WHAT IF Check report

This file was created 2017-10-18 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/pdb3wze.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    ACS MED.CHEM.LETT.            V.   6    89 2015
JRNL        REFN                   ISSN 1948-5875
JRNL        PMID   25589937
JRNL        DOI    10.1021/ML500394M

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: C 1 2 1
Number of matrices in space group: 4
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: 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: 34145.961
Volume of the Unit Cell V= 405645.406
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.970
One BIOMT matrix observed in the PDB file, but that is the unitary one
Matthews coefficient read from REMARK 280 Vm= 2.970
Vm by authors and this calculated Vm agree remarkably 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.

  299 BAX  (1201-) A  -
  301 DTT  (1203-) A  -

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.

  301 DTT  (1203-) A  -

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.

    1 GLU  ( 815-) A  -    CG
    1 GLU  ( 815-) A  -    CD
    1 GLU  ( 815-) A  -    OE1
    1 GLU  ( 815-) A  -    OE2
   21 LYS  ( 835-) A  -    CD
   21 LYS  ( 835-) A  -    CE
   21 LYS  ( 835-) A  -    NZ
   24 LYS  ( 838-) A  -    CD
   24 LYS  ( 838-) A  -    CE
   24 LYS  ( 838-) A  -    NZ
   28 ARG  ( 842-) A  -    CD
   28 ARG  ( 842-) A  -    NE
   28 ARG  ( 842-) A  -    CZ
   28 ARG  ( 842-) A  -    NH1
   28 ARG  ( 842-) A  -    NH2
And so on for a total of 80 lines.

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 (  815)   298 ( 1167) A Protein             To check
     2   299 ( 1201)   299 ( 1201) A BAX                 To check
     3   300 ( 1202)   300 ( 1202) A ACT                 To check
     4   301 ( 1203)   301 ( 1203) A DTT  <-             To check
     5   302 ( HOH )   302 ( HOH ) A water   (  107)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 298
of which 13 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 107
Residue numbers increase monotonously OK

Some numbers...

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

Warning: Analysis of bonded atoms indicate B-factor problems

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

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

Warning: Low 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

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

Note: PRO puckering phases OK

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

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: Second generation packing environment OK

Note: No series of residues with abnormal new packing environment

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

Note: His, Asn, Gln side chains OK

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: No crippling problems detected

Note: Cell parameter anomaly

Error: Bumps in your structure

Residues in need of attention

Warning: Troublesome residues