REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. Example: 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: X-ray entry specific, obtained in the eds step from REFMAC calculation.
The string "yes".
Allowable values: yes
The overall R-factor from a DCC recalculation of an electron density map. Example: Currently value is rounded to 2 decimal places. X-ray entry specific, obtained from the DCC program.
Either a decimal number or the string "NotAvailable".
The pdbx_vrpt_software used by DCC to perform the recaluclation of the electron density maps. Currently one of "CNS", "REFMAC" or "PHENIX". Example: X-ray entry specific, obtained from the DCC program.
The overall R factor from the EDS REFMAC calculation (no free set is used in this). Example: 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: 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: X-ray entry specific, obtained in the eds step.
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.
Either a decimal number or the string "NotAvailable".
Fo,Fc correlation: The difference between the observed structure factors (Fo) and the calculated structure factors (Fc) measures the correlation between the PDB_model_num and the i experimental data. Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
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 X-ray entry specific, calculated by Phenix Xtriage program.
Either a decimal number or the string "NotAvailable".
Either a decimal number or the string "NotAvailable".
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.
Either a decimal number or the string "NotAvailable".
Either a decimal number or the string "NotAvailable".
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 depositon 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.
The MolProbity conformer-match quality parameter for RNA structures. Low values are worse. Example: Specific to structures that contain RNA polymers.
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: 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: X-ray entry specific, calculated by Phenix Xtriage program.
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).
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).
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).
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).
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).
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).
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: X-ray entry specific, calculated by Phenix Xtriage program.
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 proportion of all non hydrogen atoms within density.
The proportion of backbone atoms within density.
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 pdbx_vrpt_software element in the pdbx_vrpt_sotfware_notused list.
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 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 threesigma.
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.
REFMAC scaling parameter as reported in log output line starting 'Partial structure 1: scale.' Example: 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: X-ray entry specific, obtained in the eds step from REFMAC calculation.
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 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 threesigma.
The version of CCP4 suite pdbx_vrpt_sotfware_notused used in the analysis. Example: X-ray entry specific, obtained from the eds step.
The number of centric reflections that Xtriage identifies as outliers. Example: X-ray entry specific, calculated by Phenix Xtriage program.
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).
The filename for the input chemical shifts file given to the validation pipeline. Not reported for runs at the annotation or release stage.
This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other. It is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms. For structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the well-defined (core) residues from ensemble analysis.
Only given for structures determined by NMR. The MolProbity pdbx_vrpt_clashes score for all label_atom_id pairs.
The recommended contour level for the primary map of this deposition.
The filename for the input mmCIF coordinate file given to the validation pipeline. Not reported for runs at the annotation or release stage.
Diagnostic message from the wrapper of Cyrange software which identifies the well-defined cores (domains) of NMR protein structures.
Total number of well-defined cores (domains) identified by Cyrange
Reference for the Cyrange software.
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: X-ray entry specific, obtained from the Xtriage program.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
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"
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: 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-RNAsuiteness". Note that the "high_resol_relative_percentile_RNA_suiteness" value is numerically smaller than the corresponding low value. Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness 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: 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-percent-RSRZ-outliers". Note that the "high_resol_relative_percentile_percent_RSRZ_outliers" value is numerically smaller than the corresponding low-* value. Example: 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-rama-outliers". Note that the "high_resol_relative_percentile_percent_ramachandran_outliers" value is numerically smaller than the corresponding low value. Example: Specific to structures that have a percent_ramachandran_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_rotamer_outliers" value is numerically smaller than the corresponding low value. Example: Specific to that have a percent_rotamer_outliers attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software.
The string "yes".
Allowable values: yes
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: 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-RNAsuiteness". Note that the "low_resol_relative_percentile_RNA_suiteness" value is numerically greater than the corresponding high value. Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness 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 "low_resol_relative_percentile_clashscore" value is numerically greater than the corresponding high value. Example: 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-percent-RSRZ-outliers". Note that the "low_resol_relative_percentile_percent_RSRZ_outliers" value is numerically greater than the corresponding high value. Example: 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-rama-outliers". Note that the "low_resol_relative_percentile_percent_ramachandran_outliers" value is numerically greater than the corresponding high value. Example: Specific to that have a percent_ramachandran_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 "low_resol_relative_percentile_percent_rotamer_outliers" value is numerically greater than the corresponding high value. Example: Specific to that have a percent_rotamer_outliers attribute and have been determined by X-ray crystallography. Produced by the percentiles step of the validation pipeline software.
For each Cyrange well-defined core ("cyrange_domain") the id of the PDB_model_num which is most similar to other models as measured by pairwise RMSDs over the domain. For the whole entry ("Entry"), the medoid PDB_model_num of the largest core is taken as an overall representative of the structure.
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 NMRClust software which clusters NMR models.
Total number of clusters in the NMR ensemble identified 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.
Number of models that do not belong to any cluster as deemed by NMRClust.
Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust.
Reference for the NMRClust software.
The string "yes".
Allowable values: yes
The string "yes".
Allowable values: yes
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.
This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the all-atom clashscore.
The number of PDB depositions used in the comparison when calculating the attribute "absolute-percentile-DCC_Rfree". Example: 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-RNAsuiteness". Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness 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-clashscore" Example: 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: 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-rama-outliers" Example: 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: 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: 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-RNAsuiteness". Example: Specific to entries that contain RNA polymers (and have a RNA_suiteness 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-clashscore" Example: 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: 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-rama-outliers" Example: 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: Produced by the percentiles step of the validation pipeline software.
The number of bond angless 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 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 reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. example: X-ray entry specific, obtained from the DCC 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: X-ray entry specific, calculated by Phenix Xtriage program.
Reference for the PANAV software.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
A percentage, Normally percent proportion of the total number. Between 0% and 100%.
The percentile bins that this structure would contribute to in a recalculation of percentile. The string is a comma separated list. Example: 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: An EM entry that would contribute to all and em structures bins. Example #3: A NMR entry hat would contribute to all and nmr structures bins.
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
Version and reference of the RCI software
The filename for the input mmCIF format reflection file given to the validation pipeline. Not reported for runs at the annotation or release stage.
Version of the REFMAC pdbx_vrpt_software used in the EDS step. Example: X-ray entry specific, obtained in the eds step from REFMAC calculation.
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).
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).
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).
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).
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).
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).
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 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.
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)
Version of the software for chemical shift outlier detection - currently same as revision number of the validation pipeline.
A sentence giving the result of Xtriage’s analysis on translational NCS. Example: 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: 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: 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: X-ray entry specific, obtained from the Xtriage program.
The mmCIF item names of the _refln columns used as input to the Xtriage program. Example X-ray entry specific, calculated by Phenix Xtriage program.
Generated using TypeDoc
String for B_factor_type either "PARTIAL" or "FULL".
Allowable values: FULL, PARTIAL