WHAT IF Check report

This file was created 2017-09-06 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/pdb1trs.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: Cell is 1 Angstrom cube

The unit cell in the CRYST1 card of the PDB file is given as a cube with vertices of 1 Angstrom. This is the convention for structures obtained using a method other than crystallography.

Note: Header records from PDB file

Header records from PDB file.

HEADER    ELECTRON TRANSPORT                      10-MAY-94   1TRS
THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURES
 OF THE OXIDIZED AND REDUCED STATES OF HUMAN THIOREDOXIN
ELECTRON TRANSPORT
JRNL        J.QIN,G.M.CLORE,A.M.GRONENBORN
JRNL        THE HIGH-RESOLUTION THREE-DIMENSIONAL SOLUTION
JRNL        STRUCTURES OF THE OXIDIZED AND REDUCED STATES OF
JRNL        HUMAN THIOREDOXIN.
JRNL        REF    STRUCTURE                     V.   2   503 1994
JRNL        REFN                   ISSN 0969-2126
JRNL        PMID   7922028
JRNL        DOI    10.1016/S0969-2126(00)00051-4
SYMMETRY will be unavailable for this molecule.

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.

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)   105 (  105) A Protein             /srv/data/pdb/fla...
     2   106 (  105)   106 (  105) A V O2 <-   105       /srv/data/pdb/fla...
     3   107 ( HOH )   107 ( HOH ) A water   (    7)     /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 105.
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 7
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

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?



Warning: Temperature factors given as "U", not as "B"

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

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

Note: All bond lengths OK

Note: Normal bond length variability


Warning: Directionality in bond lengths and no X-ray cell

Warning: Unusual bond angles


Note: Normal bond angle variability


Note: Residue hand check OK

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

Error: Ramachandran Z-score very low

Note: Ramachandran check

Note: Torsion angles OK

Warning: Backbone evaluation reveals unusual conformations


Error: Chi-1/chi-2 rotamer problems


Error: chi-1/chi-2 angle correlation Z-score very low

Warning: Unusual rotamers


Warning: Unusual backbone conformations


Note: Backbone conformation Z-score OK

Warning: Omega angles too tightly restrained

Warning: Unusual PRO puckering amplitudes


Note: PRO puckering phases OK

Warning: Backbone oxygen evaluation


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

Warning: Abnormal packing environment for some residues


Note: No series of residues with bad packing environment

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

Warning: No crystallisation information

Note: Water contacts OK

Note: Symmetry related water molecules check not performed

Note: Water hydrogen bonds OK

Note: His, Asn, Gln side chains OK

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

Note: Bond length variabilty Z-score high

Note: Bond angle variabilty Z-score high

Note: Average B-factor problem

Residues in need of attention

Warning: Troublesome residues