WHAT IF Check report

This file was created 2017-10-27 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.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for /srv/data/pdb/flat/pdb4klv.ent

Checks that need to be done early-on in validation

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.

  175 KLV  ( 216-) A  -

Non-validating, descriptive output paragraph

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Missing atoms



Warning: What type of B-factor?



Note: B-factor plot

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem


Warning: Tyrosine convention problem


Warning: Phenylalanine convention problem


Warning: Glutamic acid convention problem


Geometric checks

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


Error: Nomenclature error(s)


Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues


Warning: Backbone evaluation reveals unusual conformations


Error: Chi-1/chi-2 rotamer problems


Warning: Unusual rotamers


Warning: Unusual backbone conformations


Bump checks

Error: Abnormally short interatomic distances


Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Warning: Abnormal packing environment for some residues


Note: Quality value plot

Chain identifier: A

Warning: Low packing Z-score for some residues


Note: Second generation quality Z-score plot

Chain identifier: A

Water, ion, and hydrogen bond related checks

Error: Water clusters without contacts with non-water atoms


Error: Water molecules without hydrogen bonds


Error: His, Asn, Gln side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Suggestions for the refinement process

Error: Water bumps in your structure

Residues in need of attention

Warning: Troublesome residues