WHAT IF Check report

This file was created 2017-09-29 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/pdb2xyk.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.

JRNL        REF    BIOCHIM.BIOPHYS.ACTA          V.1814   810 2011
JRNL        REFN                   ISSN 0006-3002
JRNL        PMID   21070893
JRNL        DOI    10.1016/J.BBAPAP.2010.11.001

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 : 1.150
CA-only RMS fit for the two chains : 0.589

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: P 1 21 1
Number of matrices in space group: 2
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: 4
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: 29711.256
Volume of the Unit Cell V= 126177.852
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.123
BIOMT matrices observed in the PDB file: 2
Matthews coefficient read from REMARK 280 Vm= 2.070
Vm by authors and this calculated Vm agree 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.

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).

Warning: Groups attached to potentially hydrogen-bonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogen-bonding related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

   80 HIS  (  80-) A  -    NE2 bound to   260 HEM  ( 700-) A  -   FE
  209 HIS  (  80-) B  -    NE2 bound to   261 HEM  ( 701-) B  -   FE

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.

   98 ARG  (  98-) A  -    NH1
   98 ARG  (  98-) A  -    NH2
  152 ARG  (  23-) B  -    NE
  152 ARG  (  23-) B  -    CZ
  152 ARG  (  23-) B  -    NH1
  152 ARG  (  23-) B  -    NH2
  207 ARG  (  78-) B  -    CD
  207 ARG  (  78-) B  -    NE
  207 ARG  (  78-) B  -    CZ
  207 ARG  (  78-) B  -    NH1
  207 ARG  (  78-) B  -    NH2
  241 GLU  ( 112-) B  -    CG
  241 GLU  ( 112-) B  -    CD
  241 GLU  ( 112-) B  -    OE1
  241 GLU  ( 112-) B  -    OE2

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)   129 (  129) A Protein             To check
     2   130 (    1)   259 (  130) B Protein             To check
     3   260 (  700)   260 (  700) A HEM  <-             To check
     4   261 (  701)   261 (  701) B HEM  <-             To check
     5   262 ( HOH )   262 ( HOH ) A water   (   51)     To check
     6   263 ( HOH )   263 ( HOH ) B water   (   48)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 259
of which 3 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 99
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

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: 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

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

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

Error: Side chain planarity problems

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

Note: Backbone oxygen evaluation OK

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

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

Note: No series of residues with abnormal new packing environment

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

Note: Water contacts OK

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: No crippling problems detected

Note: Cell parameter anomaly

Error: Bumps in your structure

Error: Water bumps in your structure

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues