median value of the violation of a given restraint in an ensemble
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_dihedralangle_violations_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
restraint_type	text	The dihedral-angle restraint type (PHI,PSI,etc)
consistently_violated_count	integer	Number of restraints that are violated in all models
consistently_violated_percent_total	double precision	Percentage of restraints that are violated in all models against total number of restraints.
consistently_violated_percent_type	double precision	Percentage of restraints that are violated in all models against number of restraints in a given restraint type.
restraints_count	integer	Number of restraints in a given restraint type.
violated_count	integer	Number of restraints that are violated that are violated at least in one model.
percent_total	double precision	Percentage of restraints in a given restraint type.
violated_percent_total	double precision	Percentage of restraints that are violated at least in one model in given restraint type against the total restraints
violated_percent_type	double precision	Percentage of restraints that are violated at least in one model against the total number of restraints in a given restraints type
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_distance_violation_ensemble

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
dist_rest_type	text	The type of distance restraint (intraresidue, sequential, etc.)
violations_count	integer	Number of violated restraints in ensemble.
ensemble_distance_count	text	Number of violated models for given set of violated restraint
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_distance_violation_model_restraints

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
dist_rest_type	text	The type of distance restraint (intraresidue, sequential, etc.).
violations_count	integer	Number of violated restraints.
PDB_model_num	text	The model number.
ordinal	integer	Uniquely identifies each model restraint.

pdbx_vrpt_distance_violation_model_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
max_violation	double precision	The maximum value of violation of a particular restraint in an ensemble.
mean_violation	double precision	The mean value of the violation of a given restraint in an ensemble.
PDB_model_num	integer	Model identifier. If the structure does not have multiple models then PDB_model_num will be "1".
standard_deviation	double precision	The standard deviation of the value of the violations of a given restraint in an ensemble.
median_violation	double precision	The median value of the violation of a given restraint in an ensemble
ordinal	integer	Uniquely identifies each distance violation.

pdbx_vrpt_distance_violation_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
restraint_type	text	The restraint type (Intra-residue, Sequential, MediumRange, LongRange, InterChain, Total)
restraint_sub_type	text	The restraint sub type (BackboneBackbone, BackboneSidechain, SidechainSidechain, all)
consistently_violated_count	integer	Number of restraints that are violated in all models
consistently_violated_percent_total	double precision	Percentage of restraints that are violated in all models against total number of restraints
consistently_violated_percent_type	double precision	Percentage of restraints that are violated in all models against number of restraints in a given restraint type.
restraints_count	integer	Number of restraints in a given restraint type.
violated_count	integer	Number of restraints that are violated at least in one model
percent_total	double precision	Percentage of restraints in a given restraint type
violated_percent_total	double precision	Percentage of restraints that are violated at least in one model in given restraint type against the total restraints.
violated_percent_type	double precision	Percentage of restraints that are violated at least in one model against the total number of restraints in a given restraints type.
ordinal	integer	Uniquely identifies each violation summary.

pdbx_vrpt_distance_violations_ensemble_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
fraction_of_ensemble_count	integer	Number of violated models for given set of violated restraints.
fraction_of_ensemble_percent	double precision	Percentage of violated models for given set of violated restraints
id	text	Uniquely identifies each instance of this category.

pdbx_vrpt_em_2d_graph_data

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of data in this category.
graph_data_id	text	A reference to the 2D graph containing this item of data.
x_value	double precision	Data X-value.
y_value	double precision	Data Y-value.

pdbx_vrpt_em_2d_graph_info

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
graph_data_id	text	An identifier for the data set associated with this 2D graph.
graph_id	text	A unique identifier for a EM validation report 2D graph.
title	text	2D graph title.
x_axis_title	text	2D graph X-axis title.
x_axis_units	text	2D graph X-axis units. (arbitrary if not provided)
y_axis_title	text	2D graph Y-axis title.
y_axis_scale	text	2D graph Y-axis scale. (linear if not provided)
y_axis_units	text	2D graph X-axis units. (arbitrary if not provided)

pdbx_vrpt_em_details

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of data in this category.
recommended_contour_level	double precision	Recommended contour level for the primary map of this entry.

pdbx_vrpt_em_graph_atom_inclusion

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
graph_id	text	A unique identifier for a EM validation report 2D graph.
type	text	The atom type subset for this graph

pdbx_vrpt_em_graph_fsc_curve

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
graph_id	text	A unique identifier for a EM validation report 2D graph.
type	text	The fsc curve type (e.g. half_map to half_map fsc).
curve_name	text	The fsc curve name.

pdbx_vrpt_em_graph_fsc_indicator_curve

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
graph_id	text	A unique identifier for a EM validation report 2D graph.
type	text	The fsc indicator curve type (e.g. threshold).
curve_name	text	The fsc indicator curve name.
data_curve_name	text	The fsc data (curve_name) used to calculate this fsc indicator curve.

pdbx_vrpt_em_resolution_intersections

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of data in this category.
resolution_units	text	Units of resolution.
spatial_frequency_units	text	Units of spatial frequency.
correlation	double precision	fsc intersection correlation.
resolution	double precision	fsc intersection resolution.
spatial_frequency	double precision	fsc intersection spatial frequency.
curve	text	fsc curve name.
type	text	fsc curve type.

pdbx_vrpt_entity

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
id	text	Uniquely identifies each instance of this category.
type	text	Describes the percentile type being reported
description	text	The name of the entity

pdbx_vrpt_exptl

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
method	text	Experimental methods used in structure determination
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_instance_clashes

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each clash instance.
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
cid	integer	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.
clashmag	double precision	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.
dist	double precision	The distance in Angstroms between two atoms involved a clash.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.

pdbx_vrpt_instance_intra_angle_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each angle outlier.
mean	double precision	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.
stdev	double precision	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.
obs	double precision	The observed value for bond angle, that is the value fouund for the atoms involved.
Z	double precision	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.
link	text	Flag indicating that the bond involves an atom that is in another residue.
atom_1	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_2	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_3	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.

pdbx_vrpt_instance_intra_bond_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each outlier.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
atom_1	text	A label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_2	text	A label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
mean	double precision	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.
stdev	double precision	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.
obs	double precision	The observed value for the bond length. that is the value found in the structure being analyzed for the atoms involved.
Z	double precision	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.
link	text	Flag indicating that the bond involves an atom that is in another residue

pdbx_vrpt_instance_intra_plane_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each planar outlier.
type	text	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".
improper	double precision	For a type="mainchain" outlier, the improper torsion angle in degrees.
omega	double precision	For a type="peptide" outlier, the omega torsion angle in degrees.
plane_rmsd	double precision	For a type="sidechain" outlier, the root mean squared deviation from the mean plane in Angstroms.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.

pdbx_vrpt_instance_mogul_angle_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
obsval	double precision	The observed value for the bond angle that is the value found in the structure being analyzed for the atoms involved.
mean	double precision	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.
stdev	double precision	The standard deviation for the bond angle. Source is standard deviation found Mogul analysis of CSD structures that have a similar local chemistry.
numobs	integer	The number of observations found for bond length in the Mogul analysis.
Zscore	double precision	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.
mindiff	double precision	The difference to the nearest value of the bond angle found in the Mogul analysis.
atom_1	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_2	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_3	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_instance_mogul_bond_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
obsval	double precision	The observed value for the bond length that is the value found in the structure being analyzed for the atoms involved.
mean	double precision	The "ideal" value of the bond length. Source is mean value from Mogul analysis of CSD structures that have a similar local chemistry.
stdev	double precision	The standard deviation for the bond length. Source is standard deviation found from Mogul analysis of CSD structures that have a similar local chemistry.
numobs	integer	The number of observations found for bond length or bond angle or torsion angle in the Mogul analysis.
Zscore	double precision	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.
mindiff	double precision	The difference to the nearest value of the bond length found in the Mogul analysis.
atom_1	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_2	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each bond outlier.

pdbx_vrpt_instance_mogul_ring_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
atoms	text	A comma separated list of label_atom_id names.
mean	double precision	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.
mindiff	double precision	The difference to the nearest value thetorsion angle found in the Mogul analysis.
stdev	double precision	The standard deviation of the torsion angles. Source is standard deviation found in Mogul analysis of CSD structures that have a similar local chemistry.
numobs	integer	The number of observations found for torsion angles in the Mogul analysis.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each ring outlier.

pdbx_vrpt_instance_mogul_torsion_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
obsval	double precision	The observed value for the torsion angle, that is the value found in the structure being analyzed for the atoms involved.
mean	double precision	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.
mindiff	double precision	The difference to the nearest value of the torsion angle found in the Mogul analysis.
numobs	integer	The number of observations found for torsion angle in the Mogul analysis.
stdev	double precision	The standard deviation for the torsion angle. Source is standard deviation found from Mogul analysis of CSD structures that have a similar local chemistry.
local_density	double precision	The local density is the percentage of observed Mogul torsion angles within certain units of the query torsion angle.
atom_1	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_2	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_3	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_4	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each torsion outlier.

pdbx_vrpt_instance_stereo_outliers

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each stereo outlier.
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
problem	text	The type of chiral problem that the label_atom_id has. either "WRONG HAND" or "PLANAR"
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.

pdbx_vrpt_instance_symm_clashes

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each symmetry clash.
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
symop	text	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.
scid	integer	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.
clashmag	double precision	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.
dist	double precision	The distance in Angstroms between two atoms involved a clash.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.

pdbx_vrpt_model_instance

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
id	text	Uniquely identifies each instance of the model.
auth_asym_id	text	The auth_asym_id identifier for the residue is the same as in the model mmCIF item _atom_site.auth_asym_id.
auth_seq_id	integer	The authors residue number for a residue. This is obtained from _atom_site.auth_seq_id
label_comp_id	text	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.
PDB_model_num	integer	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".
label_alt_id	text	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
PDB_ins_code	text	Insertion code for residue from _atom_site.pdbx_PDB_ins_code
entity_id	text	The entity id for the residue or chain. This is a pointer to _pdbx_vrpt_entity.id
label_asym_id	text	The _atom_site.label_asym_id label for the residue. Normally this is the same as the author chain name.
label_seq_id	integer	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.
count_angle_outliers	integer	Count of number of atoms with angle outliers for this instance
count_bond_outliers	integer	Count of number of atoms with bond outliers in this instance
count_symm_clashes	integer	Count of number of symmetry related clashes for this instance.
count_chiral_outliers	integer	Count of number of chiral outliers for instance.
count_plane_outliers	integer	Count of number of planar outliers for this instance.
count_mogul_angle_outliers	integer	Count of number of angle outliers as reported by MOGUL for this instance.
count_mogul_bond_outliers	integer	Count of number of bond outliers as reported by MOGUL for this residue.
count_mogul_torsion_outliers	integer	Count of number torsion angle outliers as reported by MOGUL for this instance.
count_mogul_ring_outliers	integer	Count of number of atoms with ring outliers as reported by MOGUL for this instance.
count_clashes	integer	Count of number of atoms a with a pdbx_vrpt_instance_clashes for this instance.
ligand_of_interest	text	A flag to indicate if this instance is a ligand of interest.

pdbx_vrpt_model_instance_density

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
natoms_eds	integer	The number of atoms in the residue returned by the EDS software.
RSRCC	double precision	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.
RSR	double precision	Real Space R-value (RSR) for the residue from the EDS generated map. X-ray specific produced by the EDS step.
RSRZ	double precision	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.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each instance of this category.
EDIAm	double precision	The EDIAm score aggregates the electron density support for individual atoms (EDIA score) within a residue, evaluating the overall electron density fit for the residue. A residue with an EDIAm below 0.8 suggests that its constituent atoms display increasing inconsistency with the electron density, and should be visually inspected.
OPIA	double precision	Overall Percentage of well-resolved Interconnected Atoms score indicates the percentage of atoms within a residue where the EDIA score exceeds 0.8. A value below 50% suggests less than half of the atoms in the residue lack good electron density support and should be visually inspected.

pdbx_vrpt_model_instance_geometry

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
OWAB	double precision	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.
residue_inclusion	double precision	The proportion of all atoms of the residue in density
num_H_reduce	integer	This is the number of hydrogen atoms added and optimized by the MolProbity reduce software as part of the all-atom clashscore.
num_bonds_RMSZ	integer	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).
bonds_RMSZ	double precision	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).
num_angles_RMSZ	integer	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).
angles_RMSZ	double precision	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).
program_for_bond_angle_geometry	text	The software used to calculate the bond and angle RMSZ statistics.
average_occupancy	double precision	The average occupancy for the residue. Hydrogen atoms are excluded from consideration. X-ray specific produce by the EDS step.
ligand_chirality_outlier	text	A flag indicating of a ligand has a chirality outlier.
validate	text	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").
cyrange_domain_id	integer	Identifier of the well-defined core (domain) to which the residue belongs, as determined by Cyrange.
cis_peptide	text	A flag to indicate that the residue is a cis-peptide.
RNA_score	double precision	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.
RNA_suite	text	MolProbity RNA_suite conformation analysis. RNA specific produced by the molprobity step.
RNA_pucker	text	Placeholder for reporting RNA pucker problem from MolProbity.
flippable_sidechain	text	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.
ramachandran_class	text	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.
rotamer_class	text	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.
phi	double precision	The phi torsion angle for the residue in degrees. Protein and polypeptide specific produced by the molprobity step.
psi	double precision	The psi torsion angle for the residue in degrees. Protein and polypeptide specific produced by the molprobity step.
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_model_instance_map_fitting

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
residue_inclusion	double precision	The proportion of all atoms of the residue in density
Q_score	double precision	The Q-score for the residue in the map
instance_id	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_model_list

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
PDB_model_num	integer	The integer identifier of a Model.
nmrclust_cluster_id	text	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.
nmrclust_representative	text	A flag indicating if the given model is also the representative model of the cluster to which it belongs.

pdbx_vrpt_most_violated_dihedralangle_restraints

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
altcode_1	text	This attribute will be set if the first pdb x_vrpt_model_instance has atoms with the alternate position indicator set.
chain_1	text	The auth_asym_id identifier for the first residue or from cif item _atom_site.auth_asym_id.
resnum_1	integer	The residue number aka sequence id for the first residue. Obtained from _atom_site.auth_seq_id
resname_1	text	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
ent_1	text	The entity id for the first residue.
said_1	text	The _atom_site.label_asym_id label for the first residue. Normally this is the same as the chain.
seq_1	integer	From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num"
atom_1	text	The first atom label from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
chain_2	text	The auth_asym_id identifier for the second residue or auth_asym_id obtained from cif item _atom_site.auth_asym_id.
altcode_2	text	This attribute will be set if the second atom has the alternate position indicator set.
resnum_2	integer	The residue number aka sequence id for the second residue. Obtained from _atom_site.auth_seq_id
resname_2	text	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.
seq_2	integer	The sequence number for the second atom mrom cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num"
said_2	text	The _atom_site.label_asym_id label for the second residue. Normally this is the same as the chain.
ent_2	text	The entity id for the second residue.
atom_2	text	An label_atom_id name for the second item from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
mean_angle_violation	double precision	Mean value of dihedral-angle violation over all violated models
standard_deviation	double precision	The standard deviation of the value of the violations of a given restraint in an ensemble
median_violation	double precision	The median value of the violation of a given restraint in an ensemble
altcode_3	text	Alternate position setting for the third atom. Obtained from _atom_site.label_alt_id
chain_3	text	The auth_asym_id identifier for the third residue.
resnum_3	integer	The residue number aka sequence id for the third residue. Obtained from _atom_site.auth_seq_id.
resname_3	text	The "residue type", of the third residue.
ent_3	text	The entity id for the third residue.
said_3	text	The _atom_site.label_asym_id label for the third residue. Normally this is the same as the chain.
seq_3	integer	From cif item _atom_site.label_seq_id for the third residue.
atom_3	text	The label_atom_id name for the third atom.
altcode_4	text	This attribute will be set if the alternate position is set for the fourth atom. Obtained from _atom_site.label_alt_id
chain_4	text	The auth_asym_id identifier for the fourth residue.
resnum_4	integer	The residue number aka sequence id for the fourth residue.
resname_4	text	The "residue type", of the fourth atom. Obtained from _atom_site.auth_comp_id
ent_4	text	The entity id for the fourth atom.
said_4	text	The _atom_site.label_asym_id label for the fourth atom. Normally this is the same as the chain.
seq_4	integer	From cif item _atom_site.label_seq_id of fourth atom.
atom_4	text	The label_atom_id name for the fourth atom.
rlist_id	integer	An identifier used to uniquely identify a particular restraints loop.
rest_id	integer	An identifier used to uniquely identify a restraint with in a particular restraint loop.
violated_models	integer	number of violated models for a given restraint or set of restraints
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_most_violated_distance_restraints

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
altcode_1	text	This attribute will be set if the model has atoms with the alternate position indicator set.
chain_1	text	The auth_asym_id obtained from cif item _atom_site.auth_asym_id.
resnum_1	integer	The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id
resname_1	text	The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id
ent_1	text	The entity id for the residue or chain. This is from item _atom_site.label_entity_id.
said_1	text	The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain.
seq_1	integer	From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num"
chain_2	text	The auth_asym_id identifier for the residue.
altcode_2	text	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
atom_1	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
resnum_2	integer	The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id
resname_2	text	The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id
seq_2	integer	From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num"
said_2	text	The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain.
ent_2	text	The entity id for the residue or chain. This is from item _atom_site.label_entity_id that is a pointer to _entity.id.
atom_2	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
mean_distance_violation	double precision	Mean distance violation over the violated models
median_violation	double precision	The median value of the violation of a given restraint in an ensemble
standard_deviation	double precision	The standard deviation of the value of the violations of a given restraint in an ensemble
violated_models	integer	Number of violated models for a given restraint or set of restraints
rlist_id	integer	An identifier used to uniquely identify a particular restraints loop.
rest_id	integer	An identifier used to uniquely identify a restraint with in a particular restraint loop
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_percentile_conditions

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
percentile_list_id	text	A pointer to pdbx_vrpt_percentile_list.id.
type_id	text	A pointer to _pdbx_vrpt_percentile_type.id indicating the type
rank	double precision	The score or percentile
res_high	double precision	The high resolution limit of relative entries or '?' if all entries
res_low	double precision	The low resolution limit of relative entries or '?' if all entries
number_entries_total	integer	The number of entries is this set of entries
id	text	Uniquely identifies each instance of this category.

pdbx_vrpt_percentile_entity_view

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
conditions_id	text	Points to a specific condition.
type_id	text	A pointer to _pdbx_vrpt_percentile_type.id indicating the type
label_asym_id	text	The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain.
PDB_model_num	text	Model identifier. If the structure does not have multiple models then PDB_model_num will be "1".
entity_id	text	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.
auth_asym_id	text	The auth_asym_id identifier for the polymer.
rank	double precision	The score or percentile
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_percentile_list

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
exp_method	text	Experimental method for statistics
range	text	High resolution relative range of percentiles or 'all' to indicate all resolutions
id	text	Uniquely identifies each instance of this category.

pdbx_vrpt_percentile_type

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
id	text	Uniquely identifies each instance of this category.
type	text	Describes the percentile type being reported

pdbx_vrpt_random_coil_index

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of this category.
auth_asym_id	text	The auth_asym_id identifier for the residue or auth_asym_id obtained from cif item _atom_site.auth_asym_id.
rescode	text	The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id
auth_seq_id	integer	The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id
value	double precision	Value in ppm of a chemical shift

pdbx_vrpt_referencing_offset

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each referencing_offset.
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
uncertainty	double precision	Default uncertainty of the prediction, set to 0.05 ppm for protons and 0.5 ppm for 13C and 15N nuclei.
precision	double precision	Precision of the suggested correction, as estimated by jack-knifing algorithm.
value	double precision	Value in ppm of a chemical shift
number_of_measurements	integer	How many chemical shift values for this kind of nucleus are reported in the chemical shift list.

pdbx_vrpt_residual_angle_violations

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
max_violation	double precision	The maximum value of the dihedral-angle violation within the bin
bins	text	The violations are binned as small, medium and large violations based on its absolute value.
violations_per_model	double precision	Average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble.
ordinal	integer	Uniquely identifies each residual angle violation.

pdbx_vrpt_residual_distance_violations

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
max_violation	double precision	The maximum value of distance violation with in the given bin
bins	text	The violations are binned as small, medium and large violations based on its absolute value.
violations_per_model	double precision	Average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_restraint_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
description	text	The description of the restraint type.
value	double precision	The number of restraints or the value associated with the description.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_software

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each software used.
name	text	The name of the program.
version	text	Version string for the program. The format is software dependent.
success_y_or_n	text	Indicates if pdbx_vrpt_software for step ran successfully

pdbx_vrpt_summary

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
entry_id	text	pdbx_vrpt_summary accesion code (PDB, EMDB or BMRB)
extended_entry_id	text	pdbx_vrpt_summary extended accesion code
PDB_deposition_date	date	Date in yyyy-mm-dd format when structure was deposited to the PDB. Obtained from model file _pdbx_database_status.recvd_initial_deposition_date.
PDB_revision_number	integer	The highest number that appears in mmCIF model item _pdbx_audit_revision_history.ordinal.
PDB_revision_date	date	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
EMDB_deposition_date	date	Date in yyyy-mm-dd format when map was deposited to the EMDB.
report_creation_date	timestamp with time zone	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.
attempted_validation_steps	text	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.
ligands_for_buster_report	text	A flag indicating if there are ligands in the model used for detailed Buster analysis.
RNA_suiteness	double precision	The MolProbity conformer-match quality parameter for RNA structures. Low values are worse. Specific to structures that contain RNA polymers.

pdbx_vrpt_summary_diffraction

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
exp_method	text	Experimental method for statistics
Babinet_b	double precision	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.
bulk_solvent_b	double precision	REFMAC scaling parameter as reported in log output file. X-ray entry specific, obtained in the EDS step from REFMAC calculation.
Wilson_B_estimate	double precision	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.
I_over_sigma	text	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. <I/sigma(I)> 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.
num_miller_indices	integer	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.
Babinet_k	double precision	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.
bulk_solvent_k	double precision	REFMAC reported scaling parameter. X-ray entry specific, obtained in the EDS step from REFMAC calculation.
Padilla_Yeates_L_mean	double precision	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.
Padilla_Yeates_L2_mean	double precision	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.
DCC_R	double precision	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.
DCC_Rfree	double precision	Rfree as calculated by DCC.
EDS_R	double precision	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.
EDS_res_high	double precision	The data high resolution diffraction limit, in Angstroms, found in the input structure factor file. X-ray entry specific, obtained in the EDS step.
EDS_res_low	double precision	The data low resolution diffraction limit, in Angstroms, found in the input structure factor file. X-ray entry specific, obtained in the EDS step.
Wilson_B_aniso	text	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.
data_anisotropy	double precision	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.
trans_NCS_details	text	A sentence giving the result of Xtriage's analysis on translational NCS. X-ray entry specific, obtained from the Xtriage program.
B_factor_type	text	An indicator if isotropic B factors are partial or full values.
acentric_outliers	integer	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.
centric_outliers	integer	The number of centric reflections that Xtriage identifies as outliers. X-ray entry specific, calculated by Phenix Xtriage program.
data_completeness	double precision	The percent completeness of diffraction data.
number_reflns_R_free	integer	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.
percent_free_reflections	double precision	A percentage, Normally percent proportion of the total number. Between 0% and 100%.
percent_RSRZ_outliers	double precision	The percent of RSRZ outliers.
PDB_resolution_high	double precision	The high resolution limit of the data.
PDB_resolution_low	double precision	The low resolution limit of the diffraction data.
PDB_R	double precision	The reported R in the model file.
PDB_Rfree	double precision	The reported Rfree.
twin_fraction	text	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.
Fo_Fc_correlation	double precision	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.
ordinal	integer	Uniquely identifies each instance of this category.
density_fitness_version	text	The version of density-fitness suite programs used in the analysis.
CCP4_version	text	The version of CCP4 suite used in the analysis.
EDS_R_warning	text	Warning message when EDS calculated R vs reported R is higher than a threshold

pdbx_vrpt_summary_em

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
exp_method	text	Experimental method for statistics
contour_level_primary_map	double precision	The recommended contour level for the primary map of this deposition.
atom_inclusion_all_atoms	double precision	The proportion of all non hydrogen atoms within density.
atom_inclusion_backbone	double precision	The proportion of backbone atoms within density.
author_provided_fsc_resolution_by_cutoff_pt_143	double precision	The resolution from the intersection of the author provided fsc and the indicator curve 0.143.
author_provided_fsc_resolution_by_cutoff_pt_333	double precision	The resolution from the intersection of the author provided fsc and the indicator curve 0.333.
author_provided_fsc_resolution_by_cutoff_pt_5	double precision	The resolution from the intersection of the author provided fsc and the indicator curve 0.5.
author_provided_fsc_resolution_by_cutoff_halfbit	double precision	The resolution from the intersection of the author provided fsc and the indicator curve halfbit.
author_provided_fsc_resolution_by_cutoff_onebit	double precision	The resolution from the intersection of the author provided fsc and the indicator curve onebit.
author_provided_fsc_resolution_by_cutoff_threesigma	double precision	The resolution from the intersection of the author provided fsc and the indicator curve threesigma.
calculated_fsc_resolution_by_cutoff_pt_143	double precision	The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143.
calculated_fsc_resolution_by_cutoff_pt_333	double precision	The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333.
calculated_fsc_resolution_by_cutoff_pt_5	double precision	The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5.
calculated_fsc_resolution_by_cutoff_halfbit	double precision	The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit.
calculated_fsc_resolution_by_cutoff_onebit	double precision	The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit.
calculated_fsc_resolution_by_cutoff_threesigma	double precision	The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma.
EMDB_resolution	double precision	The resolution reported in the entry.
Q_score	double precision	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)
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_summary_entity_fit_to_map

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of this summary.
PDB_model_num	integer	The unique model number from _atom_site.pdbx_PDB_model_num.
entity_id	text	The entity id for the residue or chain.
label_asym_id	text	The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain.
auth_asym_id	text	The _atom_site.auth_asym_id identifier for the instance.
Q_score	double precision	The calculated average Q-score.
average_residue_inclusion	double precision	The average of the residue inclusions for all residues in this instance

pdbx_vrpt_summary_entity_geometry

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of this summary.
PDB_model_num	integer	The unique model number from _atom_site.pdbx_PDB_model_num.
entity_id	text	The entity id for the residue or chain.
label_asym_id	text	The _atom_site.label_asym_id label for the residue. Normally this is the same as the chain.
auth_asym_id	text	The _atom_site.auth_asym_id identifier for the instance.
angles_RMSZ	double precision	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).
bonds_RMSZ	double precision	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).
num_bonds_RMSZ	integer	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).
num_angles_RMSZ	integer	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).
average_residue_inclusion	double precision	The average of the residue inclusions for all residues in this instance

pdbx_vrpt_summary_geometry

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
percent_ramachandran_outliers	double precision	The percentage of residues with Ramachandran outliers.
clashscore	double precision	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.
angles_RMSZ	double precision	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.
bonds_RMSZ	double precision	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.
num_angles_RMSZ	integer	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.
num_bonds_RMSZ	integer	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.
percent_rotamer_outliers	double precision	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.
percent_ramachandran_outliers_full_length	double precision	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.
percent_rotamer_outliers_full_length	double precision	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.
clashscore_full_length	double precision	Only given for structures determined by NMR. The MolProbity pdbx_vrpt_instance_clashes score for all label_atom_id pairs.
num_H_reduce	integer	This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the all-atom clashscore.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_summary_nmr

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
exp_method	text	Experimental method for statistics
nmr_models_consistency_flag	text	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").
nmrclust_representative_model	integer	Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust.
medoid_model	integer	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.
nmrclust_number_of_outliers	integer	Number of models that do not belong to any cluster as deemed by NMRClust.
nmrclust_number_of_models	integer	Number of models analysed by NMRClust - should in almost all cases be the same as the number of models in the NMR ensemble.
nmrclust_number_of_clusters	integer	Total number of clusters in the NMR ensemble identified by NMRClust.
cyrange_number_of_domains	integer	Total number of well-defined cores (domains) identified by Cyrange
chemical_shift_completeness	double precision	Overall completeness of the chemical shift assignments for the well-defined regions of the structure.
chemical_shift_completeness_full_length	double precision	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).
cyrange_error	text	Diagnostic message from the wrapper of Cyrange software which identifies the well-defined cores (domains) of NMR protein structures.
ordinal	integer	Uniquely identifies each instance of this category.

pdbx_vrpt_unmapped_chemical_shift

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of this category.
auth_asym_id	text	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"
rescode	text	The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id
auth_seq_id	integer	The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
value	double precision	Value in ppm of a chemical shift
error	text	Uncertainty on a chemical shift value, if known.
ambiguity	text	Ambiguity of the chemical shift assignment as per NMR-STAR V3.1 dictionary.
diagnostic	text	Diagnostic text message when a chemical shift was not parsed or not mapped to structure.

pdbx_vrpt_unparsed_chemical_shift

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
ordinal	integer	Uniquely identifies each instance of this category.
id	text	ID of the chemical shift as parsed in the chemical shifts file.
auth_asym_id	text	The auth_asym_id identifier for the residue obtained from mmCIF item _atom_site.auth_asym_id.
rescode	text	The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id
auth_seq_id	integer	The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id
label_atom_id	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
value	double precision	Value in ppm of a chemical shift
error	text	Uncertainty on a chemical shift value - usually not available
ambiguity	text	Ambiguity of the chemical shift assignment as per NMR-STAR V3.1 dictionary.
diagnostic	text	Diagnostic text message when a chemical shift was not parsed or not mapped to structure.

pdbx_vrpt_violated_dihedralangle_restraints

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
atom_1	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_2	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
violation	double precision	The measureed violation.
atom_3	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
atom_4	text	An label_atom_id name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id.
rlist_id	integer	An identifier used to uniquely identify a particular restraints loop.
rest_id	integer	An identifier used to uniquely identify a restraint with in a particular restraint loop.
instance_id_1	text	A pointer to pdbx_vrpt_model_instance.id.
instance_id_2	text	A pointer to pdbx_vrpt_model_instance.id.
instance_id_3	text	A pointer to pdbx_vrpt_model_instance.id.
instance_id_4	text	A pointer to pdbx_vrpt_model_instance.id.
ordinal	integer	Uniquely identifies each dihedral angle restraint.

pdbx_vrpt_violated_distance_restraints

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
atom_1	text	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.
atom_2	text	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.
violation	double precision	Absolute value of the violation
rlist_id	integer	An identifier used to uniquely identify a particular restraints loop
rest_id	integer	An identifier used to uniquely identify a restraint with in a particular restraint loop
instance_id_1	text	A pointer to the first atom fro pdbx_vrpt_model_instance.id.
instance_id_2	text	A pointer to pdbx_vrpt_model_instance.id for second atom
ordinal	integer	Uniquely identifies each instance of this category.

struct_asym

Column	Type	Description
pdbid	text	PDBID of an entry. All tables/categories refer back to the PDBID in the brief_summary table.
entity_id	text	This data item is a pointer to _entity.id in the ENTITY category.
id	text	The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier.
pdbx_modified	text	This data item indicates whether the structural elements are modified.