WHAT IF Check report

This file was created 2014-06-26 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 pdb1khl.ent

Checks that need to be done early-on in validation

Error: The SCALE matrix is nonstandard The SCALE matrix given ...the PDB file


The CRYST1 cell dimensions


Note: Non crystallographic symmetry RMS plot

Chain identifiers of the two chains: A and B


Note: Non crystallographic symmetry backbone difference plot

Chain identifiers of the two chains: A and B

Warning: Ligands for which a topology was generated automatically


Non-validating, descriptive output paragraph

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem


Warning: Tyrosine convention problem


Warning: Phenylalanine convention problem


Warning: Aspartic acid convention problem


Warning: Glutamic acid convention problem


Geometric checks

Warning: Unusual bond lengths


Warning: Unusual bond angles


Error: Nomenclature error(s)


Warning: Chirality deviations detected


Error: Tau angle problems


Warning: High tau angle deviations

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues


Warning: Backbone evaluation reveals unusual conformations


Warning: Unusual backbone conformations


Warning: Omega angles too tightly restrained

Warning: Unusual PRO puckering amplitudes


Bump checks

Error: Abnormally short interatomic distances


Packing, accessibility and threading

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


Note: Quality value plot

Chain identifier: A

Note: Quality value plot

Chain identifier: B

Warning: Low packing Z-score for some residues


Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving


Error: Water molecules without hydrogen bonds


Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: Unusual water packing


Final summary

Note: Summary report for users of a structure







Note: Summary report for depositors of a structure