WHAT IF Check report

This file was created 2017-10-03 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/pdb5ph8.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                          07-FEB-17   5PH8
PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D IN
 COMPLEX WITH N09552A
PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, JMJ DOMAIN,
 EPIGENETICS, OXIDOREDUCTASE
JRNL        N.M.PEARCE,T.KROJER,A.R.BRADLEY,P.COLLINS,R.P.NOWAK,R.TALON,
JRNL        B.D.MARSDEN,S.KELM,J.SHI,C.M.DEANE,F.VON DELFT
JRNL        A MULTI-CRYSTAL METHOD FOR EXTRACTING OBSCURED
JRNL        CRYSTALLOGRAPHIC STATES FROM CONVENTIONALLY UNINTERPRETABLE
JRNL        ELECTRON DENSITY.
JRNL        REF    NAT COMMUN                    V.   8 15123 2017
JRNL        REFN                   ESSN 2041-1723
JRNL        PMID   28436492
JRNL        DOI    10.1038/NCOMMS15123

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 43 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
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: 8
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: 38264.641
Volume of the Unit Cell V= 761194.000
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.487
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= 2.260
Vm by authors and this calculated Vm agree reasonably 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.

  334 OGA  ( 403-) A  -
  345 PHT  ( 414-) A  -
  346 1XN  ( 415-) A  -

Note: Covalently bound ligands

No problems were detected that seem related to covalently bound ligands.

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.

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.

   72 ARG  (  82-) A  - Corrected
  113 ARG  ( 123-) A  - Corrected
  117 LYS  ( 127-) A  - Corrected
  177 THR  ( 187-) A  - Corrected
  186 MET  ( 196-) A  - Corrected
  218 ARG  ( 228-) A  -
  298 SER  ( 308-) A  - Corrected
  309 PHE  ( 319-) A  - Corrected
  310 SER  ( 320-) A  - Corrected
  324 ASP  ( 334-) A  - 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 (   11)   331 (  341) A Protein             /srv/data/pdb/fla...
     2   332 (  401)   332 (  401) A  ZN                 /srv/data/pdb/fla...
     3   333 (  402)   333 (  402) A  NI                 /srv/data/pdb/fla...
     4   334 (  403)   334 (  403) A OGA                 /srv/data/pdb/fla...
     5   335 (  404)   335 (  404) A EDO                 /srv/data/pdb/fla...
     6   336 (  405)   336 (  405) A EDO                 /srv/data/pdb/fla...
     7   337 (  406)   337 (  406) A EDO                 /srv/data/pdb/fla...
     8   338 (  407)   338 (  407) A EDO                 /srv/data/pdb/fla...
     9   339 (  408)   339 (  408) A EDO                 /srv/data/pdb/fla...
    10   340 (  409)   340 (  409) A EDO                 /srv/data/pdb/fla...
    11   341 (  410)   341 (  410) A SO4                 /srv/data/pdb/fla...
    12   342 (  411)   342 (  411) A SO4                 /srv/data/pdb/fla...
    13   343 (  412)   343 (  412) A SO4                 /srv/data/pdb/fla...
    14   344 (  413)   344 (  413) A SO4                 /srv/data/pdb/fla...
    15   345 (  414)   345 (  414) A PHT                 /srv/data/pdb/fla...
    16   346 (  415)   346 (  415) A 1XN                 /srv/data/pdb/fla...
    17   347 ( HOH )   347 ( HOH ) A water   (  406)     /srv/data/pdb/fla...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 331
of which 5 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 406
Residue numbers increase monotonously OK

Some numbers...

Note: Chain identifiers seem OK

Note: Ramachandran plot

Chain identifier: A

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

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


Note: Tyrosine torsion conventions OK

Warning: Phenylalanine convention problem


Note: Aspartic acid torsion conventions OK

Warning: Glutamic acid convention problem


Note: Phosphate group names OK in DNA/RNA

Note: SO4/PO4 atom names OK

Note: Heavy atom naming OK

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


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


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

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


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

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

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

Water, ion, and hydrogen bond related checks

Note: Crystallisation conditions from REMARK 280


Note: Water contacts OK

Note: No waters need moving

Note: Water hydrogen bonds OK

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

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: Bond angle variabilty Z-score low

Note: His, Asn, Gln side chain flips.

Residues in need of attention

Warning: Troublesome residues