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/pdb1y6w.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    CALCIUM-BINDING PROTEIN                 07-DEC-04   1Y6W
TRAPPED INTERMEDIATE OF CALMODULIN
EF-HAND, CALCIUM-BINDING PROTEIN, ENGINEERED DISULFIDE
JRNL        Z.GRABAREK
JRNL        STRUCTURE OF A TRAPPED INTERMEDIATE OF CALMODULIN:
JRNL        CALCIUM REGULATION OF EF-HAND PROTEINS FROM A NEW
JRNL        PERSPECTIVE.
JRNL        REF    J.MOL.BIOL.                   V. 346  1351 2005
JRNL        REFN                   ISSN 0022-2836
JRNL        PMID   15713486
JRNL        DOI    10.1016/J.JMB.2005.01.004

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

Warning: Matthews Coefficient (Vm) 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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 15298.825
Volume of the Unit Cell V= 514803.969
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z is a bit high: Vm= 4.206
One BIOMT matrix observed in the PDB file, but that is the unitary one
Matthews coefficient read from REMARK 280 Vm= 3.800
Vm by authors and this calculated Vm agree only marginally

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.

  150 MPD  ( 400-) A  -
  151 TBU  ( 500-) 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.

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.

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT CHECK neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT CHECK knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are present. So, please consider to either set the occupancy of the listed atoms at 1.0, or remove the residues from the PDB file.

  112 GLU  ( 114-) A  -    CG
  112 GLU  ( 114-) A  -    CD
  112 GLU  ( 114-) A  -    OE1
  112 GLU  ( 114-) A  -    OE2
  113 LYS  ( 115-) A  -    CG
  113 LYS  ( 115-) A  -    CD
  113 LYS  ( 115-) A  -    CE
  113 LYS  ( 115-) A  -    NZ
  114 LEU  ( 116-) A  -    CG
  114 LEU  ( 116-) A  -    CD1
  114 LEU  ( 116-) A  -    CD2

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.

   34 MSE  (  36-) A  -          OK
   49 MSE  (  51-) A  -          OK
   69 MSE  (  71-) A  -          OK
   70 MSE  (  72-) A  -          OK
   74 MSE  (  76-) A  -          OK
  107 MSE  ( 109-) A  -          OK
  122 MSE  ( 124-) A  -          OK
  142 MSE  ( 144-) A  -          OK
  143 MSE  ( 145-) A  -          OK

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 (    3)   145 (  147) A Protein             /srv/data/pdb/fla...
     2   146 (  149)   146 (  149) A  CA                 /srv/data/pdb/fla...
     3   147 (  150)   147 (  150) A  CA                 /srv/data/pdb/fla...
     4   148 (  151)   148 (  151) A  CA                 /srv/data/pdb/fla...
     5   149 (  152)   149 (  152) A  CA                 /srv/data/pdb/fla...
     6   150 (  400)   150 (  400) A MPD                 /srv/data/pdb/fla...
     7   151 (  500)   151 (  500) A TBU                 /srv/data/pdb/fla...
     8   152 ( HOH )   152 ( HOH ) A water   (   56)     /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 145
of which 4 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 56
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

Note: No missing atoms detected in residues

Warning: B-factors outside 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

Note: Arginine nomenclature OK

Note: Tyrosine torsion conventions OK

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

Note: All bond lengths OK

Note: Normal bond length variability


Note: No bond length directionality

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


Warning: chi-1/chi-2 angle correlation Z-score low

Warning: Unusual rotamers


Note: Backbone conformations OK

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

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: Too many strange amino acid residues

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


Note: Buried hydrogen bond acceptors OK

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: Non-canonical amino acids detected

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: His, Asn, Gln side chain flips.

Residues in need of attention

Warning: Troublesome residues