WHAT IF Check report

This file was created 2019-04-20 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/pdb4w88.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    HYDROLASE                               22-AUG-14   4W88
CRYSTAL STRUCTURE OF XEG5A, A GH5 XYLOGLUCAN-SPECIFIC ENDO-BETA-1,4-
 GLUCANASE FROM RUMINAL METAGENOMIC LIBRARY, IN COMPLEX WITH A
 XYLOGLUCAN OLIGOSACCHARIDE AND TRIS
GLYCOSIDE HYDROLASE, CELL WALL DEGRADING ENZYME, GH5 FAMILY,
 HYDROLASE
JRNL        C.R.DOS SANTOS,R.L.CORDEIRO,D.W.WONG,M.T.MURAKAMI
JRNL        STRUCTURAL BASIS FOR XYLOGLUCAN SPECIFICITY AND
JRNL        ALPHA-D-XYLP(1 6)-D-GLCP RECOGNITION AT THE -1 SUBSITE
JRNL        WITHIN THE GH5 FAMILY.
JRNL        REF    BIOCHEMISTRY                  V.  54  1930 2015
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   25714929
JRNL        DOI    10.1021/ACS.BIOCHEM.5B00011

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: B and A

All-atom RMS fit for the two chains : 0.401
CA-only RMS fit for the two chains : 0.047

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 A

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 31
Number of matrices in space group: 3
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
Value of Z as found on the CRYST1 card: 6
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: 48.610
Volume of the Unit Cell V= 792777.438
Space group multiplicity: 3
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z is high: Vm= 5436.312
Be aware though that the number of residues with missing atoms is: 57
BIOMT matrices observed in the PDB file: 2
But accounting for these BIOMT matrices does not make Vm reasonable yet
Matthews coefficient read from REMARK 280 Vm= 3.380
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.

   68 ASP  (  92-) B  -
   69 ARG  (  93-) B  -
   70 SER  (  94-) B  -
   71 ARG  (  95-) B  -
   72 VAL  (  96-) B  -
   73 PHE  (  97-) B  -
   74 ASP  (  98-) B  -
   75 ILE  (  99-) B  -
   76 LEU  ( 100-) B  -
   77 SER  ( 101-) B  -
   78 ASN  ( 102-) B  -
   79 ILE  ( 103-) B  -
   80 ASN  ( 104-) B  -
   81 ILE  ( 105-) B  -
   82 GLY  ( 106-) B  -
And so on for a total of 624 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.

   99 GLU  ( 125-) B  -
  122 ILE  ( 149-) B  -
  140 ASP  ( 170-) B  -
  143 ARG  ( 174-) B  -
  176 LEU  ( 211-) B  -
  181 ILE  ( 218-) B  -
  186 GLU  ( 224-) B  -
  187 PHE  ( 226-) B  -
  195 PHE  ( 235-) B  -
  202 GLY  ( 245-) B  -
  204 LYS  ( 248-) B  -
  212 GLU  ( 257-) B  -
  220 PHE  ( 268-) B  -
  230 ASP  ( 281-) B  -
  260 LEU  ( 313-) B  -
And so on for a total of 40 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.

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.

Warning: Non-canonical residue(s)

Non-canonical residues WHAT CHECK has detected any non-canonical residue(s). If they are listed here as OK, then WHAT CHECK is reasonably about the topology it determined. If the residue is labeled HARD, then it was hard to make a topology, and you might want to be critical when it comes to error messages related to this residue.

    9 MSE  ( 187-) B  -          HARD
   16 MSE  ( 234-) B  -          HARD
   17 MSE  ( 238-) B  -          HARD
   18 MSE  ( 243-) B  -          HARD
   23 MSE  ( 264-) B  -          HARD
   43 MSE  ( 187-) A  -          HARD
   50 MSE  ( 234-) A  -          HARD
   51 MSE  ( 238-) A  -          HARD
   52 MSE  ( 243-) A  -          HARD
   57 MSE  ( 264-) A  -          HARD

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 (  115)    34 (  431) B Protein             /srv/data/pdb/fla...
     2    35 (  115)    67 (  430) A Protein             /srv/data/pdb/fla...
     3    68 (   92)    68 (   92) B ASP                 /srv/data/pdb/fla...
     4    69 (   93)    69 (   93) B ARG                 /srv/data/pdb/fla...
     5    70 (   94)    70 (   94) B SER                 /srv/data/pdb/fla...
     6    71 (   95)    71 (   95) B ARG                 /srv/data/pdb/fla...
     7    72 (   96)    72 (   96) B VAL                 /srv/data/pdb/fla...
     8    73 (   97)    73 (   97) B PHE                 /srv/data/pdb/fla...
     9    74 (   98)    74 (   98) B ASP                 /srv/data/pdb/fla...
    10    75 (   99)    75 (   99) B ILE                 /srv/data/pdb/fla...
    11    76 (  100)    76 (  100) B LEU                 /srv/data/pdb/fla...
    12    77 (  101)    77 (  101) B SER                 /srv/data/pdb/fla...
    13    78 (  102)    78 (  102) B ASN                 /srv/data/pdb/fla...
    14    79 (  103)    79 (  103) B ILE                 /srv/data/pdb/fla...
    15    80 (  104)    80 (  104) B ASN                 /srv/data/pdb/fla...
And so on for a total of 630 lines.

Some numbers...

Note: Chain identifiers seem OK

Note: Ramachandran plot

Chain identifier: B

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

Warning: 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: 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: B

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

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

Note: All bond lengths OK

Warning: Low bond length variability


Note: No bond length directionality

Note: All bond angles OK

Note: Normal bond angle variability


Note: Residue hand check OK

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 check

Note: Torsion angles OK

Note: Backbone torsion angles OK

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

Note: Rotamers checked OK

Note: Backbone conformations 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


Note: No waters 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

Note: Non-canonical amino acids detected

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: Free floating waters

Residues in need of attention

Note: The residues listed in the table below need to be inspected