WHAT IF Check report

This file was created 2017-10-05 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Verification log for /srv/data/pdb/flat/pdb3dvg.ent

Checks that need to be done early-on in validation

Note: Introduction

WHAT CHECK needs to read a PDB file before it can check it. It does a series of checks upon reading the file. The results of these checks are reported in this section (section 2.1). The rest of the report will be more systematic in that section 2.2 reports on administrative problems. Section 2.3 gives descriptive output that is not directly validating things but more telling you how WHAT CHECK interpreted the input file. Section 2.4 looks at B-factors, occupancies, and the presence/absence of (spurious) atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with geometric problems like bond lengths and bond angles. Section 2.7 deals with torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen bonds, ion packing, and other things that can be summarized under the common name charge-charge interactions. Section 2.11 gives a summary of whole report and tells you (if applicable) which symmetry matrices were used. Section 2.12 tells the crystallographer which are the things most in need of manual correction. And the last section, section 2.13, lists all residues sorted by their need for visual inspection in light of the electron density.

Note: Header records from PDB file

Header records from PDB file.

HEADER    IMMUNE SYSTEM                           18-JUL-08   3DVG
CRYSTAL STRUCTURE OF K63-SPECIFIC FAB APU.3A8 BOUND TO K63-LINKED DI-
 UBIQUITIN
DI-UBIQUITIN, FAB FRAGMENT, ANTIBODY, NUCLEUS, PHOSPHOPROTEIN,
 RIBOSOMAL PROTEIN, IMMUNE SYSTEM
JRNL        K.NEWTON,M.L.MATSUMOTO,I.E.WERTZ,D.S.KIRKPATRICK,J.R.LILL,
JRNL        J.TAN,D.DUGGER,N.GORDON,S.S.SIDHU,F.A.FELLOUSE,L.KOMUVES,
JRNL        D.M.FRENCH,R.E.FERRANDO,C.LAM,D.COMPAAN,C.YU,I.BOSANAC,
JRNL        S.G.HYMOWITZ,R.F.KELLEY,V.M.DIXIT
JRNL        UBIQUITIN CHAIN EDITING REVEALED BY POLYUBIQUITIN
JRNL        LINKAGE-SPECIFIC ANTIBODIES.
JRNL        REF    CELL(CAMBRIDGE,MASS.)         V. 134   668 2008
JRNL        REFN                   ISSN 0092-8674
JRNL        PMID   18724939
JRNL        DOI    10.1016/J.CELL.2008.07.039

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: X and Y

All-atom RMS fit for the two chains : 1.149
CA-only RMS fit for the two chains : 0.745

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: X and Y

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Note: Matthews coefficient OK

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Molecular weight of all polymer chains: 63491.871
Volume of the Unit Cell V= 806272.875
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 3.175
A few residues have missing atoms that did not enter the Vm calculation
One BIOMT matrix observed in the PDB file, but that is the unitary one
Matthews coefficient read from REMARK 280 Vm= 3.030
Vm by authors and this calculated Vm agree well

Note: All atoms are sufficiently far away from symmetry axes

None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis.

Note: Chain identifiers OK

WHAT CHECK has not detected any serious chain identifier problems. But be aware that WHAT CHECK doesn't care about the chain identifiers of waters.

Administrative problems that can generate validation failures

Note: No strange inter-chain connections detected

No covalent bonds have been detected between molecules with non-identical chain identifiers.

Note: No duplicate atom names in ligands

All atom names in ligands (if any) seem adequately unique.

Note: In all cases the primary alternate atom was used

WHAT CHECK saw no need to make any alternate atom corrections (which means they either are all correct, or there are none).

Note: No residues detected inside ligands

Either this structure does not contain ligands with amino acid groups inside it, or their naming is proper (enough).

Note: No attached groups interfere with hydrogen bond calculations

It seems there are no sugars, lipids, etc., bound (or very close) to atoms that otherwise could form hydrogen bonds.

Note: No probable side chain atoms with zero occupancy detected.

Either there are no side chain atoms with zero occupancy, or the side chain atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: No probable backbone atoms with zero occupancy detected.

Either there are no backbone atoms with zero occupancy, or the backbone atoms with zero occupancy were left out of the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: All residues have a complete backbone.

No residues have missing backbone atoms.

Note: No C-alpha only residues

There are no residues that consist of only an alpha carbon atom.

Non-validating, descriptive output paragraph

Note: Content of the PDB file as interpreted by WHAT CHECK

Content of the PDB file as interpreted by WHAT CHECK. WHAT CHECK has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT CHECK output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK website.

     1     1 (    5)   210 (  214) A Protein             To check
     2   211 (    1)   431 (  221) B Protein             To check
     3   432 (   -1)   506 (   73) X Protein             To check
     4   507 (    1)   582 (   76) Y Protein             To check
     5   583 ( HOH )   583 ( HOH ) A water   (   18)     To check
     6   584 ( HOH )   584 ( HOH ) B water   (    7)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 582
of which 3 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 25

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Secondary structure

Secondary structure assignment

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Note: No rounded coordinates detected

Note: No artificial side chains detected

Warning: Missing atoms



Note: All B-factors fall in the range 0.0 - 100.0

Note: C-terminus capping




Note: Weights administratively correct

Note: Normal distribution of occupancy values



Warning: Occupancy atoms do not add up to 1.0.





Warning: What type of B-factor?



Note: Number of buried atoms with low B-factor is OK

Note: B-factor distribution normal



Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Nomenclature related problems

Note: Introduction to the nomenclature section.

Note: Valine nomenclature OK

Note: Threonine nomenclature OK

Note: Isoleucine nomenclature OK

Note: Leucine nomenclature OK

Warning: Arginine nomenclature problem


Warning: Tyrosine convention problem


Warning: Phenylalanine convention problem


Warning: Aspartic acid convention problem


Warning: Glutamic acid convention problem


Note: Phosphate group names OK in DNA/RNA

Note: Heavy atom naming OK

Note: No decreasing residue numbers

Geometric checks

Warning: Unusual bond lengths


Note: Normal bond length variability


Warning: Possible cell scaling problem

SCALE matrix obtained from PDB file


Unit Cell deformation matrix


Proposed new scale matrix


With corresponding cell


The CRYST1 cell dimensions



Note: All bond angles OK

Note: Normal bond angle variability


Error: Nomenclature error(s)


Note: Chirality OK

Note: Improper dihedral angle distribution OK

Note: Tau angles OK

Note: Normal tau angle deviations

Note: Side chain planarity OK

Note: Atoms connected to aromatic rings OK

Torsion-related checks

Note: Ramachandran Z-score OK

Note: Ramachandran check

Warning: Torsion angle evaluation shows unusual residues


Warning: Backbone evaluation reveals unusual conformations


Error: Chi-1/chi-2 rotamer problems


Error: chi-1/chi-2 angle correlation Z-score very low

Warning: Unusual rotamers


Warning: Unusual backbone conformations


Note: Backbone conformation Z-score OK

Note: Omega angle restraint OK

Warning: Unusual PRO puckering amplitudes


Warning: Unusual PRO puckering phases


Warning: Backbone oxygen evaluation


Warning: Possible peptide flips


Bump checks

Error: Abnormally short interatomic distances


Note: Some notes regarding these bumps









Packing, accessibility and threading

Note: Inside/outside distribution check

Note: Inside/Outside residue distribution normal

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Warning: Abnormal packing environment for some residues


Note: No series of residues with bad packing environment

Note: Structural average packing environment OK

Note: Quality value plot

Chain identifier: A

Note: Quality value plot

Chain identifier: B

Note: Quality value plot

Chain identifier: X

Note: Quality value plot

Chain identifier: Y

Warning: Low packing Z-score for some residues


Note: No series of residues with abnormal new packing environment

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Water, ion, and hydrogen bond related checks

Note: Crystallisation conditions from REMARK 280


Note: Water contacts OK

Note: No waters need moving

Error: Water molecules without hydrogen bonds


Error: His, Asn, Gln side chain flips


Note: Histidine type assignments


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Note: Some notes regarding these donors and acceptors


















Note: Content of the PDB file as interpreted by WHAT CHECK


Final summary

Note: Summary report







Suggestions for the refinement process

Note: Introduction to refinement recommendations

Note: Matthews coefficient problem

Note: Cell parameter anomaly

Error: Bumps in your structure

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues