WHAT IF Check report

This file was created 2017-09-10 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/pdb1xyz.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.

Warning: Triclinic cell with mixed acute and obtuse angles

The crystallographic unit cell does not conform to the convention that a triclinic cell should be specified as having either three obtuse (type II) or three acute angles (type I).

The CRYST1 cell dimensions

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha= 100.540  Beta=  83.790  Gamma= 101.640

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha= 100.540  Beta=  83.790  Gamma= 101.640

Dimensions of a reduced cell

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha=  79.460  Beta=  83.790  Gamma=  78.360

Dimensions of the conventional cell

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha=  79.460  Beta=  83.790  Gamma=  78.360

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

Note: Header records from PDB file

Header records from PDB file.

HEADER    GLYCOSYLTRANSFERASE                     07-JUN-95   1XYZ
A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO
 DISTINCT FAMILIES OF BETA-GLYCANASES
GLYCOSYL HYDROLASE, XYLANASE, FAMILY F/10 OF GLYCOSYL
 HYDROLASES, CLOSTRIDIUM THERMOCELLUM, GLYCOSYLTRANSFERASE
JRNL        R.DOMINGUEZ,H.SOUCHON,S.SPINELLI,Z.DAUTER,
JRNL        K.S.WILSON,S.CHAUVAUX,P.BEGUIN,P.M.ALZARI
JRNL        A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN
JRNL        TWO DISTINCT FAMILIES OF BETA-GLYCANASES.
JRNL        REF    NAT.STRUCT.BIOL.              V.   2   569 1995
JRNL        REFN                   ISSN 1072-8368
JRNL        PMID   7664125
JRNL        DOI    10.1038/NSB0795-569

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: A and B

All-atom RMS fit for the two chains : 0.629
CA-only RMS fit for the two chains : 0.286

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: A and B

Note: Counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Z equals the number of matrices of the space group multiplied by the number of NCS relations. These numbers seem to be consistent.

Space group as read from CRYST card: P 1
Number of matrices in space group: 1
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
but NCS matrices (but not the unitary matrix) are found labeled `dont use`: 1
SEQRES multiplicity agrees with number of MTRIX matrices labeled `dont use`
Value of Z as found on the CRYST1 card: 2
Z, spacegroup, and NCS seem to agree administratively

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: 73381.812
Volume of the Unit Cell V= 163504.234
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 1
which seems more or less consistent with the SEQRES multiplicity
because the unitary MTRIX record gets forgotten more often ...
Matthews coefficient for observed atoms and Z: Vm= 2.228
BIOMT matrices observed in the PDB file: 2
Matthews coefficient read from REMARK 280 Vm= 2.070
Vm by authors and this calculated Vm agree well

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 (  516)   320 (  835) A Protein             To check
     2   321 (  516)   640 (  835) B Protein             To check
     3   641 ( HOH )   641 ( HOH ) A water   (  234)     To check
     4   642 ( HOH )   642 ( HOH ) B water   (  223)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 640.
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 457
Residue numbers increase monotonously OK

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Note: No missing atoms detected in residues

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



Note: All occupancies seem to add up to 0.0 - 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

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

Note: Arginine nomenclature OK

Note: Tyrosine torsion conventions OK

Note: Phenylalanine torsion conventions OK

Note: Aspartic acid torsion conventions OK

Note: Glutamic acid torsion conventions OK

Note: Phosphate group names OK in DNA/RNA

Note: Heavy atom naming OK

Note: No decreasing residue numbers

Geometric checks

Warning: Unusual bond lengths


Warning: Low 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



Warning: Unusual bond angles


Note: Normal bond angle variability


Note: Residue hand check OK

Note: Chirality OK

Note: Improper dihedral angle distribution OK

Error: Tau angle problems


Warning: High tau angle deviations

Error: Side chain planarity problems


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


Note: chi-1/chi-2 angle correlation Z-score OK

Warning: Unusual rotamers


Warning: Unusual backbone conformations


Note: Backbone conformation Z-score OK

Warning: Omega angles too tightly restrained

Warning: Unusual PRO puckering amplitudes


Warning: Unusual PRO puckering phases


Note: Backbone oxygen evaluation OK

Note: Peptide bond conformations

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

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Note: Structural average packing environment OK

Note: Quality value plot

Chain identifier: A

Note: Quality value plot

Chain identifier: B

Warning: Low packing Z-score for some residues


Warning: Abnormal packing Z-score for sequential residues


Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogen bond related checks

Warning: No crystallisation information

Error: Water clusters without contacts with non-water atoms


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: No crippling problems detected

Note: Cell parameter anomaly

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues