WHAT IF Check report

This file was created 2017-10-28 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/pdb4lmr.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                          10-JUL-13   4LMR
CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM BACILLUS CEREUS ATCC
 14579, NYSGRC TARGET 029452
STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NYSGRC, PSI-
 BIOLOGY, NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM,
 OXIDOREDUCTASE
JRNL        V.N.MALASHKEVICH,J.B.BONANNO,R.BHOSLE,R.TORO,B.HILLERICH,
JRNL        A.GIZZI,S.GARFORTH,A.KAR,M.K.CHAN,J.LAFLUER,H.PATEL,
JRNL        B.MATIKAINEN,S.CHAMALA,S.LIM,A.CELIKGIL,G.VILLEGAS,B.EVANS,
JRNL        J.LOVE,A.FISER,K.KHAFIZOV,R.SEIDEL,S.C.ALMO
JRNL        CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM BACILLUS
JRNL        CEREUS ATCC 14579, NYSGRC TARGET 029452
JRNL        REF    TO BE PUBLISHED
JRNL        REFN

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 : 0.778
CA-only RMS fit for the two chains : 0.395

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: I 41 2 2
Number of matrices in space group: 16
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: 32
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: 67481.172
Volume of the Unit Cell V= 5310225.0
Space group multiplicity: 16
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z is high: Vm= 4.918
BIOMT matrices observed in the PDB file: 2
Matthews coefficient read from REMARK 280 Vm= 4.390
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.

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.

   22 MSE  (  24-) A  -          OK
   46 MSE  (  48-) A  -          OK
  108 MSE  ( 110-) A  -          OK
  156 MSE  ( 158-) A  -          OK
  236 MSE  ( 238-) A  -          OK
  308 MSE  ( 310-) A  -          OK
  334 MSE  (  24-) B  -          OK
  358 MSE  (  48-) B  -          OK
  420 MSE  ( 110-) B  -          OK
  468 MSE  ( 158-) B  -          OK
  548 MSE  ( 238-) B  -          OK
  620 MSE  ( 310-) B  -          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)   312 (  314) A Protein             /srv/data/pdb/fla...
     2   313 (    3)   624 (  314) B Protein             /srv/data/pdb/fla...
     3   625 (  314)   625 (  314) A L O2 <-   312       /srv/data/pdb/fla...
     4   626 (  314)   626 (  314) B L O2 <-   624       /srv/data/pdb/fla...
     5   627 ( HOH )   627 ( HOH ) A water   (   88)     /srv/data/pdb/fla...
     6   628 ( HOH )   628 ( HOH ) B water   (   45)     /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 624
of which 20 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 133
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

Warning: B-factors outside 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

Warning: Arginine nomenclature problem


Note: Tyrosine torsion conventions OK

Note: Phenylalanine torsion conventions OK

Note: Aspartic acid torsion conventions OK

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

Warning: Unusual bond lengths


Note: Normal 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


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


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


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: 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

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


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: Matthews coefficient problem

Note: Cell parameter anomaly

Note: Non-canonical amino acids detected

Error: Bumps in your structure

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues