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This is a XML schema for checking entry-specific validation
XML documents from wwPDB. 

versions published:
v1      2014/02/20  http://wwpdb.org/validation/schema/wwpdb_validation_v1.xsd
v002    2016/02/25  http://wwpdb.org/validation/schema/wwpdb_validation_v002.xsd
v002    2017/08/31  http://wwpdb.org/validation/schema/wwpdb_validation_v002.xsd (with annotations)
v003    2019/05/27  http://wwpdb.org/validation/schema/wwpdb_validation_v003.xsd (added local_density, no-ligands-for-buster-report ligands-for-buster-report attribute)
v004    2019/10/16  http://wwpdb.org/validation/schema/wwpdb_validation_v004.xsd (added em validation)
v004    2019/11/18  http://wwpdb.org/validation/schema/wwpdb_validation_v004.xsd (Updated FSC representation)
v004    2020/02/18  http://wwpdb.org/validation/schema/wwpdb_validation_v004.xsd (Added EMDB-deposition-date and EMDB-resolution)
v004    2020/10/06  http://wwpdb.org/validation/schema/wwpdb_validation_v004.xsd (Added raw map rotationally averaged power spectrum)
v005    2020/10/02  http://wwpdb.org/validation/schema/wwpdb_validation_v005.xsd (Added NMR Restraints analysis xml schema)
v5.01   2020/12/10  http://wwpdb.org/validation/schema/wwpdb_validation_v5.01.xsd (cleanup of NMR restraint definitions)
v6.00   2020/01/10  http://wwpdb.org/validation/schema/wwpdb_validation_v6.00.xsd (change attribute names for NMR restraint definitions for consistency)
v6.01   2022/07/20  http://wwpdb.org/validation/schema/wwpdb_validation_v6.01.xsd (Added Q_score)
v6.02   2022/07/20  http://wwpdb.org/validation/schema/wwpdb_validation_v6.02.xsd (Added bmrb_id)
v6.03   2024/08/09  http://wwpdb.org/validation/schema/wwpdb_validation_v6.03.xsd (Added EDIAm, OPIA scores, density-fitness version, removed RefmacVersion)
v6.04   2024/11/11  http://wwpdb.org/validation/schema/wwpdb_validation_v6.04.xsd (Added eds_rfactor_warning, add back RefmaxVersion for backwards compatibilty)

$Revision$
*****************************************************************

Entry contains most information that has a single value for the structure analyzed and in the run. This flag indicates where restraints data is provided or not. If yes, then only chemical shift data provided in parsable format. A "Model" 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. The integer identifier of a Model. 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 if this value is integer. If the value is "outlier" - the given model is sufficiently different from other models in the ensemble. A flag (with allowed values "True" and "False" indicating if the given model is also the representative model of the cluster to which it belongs. A "ModelledSubgroup" is an individual occurrence of a residue. If there are alternate atoms in the residue each alternate and any alternate atoms is a separate ModelledSubgroup. If there are multiple models then each of these is a separate subgroup. 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". Each separate chain in the structure is a "ModelledEntityInstance". In the case of multiple models each individual model is a "ModelledEntityInstance" on its own. EM validation information which is not tied to a specific chain or residue. The recommended contour level for the primary map of this entry A shared element for storing graphs, contains X and Y coordinates for a single point. Axis labels and scales should be stored in the parent element Used for storing graph data. Titles must be given if more than one curve of this type is present. Scales will be assumed to be linear if not provided. Units will be assumed to be arbitrary if empty or not provided. Used for storing the data fsc curves. The type denotes what files the curve was calculated from e.g. "half_map to half_map fsc" Used for storing the fsc indicator curves. The data_curve refers to the fsc_curve which this indicator curve is made against. The type denotes which threshold is used. Contains the data required to plot the map-value distribution graph for the primary map Contains the data required to plot the rotationally averaged power spectrum graph for the primary map Contains the data required to plot the rotationally averaged power spectrum graph for the raw map Contains the data required to plot the volume estimate for the primary map Contains an element for each atom inclusion graph line Contains the data required to plot atom inclusion for for all atoms. Contains the data required to plot the atom inclusion for the backbone. Contains all fsc information. Including fsc curves, fsc indicator curves and fsc intersections Contains intersections between fsc_curves and their corresponding fsc_indicator_curves The unit of resolution The unit of spatial frequency Contains information regarding a fsc intersection Contains fsc data curves Contains the plots for the fsc indicator curves 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. 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. 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. ID of the chemical shift as parsed in the chemical shifts file. 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. Description of the missing but required data item (tag). The name of the missing data item (tag). 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. 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. The mean value of the chemical shift expected from the BMRB statistics Method to determine the expected value and standard deviation. At present this is limited to BMRB statistics. PANAV software is used to calculate suggested referencing correction for each chemical shift list. Default uncertainty of the prediction, set to 0.05 ppm for protons and 0.5 ppm for 13C and 15N nuclei. Precision of the suggested correction, as estimated by jack-knifing algorithm. How many chemical shift values for this kind of nucleus are reported in the chemical shift list. For the well-defined regions of the structure, what is the completeness of chemical shift assignments for the typically assigned nuclei. "Type" refers to a subset of assignments: overall, backbone, aliphatic sidechain, aromatic protein rings, nucleic acid base and ribose or deoxyribose ring. For the complete structure, what is the completeness of chemical shift assignments for the typically assigned nuclei. "Type" refers to a subset of assignments: overall, backbone, aliphatic sidechain, aromatic protein rings, nucleic acid base and ribose or deoxyribose ring. A list of programs used by the validation pipeline. An individual program used by the validation pipeline. Normally this corresponds to a "step" but not always. The name of the program. For example: name="mogul". This aims to provide a comma seperate list of the xml attributes/elements that program supplied. The list is in an arbitrary order that can vary. Example: properties="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 properties list includes "mogul-angle-outlier" but the attribute is "mog-angle-outlier". Version string for the program. Format program dependent. Example: version="1.7.2 (RC1), CSD as538be (2017)" 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: <bond-outlier atom0="C" atom1="OXT" mean="1.229" obs="1.327" stdev="0.019" z="5.16"/> 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. Example: < atom0="C" atom1="N" atom2="CA" link="yes" mean="121.700" obs="139.881" stdev="2.500" z="7.27"/> 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. The type of chiral problem that the atom has. either "WRONG HAND" or "PLANAR" 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. Examples: <plane-outlier improper="-13.96" type="mainchain"/> <plane-outlier omega="-145.49" type="peptide"/> <plane-outlier planeRMSD="0.17" type="sidechain"/> The type of chiral problem that the atom has. One of: (A) "mainchain": The N atom 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 atom from the plane. Expected value of such distances have been pre-calculated from data analysis (wwPDB, 2012). If an atom 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". For a type="mainchain" outlier, the improper torsion angle in degrees. For a type="peptide" outlier, the omega torsion angle in degrees. For a type="sidechain" outlier, the root mean squared deviation from the mean plane in Angstroms. A MolProbity all-atom clash 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. Example: <clash atom="HB3" cid="7" clashmag="0.44" dist="2.57"/> An identifier that cross references the other atom in the clash. The two atoms in the clash will have the same unique cid. The "magnitude" of the clash in Angstroms assessed by MolProbity. The MolProbity "magnitude" of a clash is defined as the difference between the observed interatomic distance and the sum of the van der Waals radii of the atoms involved. A symmetry-related clash identified by Validation-pack. Symmetry related clashes are too-close contacts between two atoms across a crystallographic symmetry contact. Only relevant to crystallographic structures. Example: <symm-clash atom="O" clashmag="0.79" dist="1.41" scid="0" symop="2_657"/> From mmcif item "_pdbx_validate_symm_contact". The symmetry operator for the atom 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. An identifier that cross references the other atom in the clash. The two atoms in the clash will have the same unique scid. The "magnitude" of the clash in Angstroms assessed by Validation-pack. In this case, the "magnitude" of a clash is defined as 2.2 Angstrom (or 1.6 Angstrom if either atom is a hydrogen atom) minus the interatomic distance. Bond outlier for ligand or modified amino acid/nucleic acid identified by the Mogul program. It will involve two atoms. The obsval, mean, mindiff, stdev will all be in Angstroms units. The Mogul program (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) Example: <mog-bond-outlier Zscore="2.25" atoms="C1,C6" mean="1.53" mindiff="0.00" numobs="128" obsval="1.56" stdev="0.01"/> Bond angle outlier for ligand or modified amino acid/nucleic acid identified by the Mogul program. It involves three atoms. The obsval, mean, mindiff, stdev will all be in degrees. The Mogul program (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). Torsion angle outlier for ligand or modified amino acid/nucleic acid identified by the Mogul program. It will involve four atoms. The obsval, mean, mindiff, stdev will all be in degrees. The Mogul program (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). 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 program (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). String for B_factor_type either "PARTIAL" or "FULL". The string "yes". The string "NotAvailable". Either a decimal number or the string "NotAvailable". A percentage, Normally percent proportion of the total number. Between 0% and 100%. Structures are judged in comparison to previously deposited PDB entries. The comparison is carried out by calculation of the percentile rank, i.e. the percentage of entries that are equal or poorer than this structure in terms of a quality indicator. Percentile ranks range from 0 (the worst) to 100 (the best). An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. An identifier for the structure. For released or annotated structures this will be the PDB ID currently 4 characters, for example "1CBS". For reports produced during initial depositon process a deposition ID will be given instead, for example "D_1000219513". An identifier for the map For released or annotated structures this will be the EMDB ID EMD-\d{4-5} eg "EMD-1001", "EMD-12325" Date in yyyy-mm-dd format when structure was deposited to the PDB. Obtained from mmCIF table _database_PDB_rev item _database_PDB_rev.date_original Reports produced by the validation server or during the initial deposition process should not have this item. If there is a difficulty parsing the item then "unknown" will be given. Date in yyyy-mm-dd format when map was deposited to the EMDB. Reports produced by the validation server or during the initial deposition process should not have this item. If there is a difficulty parsing the item then "unknown" will be given. The last highest number that appears in mmCIF item _database_PDB_rev.num. Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). If the input mmCIF coordinate file lacks the information then a value of -1 is supplied. Date in yyyy-mm-dd format when the structure was last revised by PDB. Obtained from mmCIF table _database_PDB_rev item _database_PDB_rev.date Reports produced by the validation server or during the initial deposition process should not have this item. If there is a difficulty parsing the item then "unknown" will be given. For X-ray entries: data high resolution diffraction limit in Angstroms as reported in the input mmCIF file, normally taken from mmcif item _refine.ls_d_res_high or if this is not found _reflns.d_resolution_high. For EM entries: The final resolution, in Angstroms, of the 3d reconstruction as reported in the input mmCIF file, taken from _em_3d_reconstruction.resolution. If not available then item will be absent or set to "NotAvailable". For X-ray entries: lower data resolution diffraction limit, in Angstroms, as reported in the input mmCIF file, normally taken from mmcif item _refine.ls_d_res_high or if this is not found _reflns.d_resolution_high. The resolution reported to the EMDB. The residual R-factor reported in the input mmCIF file. The value will be taken from mmcif item _refine.ls_R_factor_all or if this not found _refine.ls_R_factor_obs or if this is not found _refine.ls_R_factor_R_work. The R-factor is measure of the agreement between the crystallographic model and the experimental X-ray diffraction data. If not available then item will be absent or set to "NotAvailable". The residual R-factor for free reflections in the refinement reported in the input mmCIF file. The value will be taken from mmcif item _refine.ls_R_factor_R_free. If not available then item will be absent or set to "NotAvailable". Comma separated list of the _entity.id's for the molecular entities that are present in the structure and have _entity_poly.type indicating that they are protein, RNA or DNA: that is in the list 'polypeptide(L)', 'polypeptide(D)', 'polyribonucleotide, 'polydeoxyribonucleotide' or 'polydeoxyribonucleotide/polyribonucleotide hybrid'. Normally the entity.id's are integer numbers but not necessarily so. Example protein-DNA-RNA-entities="1,2,3" The structure is a Calpha only model. Currently implementation uses test that the structure has more than 30 atoms with the name CA and that number of atoms with name CA is greater than 1/3 of the total number of atoms. Currently test only applied in the EDS step so will be only set for X-ray structures. The date, time and time-zone that the validation XML file was created. The string will be formatted like "Feb 7, 2017 -- 12:32 pm GMT". The filename for the input mmCIF coordinate file given to the validation pipeline. Not reported for runs at the annotation or release stage. The filename for the input mmCIF format reflection file given to the validation pipeline. Not reported for runs at the annotation or release stage. The filename for the input chemical shifts file given to the validation pipeline. Not reported for runs at the annotation or release stage. 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 that was successfully completed will result in a program element in the programs list. This will be set to "yes" when there were no ligands or modified residues found in the structure and consequently Mogul has not been run. This will be set to "yes" when buster-report program was not run. This will be set to "yes" when buster-report program was run. 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) 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. 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. 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. 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. This is the number of hydrogen atoms added and optimized by the MolProbity reduce program as part of the all-atom clashscore. This score is derived from the number of pairs of atoms in the model that are unusually close to each other. It is calculated by the MolProbity program and expressed as the number or such clashes per thousand atoms. For structures determined by NMR the clashscore value here will only consider atom pairs in the well-defined (core) residues from ensemble analysis. Only given for structures determined by NMR. The MolProbity clash score for all atom pairs. The MolProbity conformer-match quality parameter for RNA structures. Low values are worse. Example: RNAsuiteness="0.89" Specific to structures that contain RNA polymers. The MolProbity Ramachandran outlier score (a percentage). A residue is considered to be a Ramachandran plot outlier if the combination of its phi and psi torsion angles is unusual, as assessed by MolProbity. The Ramachandran outlier score for an entry is calculated as the percentage of Ramachandran outliers with respect to the total number of residues in the entry for which the outlier assessment is available. Example: percent-rama-outliers="0.00" Specific to structures that contain protein chains. For NMR structures only the well-defined (core) residues from ensemble analysis will be considered. 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. 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. 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. The version of density-fitness suite programs used in the analysis. Example: density-fitnessVersion="1.0.0". X-ray entry specific, obtained from the eds step. The version of CCP4 suite programs used in the analysis. Example: CCP4version="6.5.0". X-ray entry specific, obtained from the eds step. The data high resolution diffraction limit, in Angstroms, obtained from cif item _reflns.d_resolution_high. X-ray entry specific. The data low resolution diffraction limit, in Angstroms, obtained from cif item _reflns.d_resolution_low. X-ray entry specific. The mmCIF item names of the _refln columns used as input to the Xtriage program. Example xtriage_input_columns="F_meas_au,F_meas_sigma_au". X-ray entry specific, calculated by Phenix Xtriage program. 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. Example: acentric_outliers="1". X-ray entry specific, calculated by Phenix Xtriage program. The number of centric reflections that Xtriage identifies as outliers. Example: centric_outliers="5". X-ray entry specific, calculated by Phenix Xtriage program. 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. Example IoverSigma="3.77(1.79A)". X-ray entry specific, calculated by Phenix Xtriage program. 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. Example: numMillerIndices="14678" X-ray entry specific, calculated by Phenix Xtriage program. 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. Example: WilsonBestimate="14.785" X-ray entry specific, calculated by Phenix Xtriage program. 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. Example: WilsonBaniso="[16.802,17.606,11.032,0.000,0.000,0.000]" X-ray entry specific, calculated by Phenix Xtriage program. 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). Example: DataAnisotropy="0.434". X-ray entry specific, obtained from the Xtriage program. A sentence giving the result of Xtriage’s analysis on translational NCS. Example: TransNCS="The largest off-origin peak in the Patterson function is 8.82% of the height of the origin peak. No significant pseudotranslation is detected." X-ray entry specific, obtained from the Xtriage program. Padilla and Yeates twinning parameter <|L|>. Theoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case. Example: TwinL="0.495". X-ray entry specific, obtained from the Xtriage program. Padilla and Yeates twinning parameter <|L**2|>. Theoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case. Example: TwinL2="0.312". X-ray entry specific, obtained from the Xtriage program. Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated list of operators with fractions is givens Example: TwinFraction="h,h-k,h-l:0.477;-h,-h+k,-l:0.020;-h,-k,-h+l:0.017". X-ray entry specific, obtained from the Xtriage program. Whether the B factor is FULL or PARTIAL. Normally B factors are FULL. Example: B_factor_type="FULL". X-ray entry specific, obtained from the DCC program. The number of expected diffraction spots is a function of data resolution and the space group. This metric describes the number of recorded reflections as a percentage of the number expected. Example: "DataCompleteness="95.71"" X-ray entry specific, obtained from the REFMAC program, during the EDS calculation. The overall R-factor from a DCC recalculation of an electron density map. Example: DCC_R="0.18". Currently value is rounded to 2 decimal places. X-ray entry specific, obtained from the DCC program. The free R-factor from a DCC recalculation of the electron density maps for the deposited coordinates and structure factors. Example: DCC_Rfree="0.19". Currently value is rounded to 2 decimal places. X-ray entry specific, obtained from the DCC program. The program used by DCC to perform the recaluclation of the electron density maps. Currently one of "CNS", "REFMAC" or "PHENIX". Example: DCC_refinement_program="CNS". X-ray entry specific, obtained from the DCC program. The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. example: num-free-reflections="1479". X-ray entry specific, obtained from the DCC program. The percentage reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. Example: percent-free-reflections="10.17". X-ray entry specific, obtained from the DCC program. Version of the REFMAC program used in the EDS step. Example: RefmacVersion="5.8.0135". X-ray entry specific, obtained in the eds step from REFMAC calculation. The overall R factor from the EDS REFMAC calculation (no free set is used in this). Example: EDS_R="0.18". Currently value is rounded to 2 decimal places. X-ray entry specific, obtained in the eds step from REFMAC calculation. The data high resolution diffraction limit, in Angstroms, found in the input structure factor file. Example: EDS_resolution="1.80". X-ray entry specific, obtained in the eds step. The data low resolution diffraction limit, in Angstroms, found in the input structure factor file. Example: EDS_resolution_low="14.93". X-ray entry specific, obtained in the eds step. 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 i experimental data. Example: EDS_resolution_low="14.93". X-ray entry specific, obtained in the eds step from REFMAC calculation. REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. Example: babinet_b="141.456". X-ray entry specific, obtained in the eds step from REFMAC calculation. REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. Example: babinet_k="0.156" X-ray entry specific, obtained in the eds step from REFMAC calculation. REFMAC scaling parameter as reported in log output line starting 'Partial structure 1: scale.' Example: bulk_solvent_b="72.956" X-ray entry specific, obtained in the eds step from REFMAC calculation. REFMAC scaling parameter as reported in log output line starting 'Partial structure 1: scale.' Example: bulk_solvent_k="0.401" X-ray entry specific, obtained in the eds step from REFMAC calculation. The proportion of residues that are RSRZ outliers reported as a percentage. An RSRZ outlier is a residue that has an RSRZ greater than 2. For a description of the how RSRZ provides a measure of the fit between the model and electron density, see: https://wwpdb.org/validation/2016/XrayValidationReportHelp#fit_model_data. Example: percent-RSRZ-outliers="3.88" X-ray entry specific, obtained in the eds step from REFMAC calculated electron density map. Warning message from EDS if the R factor caculated by EDS (EDS_R) is more than 5% different than the depositor provided one (PDB-R). 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"). Diagnostic message from the wrapper of Cyrange software which identifies the well-defined cores (domains) of NMR protein structures. Reference for the Cyrange software. Diagnostic message from the wrapper of NMRClust software which clusters NMR models. Reference for the NMRClust software. Overall representative model of the NMR ensemble as identified by NMRClust. 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 ("Entry"), the medoid model of the largest core is taken as an overall representative of the structure. Number of models that do not belong to any cluster as deemed by NMRClust. Number of models analysed by NMRClust - should in almost all cases be the same as the number of models in the NMR ensemble. Total number of clusters in the NMR ensemble identified by NMRClust. Total number of well-defined cores (domains) identified by Cyrange Overall completeness of the chemical shift assignments for the well-defined regions of the structure. 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). Reference for the PANAV software. Version and reference of the RCI software Version of the software for chemical shift outlier detection - currently same as revision number of the validation pipeline. The recommended contour level for the primary map of this deposition. The proportion of all non hydrogen atoms within density. The proportion of backbone atoms within density. The resolution from the intersection of the author provided fsc and the indicator curve 0.143. The resolution from the intersection of the author provided fsc and the indicator curve 0.333. The resolution from the intersection of the author provided fsc and the indicator curve 0.5. The resolution from the intersection of the author provided fsc and the indicator curve halfbit. The resolution from the intersection of the author provided fsc and the indicator curve onebit. The resolution from the intersection of the author provided fsc and the indicator curve threesigma. The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143. The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333. The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5. The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit. The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit. The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma. The percentile bins that this structure would contribute to in a recalculation of percentile. The string is a comma separated list. Example: percentilebins="all,1.8,xray": An X-ray entry with a resolution of 1.8 Angstroms, that would contribute to bins all structures, what ever bin 1.8 Angstrom resolution is in and the all xray bin. Example #2: percentilebins="all,em": An EM entry that would contribute to all and em structures bins. Example #3: percentilebins="all,nmr": A NMR entry hat would contribute to all and nmr structures bins. Will be set to "true" if no property was found to do percentile analysis on. Please note that currently due to a bug that this attribute is "true" erronously for NMR structures. The "all" percentile rank for the property RNAsuiteness (the MolProbity conformer-match quality parameter for RNA structures). The comparison will be to: * For X-ray structures: the set of all structures determined by X-ray crystallography ... * For NMR and EM structures: the set of all PDB structures ... deposited, up to the date included in the program name="percentiles" version, where the RNAsuiteness was successfully calculated. Example: absolute-percentile-RNAsuiteness="99.7" Specific to entries that contain RNA polymers (and have a RNAsuiteness attribute). Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-RNAsuiteness". Example: numPDBids-absolute-percentile-RNAsuiteness="2435". Specific to entries that contain RNA polymers (and have a RNAsuiteness attribute). Produced by the percentiles step of the validation pipeline software. The "relative" percentile rank for the property RNAsuiteness (the MolProbity conformer-match quality parameter for RNA structures). The comparison will be to: * For X-ray structures: the subset of structures structures determined by X-ray crystallography, that have a similar resolution ("PDB-resolution") to this entry, ... * For structures determined by NMR: the subset of structures determined by NMR ... * For structures determined by EM: the subset of structures determined by EM ... ... deposited up to the date included in the program name="percentiles" version and where the RNAsuiteness was successfully calculated. Example: absolute-percentile-RNAsuiteness="99.7" Specific to entries that contain RNA polymers (and have a RNAsuiteness attribute). Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "relative-percentile-RNAsuiteness". Example: numPDBids-absolute-percentile-RNAsuiteness="2435". Specific to entries that contain RNA polymers (and have a RNAsuiteness attribute). Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-RNAsuiteness". Note that the "low-resol-relative-percentile-RNAsuiteness" value is numerically greater than the corresponding high value. Example: low-resol-relative-percentile-RNAsuiteness="2.6". Specific to entries that contain RNA polymers (and have a RNAsuiteness attribute), and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-RNAsuiteness". Note that the "high-resol-relative-percentile-RNAsuiteness" value is numerically smaller than the corresponding low value. Example: high-resol-relative-percentile-RNAsuiteness="2.6". Specific to entries that contain RNA polymers (and have a RNAsuiteness attribute), and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The "all" percentile rank for the property clashscore (the MolProbity all-atom too-close contacts parameter). The comparison will be to: * For X-ray structures: the set of all structures determined by X-ray crystallography ... * For NMR and EM structures: the set of all PDB structures ... deposited, up to the date included in the program name="percentiles" version, where the clashscore was successfully calculated. Example: absolute-percentile-clashscore="71.6" Only calculated if clashscore is available. Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-clashscore" Example: numPDBids-absolute-percentile-clashscore="112137" Produced by the percentiles step of the validation pipeline software. The "relative" percentile rank for the property clashscore (the MolProbity all-atom too-close contacts parameter). The comparison will be to: * For X-ray structures: the subset of structures structures determined by X-ray crystallography, that have a similar resolution ("PDB-resolution") to this entry, ... * For structures determined by NMR: the subset of structures determined by NMR ... * For structures determined by EM: the subset of structures determined by EM ... ... deposited up to the date included in the program name="percentiles" version and where the clashscore was successfully calculated. Example: relative-percentile-clashscore="64.4" Only calculated if clashscore is available. Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "relative-percentile-clashscore" Example: numPDBids-relative-percentile-clashscore="5742". Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-clashscore". Note that the "low-resol-relative-percentile-clashscore" value is numerically greater than the corresponding high value. Example: low-resol-relative-percentile-clashscore="1.8". Specific to that have a clashscore attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-clashscore". Note that the "high-resol-relative-percentile-clashscore" value is numerically smaller than the corresponding low value. Example: high-resol-relative-percentile-clashscore="1.8". Specific to that have a clashscore attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The "all" percentile rank for the property percent-rama-outliers (the MolProbity Ramachandran outlier score). The comparison will be to: * For X-ray structures: the set of all structures determined by X-ray crystallography ... * For NMR and EM structures: the set of all PDB structures ... deposited, up to the date included in the program name="percentiles" version, where the percent-rama-outliers was successfully calculated. Example: absolute-percentile-percent-rama-outliers="100.0" Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-percent-rama-outliers" Example: numPDBids-absolute-percentile-percent-rama-outliers="110173". Produced by the percentiles step of the validation pipeline software. The "relative" percentile rank for the property percent-rama-outliers (the MolProbity Ramachandran outlier score). The comparison will be to: * For X-ray structures: the subset of structures structures determined by X-ray crystallography, that have a similar resolution ("PDB-resolution") to this entry, ... * For structures determined by NMR: the subset of structures determined by NMR ... * For structures determined by EM: the subset of structures determined by EM ... ... deposited up to the date included in the program name="percentiles" version and where the percent-rama-outliers was successfully calculated. Example: relative-percentile-percent-rama-outliers="100.0". Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-rama-outliers" Example: numPDBids-relative-percentile-percent-rama-outliers="5676". Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-rama-outliers". Note that the "low-resol-relative-percentile-percent-rama-outliers" value is numerically greater than the corresponding high value. Example: low-resol-relative-percentile-percent-rama-outliers="1.8". Specific to that have a percent-rama-outliers attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-rama-outliers". Note that the "high-resol-relative-percentile-percent-rama-outliers" value is numerically smaller than the corresponding low value. Example: high-resol-relative-percentile-percent-rama-outliers="1.8". Specific to structures that have a percent-rama-outliers attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The "all" percentile rank for the property percent-rota-outliers (the MolProbity sidechain outlier score). The comparison will be to: * For X-ray structures: the set of all structures determined by X-ray crystallography ... * For NMR and EM structures: the set of all PDB structures ... deposited, up to the date included in the program name="percentiles" version, where the percent-rota-outliers was successfully calculated. Example: absolute-percentile-percent-rota-outliers="54.2" Only calculated if percent-rota-outliers is available. Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-percent-rota-outliers" Example: numPDBids-absolute-percentile-percent-rota-outliers="112137" Produced by the percentiles step of the validation pipeline software. The "relative" percentile rank for the property percent-rota-outliers (the MolProbity sidechain outlier score). The comparison will be to: * For X-ray structures: the subset of structures structures determined by X-ray crystallography, that have a similar resolution ("PDB-resolution") to this entry, ... * For structures determined by NMR: the subset of structures determined by NMR ... * For structures determined by EM: the subset of structures determined by EM ... ... deposited up to the date included in the program name="percentiles" version and where the percent-rota-outliers was successfully calculated. Example: relative-percentile-percent-rota-outliers="64.4" Only calculated if percent-rota-outliers is available. Produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-rota-outliers" Example: numPDBids-relative-percentile-percent-rota-outliers="5742". Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-rota-outliers". Note that the "low-resol-relative-percentile-percent-rota-outliers" value is numerically greater than the corresponding high value. Example: low-resol-relative-percentile-percent-rota-outliers="1.8". Specific to that have a percent-rota-outliers attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-rota-outliers". Note that the "high-resol-relative-percentile-percent-rota-outliers" value is numerically smaller than the corresponding low value. Example: high-resol-relative-percentile-percent-rota-outliers="1.8". Specific to that have a percent-rota-outliers attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software. The "all" percentile rank for the property DCC_Rfree (the free R-factor from a DCC recalculation of the electron density maps for the deposited coordinates and structure factors). The comparison will be to the set of all structures determined by X-ray crystallography deposited, up to the date included in the program name="percentiles" version, where the DCC_Rfree was successfully calculated. Example: absolute-percentile-DCC_Rfree="90.6". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-DCC_Rfree". Example: numPDBids-absolute-percentile-DCC_Rfree="100719". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The "similar" percentile rank for the property DCC_Rfree (the free R-factor from a DCC recalculation of the electron density maps for the deposited coordinates and structure factors). The comparison will be to the subset of structures determined by X-ray crystallography deposited, up to the date included in the program name="percentiles" version, where the DCC_Rfree was successfully calculated that have a similar resolution ("PDB-resolution"). Example: relative-percentile-DCC_Rfree="92.9". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "relative-percentile-DCC_Rfree". Example: numPDBids-relative-percentile-DCC_Rfree="4827". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-DCC_Rfree". Note that the "low-resol-relative-percentile-DCC_Rfree" value is numerically greater than the corresponding high value. Example: low-resol-relative-percentile-DCC_Rfree="10.0" X-ray entry specific, produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-DCC_Rfree". Note that the "high-resol-relative-percentile-DCC_Rfree" value is numerically smaller than the corresponding low-* value. Example: high-resol-relative-percentile-DCC_Rfree="3.7" X-ray entry specific, produced by the percentiles step of the validation pipeline software. The "all" percentile rank for the property percent-RSRZ-outliers (The proportion of residues that are RSRZ outliers reported as a percentage). The comparison will be to the set of all structures determined by X-ray crystallography deposited, up to the date included in the program name="percentiles" version, where the percent-RSRZ-outliers was successfully calculated. Example: absolute_RSRZ_percentile="83.82" N.B. this is the chain/model equivalent of the overall (all chain) category "absolute-percentile-percent-RSRZ-outliers" X-ray entry specific, produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-percent-RSRZ-outliers". Example: numPDBids-absolute-percentile-percent-RSRZ-outliers="101464". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The "similar" percentile rank for the property percent-RSRZ-outliers (The proportion of residues that are RSRZ outliers reported as a percentage). The comparison will be to the subset of structures determined by X-ray crystallography deposited, up to the date included in the program name="percentiles" version, where the percent-RSRZ-outliers was successfully calculated that have a similar resolution ("PDB-resolution"). Example: relative-percentile-percent-RSRZ-outliers="100.0". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The number of PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-RSRZ-outliers". Example: numPDBids-relative-percentile-percent-RSRZ-outliers="4906" X-ray entry specific, produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-RSRZ-outliers". Note that the "low-resol-relative-percentile-percent-RSRZ-outliers" value is numerically greater than the corresponding high value. Example: low-resol-relative-percentile-percent-RSRZ-outliers="1.8". X-ray entry specific, produced by the percentiles step of the validation pipeline software. The resolution bin limit in Angstroms for PDB depositions used in the comparison when calculating the attribute "relative-percentile-percent-RSRZ-outliers". Note that the "high-resol-relative-percentile-percent-RSRZ-outliers" value is numerically smaller than the corresponding low-* value. Example: high-resol-relative-percentile-percent-RSRZ-outliers="1.8". X-ray entry specific, produced by the percentiles step of the validation pipeline software. Value in ppm of a chemical shift Uncertainty on a chemical shift value - usually not available Ambiguity of the chemical shift assignment as per NMR-STAR V3.1 dictionary. Diagnostic text message when a chemical shift was not parsed or not mapped to structure. 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 typically assigned nuclei of a given "type" (e.g., backbone) and "element" (13C)in the structure that lack a chemical shift assignment 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. The chemical element (isotope) for which the assignment completeness is calculated. An integer identifier of a chemical shifts file. The name of the chemical shifts file supplied to the validation pipeline. Label of the section that actually contains chemical shifts. Identifier of the chemical shift list in the file. 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 chemical shifts that could not be mapped to structure. Currently not used. Reserved for ambiguous mappings. Number of chemical shifts successfully mapped to the structure. Number of chemical shifts successfully parsed. Total number of records in the chemical shift list. Number of chemical shifts that could not be parsed. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" An atom name for the first atom in a bond or angle outlier. Atom names are from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" An atom name for the second atom in a bond or angle outlier. Atom names are from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="CE2" An atom name for third atom in an angle outlier. Atom names are from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" A comma separated list of atom names. Example: atoms="O5,C1,C2" The observed value for the bond length or bond angle, that is the value found in the structure being analyzed for the atoms involved. Units depend on the parameter being analyzed. Example: obsval="126.83" The observed value for the bond length or bond angle or torsion angle, that is the value found in the structure being analyzed for the atoms involved. Units depend on the parameter being analyzed. Example: obsval="126.83" The "ideal" value of the bond length or bond angle or torsion 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. Units depend on the parameter being analyzed. Example: mean="124.51" The standard deviation for the bond length or bond angle or torsion 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. Units depend on the parameter being analyzed. Example: stdev="1.12" The local density is the percentage of observed Mogul torsion angles within certain units of the query torsion angle. Units depend on the parameter being analyzed. Example: local_density="17.5" The number of observations found for bond length or bond angle or torsion angle in the Mogul analysis. Example: numobs="87" 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. Example: Zscore="-2.40" 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. Example: Zscore="-2.40" The Zscore of the deviation of the bond length or bond angle in the model 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. Units depend on the parameter being analyzed. Example: z="7.27" The difference to the nearest value of the bond length or bond angle or torsion angle found in the Mogul analysis. Units depend on the parameter being analyzed. The bond or bond angle involves one or atom that is in another residue. Example: link="yes" The distance in Angstroms between two atoms involved a clash. The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example rescode="GLY" (Only used in NMR specific definitions same as "resname".) The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Model identifier. Normally an integer but can be a string of up to 10 characters If the structure does not have multiple models then model will be "1". Example: model="1". This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. If the residue is a ligand and involved in clashes this will be set to yes: Example: ligand_clashes_outlier="yes". If the residue is a ligand and involved in clashes then this will be the number of MolProbity All-atom clashes for the subgroup. Example: ligand_num_clashes="7" l If the residue is a ligand and involved in clashes then this will be the number of symmetry related ("symm-clash") clashes identified by Validation-pack Example: ligand_num_symm_clashes="1" Will be set to "yes" if the residue is a ligand and has a chiral atom problem compared to the PDB chemical component definition. Example: ligand_chirality_outlier="yes". This residue is linked to the next residue by a peptide bond that has a cis rather than trans conformation. Example: cis_peptide="yes" The number atoms in the residue that the EDS software returns. X-ray specific produce by the EDS step. Example NatomsEDS="8". Identifier of the well-defined core (domain) to which the residue belongs, as determined by Cyrange. 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"). Real Space R-value (RSR) for the residue from the EDS generated map. Example: rsr="0.106" X-ray specific produce by the EDS step. 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. Example: rscc="0.950" X-ray specific produce by the EDS step. 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. Example: rsrz="-0.453" X-ray specific produce by the EDS step. 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. Example: EDIAm="1.04" X-ray specific produce by the EDS step. 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. Example: OPIA="87.5" X-ray specific produce by the EDS step. The Occupancy-Weighted Average B (OWAB) value per residue (in units Angstroms squared). This value is calculated by multiplying the B factor for each atom in the residue by its occupancy and then averaging this value over all atoms in the residue. Example: owab="31.210" X-ray specific produce by the EDS step. The average occupancy for the residue. Hydrogen atoms are excluded from consideration. Example: avgoccu="1.000" X-ray specific produce by the EDS step. This is the Local Ligand Density Fit (LLDF) for a ligand. LLDF compares the RSR of the non-standard residue to the mean and standard deviation of RSR for the neighbouring polymeric standard amino acids or nucleotides. Neighbouring polymeric residues are identified, as any standard amino acid or nucleotide that lies within 5.0 Angstrom distance of the ligand or non standard residue, using the NCONT program from CCP4. The mean and standard deviation of RSR values is then calculated for these neighbouring residues and this is compared to the RSR value of the non-standard residue to calculate a Z-score. If there are less than two neighbouring residues within 5.0 Å of the instance then LLDF cannot be calculated. Example: ligRSRZ="1.24" X-ray specific produce by the EDS step. A unique integer key for each LLDF calculation identifying the neighbouring polymeric residues for the residue identified as being with 5.0 Angstrom distance of the ligand or non standard residue. If a residue is involved in two or more LLDF calculations then there will be a comma separated list. Example: lig_rsrz_nbr_id="1" Example: lig_rsrz_nbr_id="1,2" X-ray specific produce by the EDS step. LLDF calculation: the mean RSR value for the residues within 5.0 Angstrom distance of the ligand. Currently the value is rounded to two decimal places so it would not be possible to actually use it practially. Example: ligRSRnbrMean="0.08" X-ray specific produce by the EDS step. LLDF calculation: the mean RSR value for the residues within 5.0 Angstrom distance of the ligand. Currently the value is rounded to two decimal places so it would not be possible to actually use it practically. Example: ligRSRnbrStdev="0.01" X-ray specific produce by the EDS step. LLDF calculation: the number of residues identified within 5.0 Angstrom distance of the ligand used in the calculation Example: ligRSRnumnbrs="23" X-ray specific produce by the EDS step. MolProbity Ramachandran plot classification for this residue one of "Favored", "Allowed" or "OUTLIER". Example: rama="Favored" Protein and polypeptide specific produced by the molprobity step. The phi torsion angle for the residue in degrees. Example: phi="-131.0". Protein and polypeptide specific produced by the molprobity step. The psi torsion angle for the residue in degrees. Example: psi="151.6". Protein and polypeptide specific produced by the molprobity step. 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: rota="mt" rota="t" rota="OUTLIER" rota="m" rota="p" rota="m-20" rota="m-85" rota="tp" rota="t80" rota="mt-10" rota="Cg_endo" rota="Cg_exo" Protein and polypeptide specific produced by the molprobity step. 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. 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. Example: RNAscore="0.84" MolProbity RNAsuite conformation analysis. RNA specific produced by the molprobity step. Placeholder for reporting RNA pucker problem from MolProbity. Not actually used at present, due to bug? This will be set to "yes" if the residue is ignored for Mogul validation of bond geometry. For instance monoatomic ions such as sodium resname="NA" will have mogul-ignore="yes". Produced by the mogul step. The root-mean-square value of the Z-scores of bond angles for the residue in degrees. Example: angles_rmsz="0.71". Mogul identifies structures with a similar bond angle in CSD small molecule crystal structure. The Z-score is the deviation of the observed angle from the mean found in the Mogul survey divided by the Mogul standard deviation. The individual Z-scores are then combined to calculate a root-mean-square value. Produced by the mogul step. The root-mean-square value of the Z-scores of bond lengths for the residue in Angstroms. Example: bonds_rmsz="0.47". Mogul identifies structures with a similar bond length in CSD small molecule crystal structure. The Z-score is the deviation of the observed length from the mean found in the Mogul survey divided by the Mogul standard deviation. The individual Z-scores are then combined to calculate a root-mean-square value. Produced by the mogul step. The number of bond angles from the residue that are used in the calculation of "mogul_angles_rmsz". Example: mogul_rmsz_numangles="26" Produced by the mogul step. The number of bond lengths from the residue that are used in the calculation of "mogul_lengths_rmsz". Example: mogul_rmsz_numlengths="16" Produced by the mogul step. This will be set to "yes" if that more than 40% of bonds, angles, torsions, and rings are found in the Mogul analysis to be outliers. Produced by the mogul step. This will be set to "yes" if EDS finds that the ligand has an issue with electron density fit. is used where the residue has Real-Space R-value (RSR) exceeding 0.5 or a Local Ligand Density Fit value (LLDF) is greater than 2. Note that the LLDF calculation is still under development and the methods and criterion for identifying outlier will be refined following analysis of a large test set of ligands. X-ray specific produce by the EDS step. The proportion of all atoms of the residue in density Q-Score value Identifier of the well-defined core Number of omissions from the contiguous protein chain within the individual well-defined core (domain). Number of residues composing the individual well-defined core (domain). What fraction the individual core contributes to the total well-defined portion of the protein. Average pairwise backbone RMSD of the individual well-defined core (domain) over the ensemble. Average RMSD between the medoid model and other members of the ensemble. Simplified description of the residue composition of the individual well-defined core (domain). The "all" percentile rank for the property percent-RSRZ-outliers for the chain/model (The proportion of residues that are RSRZ outliers reported as a percentage). The comparison will be to the set of all structures determined by X-ray crystallography deposited, up to the date included in the program name="percentiles" version, where the percent-RSRZ-outliers was successfully calculated. Example: absolute_RSRZ_percentile="39.90" N.B. this is the chain/model equivalent of the overall (all chain) category "absolute-percentile-percent-RSRZ-outliers" X-ray entry specific, produced by the percentiles step of the validation pipeline software. The "similar" percentile rank for the property percent-RSRZ-outliers for the chain/model (The proportion of residues that are RSRZ outliers reported as a percentage). The comparison will be to the subset of structures determined by X-ray crystallography deposited, up to the date included in the program name="percentiles" version, where the percent-RSRZ-outliers was successfully calculated that have a similar resolution ("PDB-resolution"). Example: relative_RSRZ_percentile="34.81" N.B. this is the chain/model equivalent of the overall (all chain) category "absolute-percentile-percent-RSRZ-outliers" X-ray entry specific, produced by the percentiles step of the validation pipeline software. The "all" percentile rank for the property percent-rama-outliers for the chain/model (the MolProbity Ramachandran outlier score). The comparison will be to: * For X-ray structures: the set of all structures determined by X-ray crystallography ... * For NMR and EM structures: the set of all PDB structures ... deposited, up to the date included in the program name="percentiles" version, where the percent-rama-outliers was successfully calculated. Example: absolute_rama_percentile="9.27" N.B. this is the chain/model equivalent of the overall (all chain) category "absolute-percentile-percent-rama-outliers" Produced by the percentiles step of the validation pipeline software. The "relative" percentile rank for the property percent-rama-outliers for the chain/model (the MolProbity Ramachandran outlier score). The comparison will be to: * For X-ray structures: the subset of structures structures determined by X-ray crystallography, that have a similar resolution ("PDB-resolution") to this entry, ... * For structures determined by NMR: the subset of structures determined by NMR ... * For structures determined by EM: the subset of structures determined by EM ... ... deposited up to the date included in the program name="percentiles" version and where the percent-rama-outliers was successfully calculated. Example: relative_rama_percentile="47.81" N.B. this is the chain/model equivalent of the overall (all chain) category "relative-percentile-percent-rama-outliers" Produced by the percentiles step of the validation pipeline software. The "all" percentile score for the chain/model based on the percentage of sidechain outliers for the chain/model. (the MolProbity sidechain outlier score). The comparison will be to: * For X-ray structures: the set of all structures determined by X-ray crystallography ... * For NMR and EM structures: the set of all PDB structures ... deposited, up to the date included in the program name="percentiles" version, where the percent-rota-outliers was successfully calculated. Example: absolute_sidechain_percentile="54.16" Only calculated if percent-rota-outliers is available. N.B. this is the chain/model equivalent of the overall (all chain) category "absolute-percentile-percent-rota-outliers" Produced by the percentiles step of the validation pipeline software. The "relative" percentile rank for the property percent-rota-outliers for this chain/model. (the MolProbity sidechain outlier score). The comparison will be to: * For X-ray structures: the subset of structures structures determined by X-ray crystallography, that have a similar resolution ("PDB-resolution") to this entry, ... * For structures determined by NMR: the subset of structures determined by NMR ... * For structures determined by EM: the subset of structures determined by EM ... ... deposited up to the date included in the program name="percentiles" version and where the percent-rota-outliers was successfully calculated. Example: relative_sidechain_percentile="1.44". Only calculated if percent-rota-outliers is available. N.B. this is the chain/model equivalent of the overall (all chain) category "relative-percentile-percent-rota-outliers" Produced by the percentiles step of the validation pipeline software. The average of the residue inclusions for all residues in this chain An identifier used to uniquely identify a particular restraints loop in the NMR-STAR file An identifier used to uniquely identify a restraint with in a particular restraint loop in NMR-STAR file The absolute value of the distance violation measured in Angstrom. The absolute value of the dihedal-angle violation measured in degrees Distance violation calculated by BMRB restraints validation package. If a given pair of atom/group of atoms are not with in the expected range given by NOE distance restraint, then the absolute value of how far away from the expected rage is given as violation An identifier used to uniquely identify a particular restraints loop in the NMR-STAR file An identifier used to uniquely identify a restraint with in a particular restraint loop in NMR-STAR file The absolute value of the distance violation measured in Angstrom. Dihedral-angle violation is calculated by BMRB restraints validation package. If a given dihedral-angle is not with in the expected range given by dihedral-angle restraints, then the absolute value of how far away from the expected rage is given as violation. An identifier used to uniquely identify a particular restraints loop in the NMR-STAR file An identifier used to uniquely identify a restraint with in a particular restraint loop in NMR-STAR file The absolute value of the dihedral-angle violation measure in degrees Number of restraints in a given restraint type Number of violated restraints The maximum value of violation of a particular restraint in an ensemble The mean value of the violation of a given restraint in an ensemble The standard deviation of the value of the violations of a given restraint in an ensemble The median value of the violation of a given restraint in an ensemble Summary of NMR distance and dihedral-angle restraints generated by BMRB Restraints analysis package Summary of conformationally restriction restraints. All redundant and duplicate restraints are filtered Number of restraints in different restraint categories are listed here The description of the restraint type The number of restraints or the value associated with the description Summary of distance violations in different bins based on its magnitude of violation Distance Violation statistics with in the bin The maximum value of distance violation with in the given bin The violations are binned as small, medium and large violations based on its absolute value. Average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble. Summary of dihedral-angle violations in different bins based on its magnitude of violation Dihedral-angle violation statistics with in the bin The maximum value of the dihedral-angle violation with in the bin The violations are binned as small, medium and large violations based on its absolute value. Average number of violations per model is calculated by dividing the total number of violations in each bin by the size of the ensemble. Analysis results of NOE distance restraints in different models in the NMR ensemble Statistics about violated and consistently violated restraints. Restraints that are violated all modules are called consistently violated restraints. Violated and consistently violated statistics in different restraints type The restraint type (Intra-residue, Sequential, MediumRange, LongRange, InterChain, Total) The restraint sub type (BackboneBackone, BackboneSidechain, SidechainSidechain, all) Number of restraints that are violated in all models Percentage of restraints that are violated in all models against total number of restraints Percentage of restraints that are violated in all models against number of restraints in a given restraint type Number of restraints in a given restraint type Number of restraints that are violated that are violated at least in one model Percentage of restraints in a given restraint type Percentage of restraints that are violated at least in one model in given restraint type against the total restraints Percentage of restraints that are violated at least in one model against the total number of restraints in a given restraints type List of number of violated distance restraints in each model Number of violated restraints in a given model The type to distance restraint (intraresidue, sequential, etc.. ) The type of distance restraint(intraresidue, sequential, etc...) Number of violated restraints The maximum value of violation of a particular restraint in an ensemble The mean value of the violation of a given restraint in an ensemble The standard deviation of the value of the violations of a given restraint in an ensemble Distance violation statistics in an ensemble Number of violated models for a given set of restraints The type to distance restraint (intraresidue, sequential, etc.. ) The type of distance restraint(intraresidue, sequential, etc...) Number of violated models for given set of violated restraints Percentage of violated models for given set of violated restraints Restraints that are violated in more than one models Restraints that are violated in 'n' models This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" 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. Example: ent="3". Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" Mean distance violation over the violated models Standard deviation of the absolute value of the violations Number of violated models for a given restraint or set of restraints List of all violated restraints Details about particular violation This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" 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. Example: ent="3". Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" absolute value of the violation Analysis results of dihedral-angle restrains in the ensemble Statistics about violated and consistently violated restraints. Restraints that are violated all models are called consistently violated restraints. Violated and consistently violated statistics in different restraints type The dihedral-angle restraint type (PHI,PSI,etc) Number of restraints that are violated in all models Percentage of restraints that are violated in all models against total number of restraints Percentage of restraints that are violated in all models against number of restraints in a given restraint type Number of restraints in a given restraint type Number of restraints that are violated that are violated at least in one model Percentage of restraints in a given restraint type Percentage of restraints that are violated at least in one model in given restraint type against the total restraints Percentage of restraints that are violated at least in one model against the total number of restraints in a given restraints type List of number of violated dihedral-angle restraints in each model Number of violated restraints ina given model The type to dihedral-angle restraint (PHI,PSIetc ) and its violations The type of dihedral-angle restraint(PHI,PSI,etc) Number of violated restraints Dihedral-angle violation statistics in the ensemble Number of violated models for a given set of restraints The type to dihedral-angle restraint (PHI,PSIetc ) and its violations The type of dihedral-angle restraint(PHI,PSI,etc) Number of violated models for given set of violated restraints Percentage of violated models for given set of violated restraints Dihedral-angle restraints that are violated in more than one model Restraints that are violated in 'n' models This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" 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. Example: ent="3". Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" Mean value of dihedral-angle violation over all violated models Standard deviation of the value of the restraint violation over all violated models This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" number of violated models for a given restraint or set of restraints List of all dihedral-angle violations Details about particular dihedral-angle violation This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" 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. Example: ent="3". Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" This attribute will be set if the ModelledSubgroup has atoms with the alternate position indicator set. Normally one character but can be up to 3. Example altcode="A" Obtained from _atom_site.label_alt_id The chain identifier for the residue or chain obtained from cif item _atom_site.auth_asym_id. Currently this is limited to 5 characters. Example: chain="A" The residue number aka sequence id for a residue. Obtained from _atom_site.auth_seq_id Example: resnum="8" The "residue type", this is the name of the chemical component from the PDB chemical component dictionary. Obtained from _atom_site.auth_comp_id Example resname="GLY" Insertion code for residue from _atom_site.pdbx_PDB_ins_code Example: icode=" " 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. Example: ent="3". The_atom_site.label_asym_id label for the residue. Normally this is the same as the chain. Example: said="A" From cif item _atom_site.label_seq_id "a pointer to _entity_poly_seq.num" Example: seq="20" for a residue in a polymer Example: seq="." for a non-polymeric residue eg ligand or water. An atom name from cif item _atom_site.label_atom_id and _chem_comp_atom.atom_id. Currently limited to 4 characters. Example: atom="NE2" An identifier for the structure. For released or annotated structures this will be the PDB ID currently 4 characters, for example "1CBS". For reports produced during initial depositon process a deposition ID will be given instead, for example "D_1000219513".