WHAT IF Check report

This file was created 2019-07-11 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/pdb4z0z.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    OXIDOREDUCTASE                          26-MAR-15   4Z0Z
INACTIVE AURONE SYNTHASE (POLYPHENOL OXIDASE) FROM NATURAL SOURCE,
 SULFOHISTIDINE ~ 90 %
POLYPHENOL OXIDASE, TYPE III COPPER PROTEIN, SULFOHISTIDINE,
 INACTIVATION, OXIDOREDUCTASE
JRNL        C.MOLITOR,S.G.MAURACHER,A.ROMPEL
JRNL        AURONE SYNTHASE IS A CATECHOL OXIDASE WITH HYDROXYLASE
JRNL        ACTIVITY AND PROVIDES INSIGHTS INTO THE MECHANISM OF PLANT
JRNL        POLYPHENOL OXIDASES.
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 113 E1806 2016
JRNL        REFN                   ESSN 1091-6490
JRNL        PMID   26976571
JRNL        DOI    10.1073/PNAS.1523575113

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.143
CA-only RMS fit for the two chains : 0.128

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and B

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 C

All-atom RMS fit for the two chains : 0.209
CA-only RMS fit for the two chains : 0.202

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and C

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.189
CA-only RMS fit for the two chains : 0.178

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and D

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.212
CA-only RMS fit for the two chains : 0.204

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: B and C

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.126
CA-only RMS fit for the two chains : 0.114

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: B and D

Note: NCS statistics suppressed

There are more pairs of NCS equivalent molecules, but the statistics will not be shown.

Note: No crystallographic symmetry between molecules

No extra crystallographic symmetry was observed between the independent molecules.

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 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 4
Highest polymer chain multiplicity according to SEQRES: 4
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Z, spacegroup, and NCS seem to agree administratively

Error: Matthews Coefficient (Vm) very high

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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 3508.991
Volume of the Unit Cell V= 736229.188
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z is high: Vm= 104.906
Be aware though that the number of residues with missing atoms is: 156
BIOMT matrices observed in the PDB file: 5
But accounting for these BIOMT matrices does not make Vm reasonable yet
Matthews coefficient read from REMARK 280 Vm= 2.210
Vm by authors and this calculated Vm do not agree very 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.

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT CHECK uses a local copy of the CCP4 monomer library to generate topology information for ligands. Be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology entry first. This topology is either present in the monomer library, or as a libcheck-generated file in the local directory.

  158 ILE  (   3-) A  -
  161 ILE  (   8-) A  -
  164 ILE  (  11-) A  -
  165 ASP  (   7-) A  -
  166 LYS  (  13-) A  -
  167 CYS  (  12-) A  -
  168 ASP  (  14-) A  -
  171 GLY  (  18-) A  -
  172 ILE  (  19-) A  -
  173 GLY  (  20-) A  -
  176 GLY  (  24-) A  -
  177 GLU  (  23-) A  -
  178 ILE  (  26-) A  -
  182 LYS  (  30-) A  -
  183 CYS  (  31-) A  -
And so on for a total of 536 lines.

Warning: Covalently bound ligands

The ligands in this table are covalently bound to something else. It is already difficult to automatically generate topologies for ligands, but when they are covalently bound to something it becomes even more complicated to do everything right. So, if you get weird error messages that seem related to this covalent bond, then please feel free to ignore those, or even better, make a topology entry by hand.

The comment `Other ligand` indicates that the covalent bond is to another ligand. In that case you might want to convert the two ligands into one bigger ligand.

  158 ILE  (   3-) A  -
  161 ILE  (   8-) A  -
  164 ILE  (  11-) A  -          Other ligand
  165 ASP  (   7-) A  -
  166 LYS  (  13-) A  -          Other ligand
  167 CYS  (  12-) A  -          Other ligand
  168 ASP  (  14-) A  -          Other ligand
  171 GLY  (  18-) A  -          Other ligand
  172 ILE  (  19-) A  -          Other ligand
  173 GLY  (  20-) A  -          Other ligand
  176 GLY  (  24-) A  -
  177 GLU  (  23-) A  -
  178 ILE  (  26-) A  -
  182 LYS  (  30-) A  -          Other ligand
  183 CYS  (  31-) A  -          Other ligand
And so on for a total of 496 lines.

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.

Warning: Duplicate atom names detected in ligands

The pairs of atoms listed in the table below sit in the same ligand, or co-factor, and have the same name.

The PDB holds a large series of co-factors that consist of multiple, identical building blocks. Often the names of atoms in these building blocks are made unique by adding an A,B,C, etc., in front of their name. For example, AO11, AO12, BO11, BO22 for 4 Oxygens. The limitations of the PDB format make it difficult (albeit not impossible) to avoid this. WHAT CHECK deals with this problem by stripping the leading A,B,C, etc., from the names. This way the atom names make chemical sense again, but they loose their uniqueness. Although this seems to generate few problems, it cannot be guaranteed that certain error messages are the direct or indirect result of this nomenclature problem. It is possible that these duplications are the result of earlier atom name corrections by WHAT CHECK.

  414 HS8  ( 252-) A  -    O     414 HS8  ( 252-) A  -    O

Warning: Alternate atom problems

The residues listed in the table below have alternate atoms that do not follow normal logic (like the first of the atoms gets label A and has the highest occupancy). Residues listed here have at least one such problem. The Note Mixed means that the the best solution found by WHAT CHECK has mixed alternate atom labels. If the Note contains Occupancy, then at in at least one case does the not-used alternate atom have a higher occupancy then the one used. Corrected in the Note means that WHAT CHECK found a solution, but that does not mean it is guaranteed solved. If you find weird problems for this residue later-on in the report, especially when those are rotamer or bump related, please look at this residue in the PDB file itself, solve the problem by hand, and run WHAT CHECK again.

  539 SER  (  17-) B  - Corrected
 1272 SER  (  17-) D  - Corrected

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 (    1)    38 (  344) A Prote<-             /srv/data/pdb/fla...
     2    39 (  441)    39 (  441) E Prote<<             /srv/data/pdb/fla...
     3    40 (    1)    77 (  344) B Prote<-             /srv/data/pdb/fla...
     4    78 (  441)    78 (  441) F Prote<-             /srv/data/pdb/fla...
     5    79 (    1)   116 (  344) C Prote<-             /srv/data/pdb/fla...
     6   117 (  441)   117 (  441) G Prote<<             /srv/data/pdb/fla...
     7   118 (    1)   155 (  344) D Prote<-             /srv/data/pdb/fla...
     8   156 (  441)   156 (  441) H Prote<<             /srv/data/pdb/fla...
     9   157 (     )   157 (     )        <=             /srv/data/pdb/fla...
    10   158 (    3)   158 (    3) A ILE  <=             /srv/data/pdb/fla...
    11   159 (     )   159 (     )        <=             /srv/data/pdb/fla...
    12   160 (     )   160 (     )        <=             /srv/data/pdb/fla...
    13   161 (    8)   161 (    8) A ILE  <-             /srv/data/pdb/fla...
    14   162 (     )   162 (     )        <=             /srv/data/pdb/fla...
    15   163 (     )   163 (     )        <=             /srv/data/pdb/fla...
And so on for a total of 1490 lines.

Some numbers...

Note: Chain identifiers seem OK

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: Unexpected atoms encountered

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



Note: All occupancies seem to add up to 0.0 - 1.0.

Warning: Ligand with individual atomic occupancies



Warning: What type of B-factor?



Note: Insufficient residues for statistics

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: C

Note: B-factor plot

Chain identifier: D

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

Warning: Heavy atom naming convention problem


Note: No decreasing residue numbers

Geometric checks

Note: All bond lengths OK

Warning: Low bond length variability


Note: No bond length directionality

Note: All bond angles OK

Warning: Low bond angle variability


Note: Residue hand check OK

Note: Chirality OK

Note: Improper dihedral angle distribution OK

Note: Tau angle distribution not determined

Note: Side chain planarity OK

Note: Atoms connected to aromatic rings OK

Torsion-related checks

Note: Ramachandran check

Note: Torsion angles OK

Note: Backbone torsion angles OK

Note: Chi-1/chi-2 rotamer normality OK

Warning: Backbone conformation Z-score undetermined

Note: Omega angle restraint OK

Note: No prolines in structure

Note: Backbone oxygen evaluation OK

Note: Peptide bond conformations

Bump checks

Error: Abnormally short interatomic distances


Note: Some notes regarding these bumps









Water, ion, and hydrogen bond related checks

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


Note: Crystallisation conditions from REMARK 280


Error: Water clusters without contacts with non-water atoms


Warning: Water molecules need moving


Error: Water molecules without hydrogen bonds


Final summary

Note: Summary report







Suggestions for the refinement process

Note: Introduction to refinement recommendations

Warning: Validation report has little value

Note: Matthews coefficient problem

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues