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/pdb3w9e.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    ACTA CRYSTALLOGR.,SECT.D      V.  69  1935 2013
JRNL        REFN                   ISSN 0907-4449
JRNL        PMID   24100313
JRNL        DOI    10.1107/S0907444913016776

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 21 21 21
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: 71497.195
Volume of the Unit Cell V= 889911.062
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 3.112
One BIOMT matrix observed in the PDB file, but that is the unitary one
Matthews coefficient read from REMARK 280 Vm= 2.750
Vm by authors and this calculated Vm agree reasonably 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.

  660 BMA  ( 303-) C  -
  661 MAN  ( 304-) C  -

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.

  660 BMA  ( 303-) C  -

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.

  657 NAG  ( 302-) C  -    O4  bound to   660 BMA  ( 303-) C  -    C1

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.

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 (   25)   229 (  253) C Protein             /srv/data/pdb/fla...
     2   230 (    1)   444 (  222) A Protein             /srv/data/pdb/fla...
     3   445 (    1)   655 (  211) B Protein             /srv/data/pdb/fla...
     4   656 (  301)   656 (  301) C Sugar               /srv/data/pdb/fla...
     5   657 (  302)   657 (  302) C Sugar<-             /srv/data/pdb/fla...
     6   658 (  305)   658 (  305) C Sugar               /srv/data/pdb/fla...
     7   659 (  222)   659 (  222) A P O2 <-   444       /srv/data/pdb/fla...
     8   660 (  303)   660 (  303) C BMA  <-             /srv/data/pdb/fla...
     9   661 (  304)   661 (  304) C MAN                 /srv/data/pdb/fla...
    10   662 ( HOH )   662 ( HOH ) C water   (   87)     /srv/data/pdb/fla...
    11   663 ( HOH )   663 ( HOH ) A water   (   90)     /srv/data/pdb/fla...
    12   664 ( HOH )   664 ( HOH ) B water   (   75)     /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 655
of which 17 have poor or (essentially) missing atoms
No nucleic acids observed in input file
Number of (recognized) sugars: 3
 of which one has poor or (essentially) missing atoms')

Some numbers...

Note: Ramachandran plot

Chain identifier: C

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: C

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

Note: Arginine nomenclature OK

Warning: Tyrosine convention problem

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

Warning: Unusual bond angles

Note: Normal bond angle variability

Error: Nomenclature error(s)

Note: Chirality OK

Note: Improper dihedral angle distribution OK

Error: Tau angle problems

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: C

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: C

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: C

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: No crippling problems detected

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues