WHAT IF Check report

This file was created 2017-10-17 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/pdb3vt4.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.

  252 5YI  ( 500-) A  -

Non-validating, descriptive output paragraph

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: C

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

Warning: What type of B-factor?

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Tyrosine convention problem

Warning: Phenylalanine convention problem

Warning: Aspartic acid convention problem

Warning: Glutamic acid convention problem

Geometric checks

Warning: Low bond length variability

Warning: Low bond angle variability

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

Warning: Possible peptide flips

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

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: Bumps in your structure

Residues in need of attention

Warning: Troublesome residues