WHAT IF Check report

This file was created 2017-09-10 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/pdb1xyz.ent

Checks that need to be done early-on in validation

Warning: Triclinic cell with mixed acute and obtuse angles

The crystallographic unit cell does not conform to the convention that a triclinic cell should be specified as having either three obtuse (type II) or three acute angles (type I).

The CRYST1 cell dimensions

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha= 100.540  Beta=  83.790  Gamma= 101.640

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha= 100.540  Beta=  83.790  Gamma= 101.640

Dimensions of a reduced cell

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha=  79.460  Beta=  83.790  Gamma=  78.360

Dimensions of the conventional cell

    A    =  47.100  B   =  51.100  C    =  70.740
    Alpha=  79.460  Beta=  83.790  Gamma=  78.360

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.629
CA-only RMS fit for the two chains : 0.286

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Non-validating, descriptive output paragraph

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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: B

Geometric checks

Warning: Unusual bond lengths


Warning: Low bond length variability


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: Tau angle problems


Warning: High tau angle deviations

Error: Side chain planarity problems


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: Omega angles too tightly restrained

Warning: Unusual PRO puckering amplitudes


Warning: Unusual PRO puckering phases


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


Warning: Abnormal packing environment for sequential residues


Note: Quality value plot

Chain identifier: A

Note: Quality value plot

Chain identifier: B

Warning: Low packing Z-score for some residues


Warning: Abnormal packing Z-score for sequential residues


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

Warning: No crystallisation information

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


Warning: Buried unsatisfied hydrogen bond acceptors


Suggestions for the refinement process

Error: Bumps in your structure

Residues in need of attention

Warning: Troublesome residues