WHAT IF Check report

This file was created 2017-08-29 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/pdb1kj3.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.

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  66.240  B   =  90.630  C    =  89.580
    Alpha=  90.000  Beta= 111.510  Gamma=  90.000

Dimensions of a reduced cell

    A    =  66.240  B   =  89.580  C    =  90.630
    Alpha=  90.000  Beta=  90.000  Gamma=  68.490

Dimensions of the conventional cell

    A    =  66.240  B   = 166.683  C    =  90.630
    Alpha=  90.000  Beta=  90.000  Gamma=  90.189

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 | -1.000000  0.000000 -2.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional cell: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Note: Header records from PDB file

Header records from PDB file.

HEADER    IMMUNE SYSTEM                           04-DEC-01   1KJ3
MHC CLASS I H-2KB MOLECULE COMPLEXED WITH PKB1 PEPTIDE
MHC CLASS I, H-2KB, PMHC COMPLEX, ALLOGENEIC, IMMUNE SYSTEM
JRNL        J.B.REISER,C.GREGOIRE,C.DARNAULT,T.MOSSER,
JRNL        A.GUIMEZANES,A.M.SCHMITT-VERHULST,
JRNL        J.C.FONTECILLA-CAMPS,G.MAZZA,B.MALISSEN,D.HOUSSET
JRNL        A T CELL RECEPTOR CDR3BETA LOOP UNDERGOES
JRNL        CONFORMATIONAL CHANGES OF UNPRECEDENTED MAGNITUDE
JRNL        UPON BINDING TO A PEPTIDE/MHC CLASS I COMPLEX.
JRNL        REF    IMMUNITY                      V.  16   345 2002
JRNL        REFN                   ISSN 1074-7613
JRNL        PMID   11911820
JRNL        DOI    10.1016/S1074-7613(02)00288-1

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: H and I

All-atom RMS fit for the two chains : 0.686
CA-only RMS fit for the two chains : 0.463

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: H and I

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: P and Q

All-atom RMS fit for the two chains : 0.244
CA-only RMS fit for the two chains : 0.127

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: P and Q

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: L and M

All-atom RMS fit for the two chains : 0.398
CA-only RMS fit for the two chains : 0.150

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: L and M

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

Note: Counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Z equals the number of matrices of the space group multiplied by the number of NCS relations. These numbers seem to be consistent.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, spacegroup, and NCS seem to agree administratively

Note: Matthews coefficient OK

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Molecular weight of all polymer chains: 89392.469
Volume of the Unit Cell V= 500300.969
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.798
BIOMT matrices observed in the PDB file: 2
Matthews coefficient read from REMARK 280 Vm= 2.790
Vm by authors and this calculated Vm agree remarkably well

Note: All atoms are sufficiently far away from symmetry axes

None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis.

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.

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT CHECK neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT CHECK knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are present. So, please consider to either set the occupancy of the listed atoms at 1.0, or remove the residues from the PDB file.

  279 PRO  ( 278-) H  -    CB
  279 PRO  ( 278-) H  -    CG

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT CHECK neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT CHECK will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  279 PRO  ( 278-) H  -    N
  279 PRO  ( 278-) H  -    CA
  279 PRO  ( 278-) H  -    C
  279 PRO  ( 278-) H  -    O

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 (    0)   279 (  278) H Protein             /srv/data/pdb/fla...
     2   280 (    1)   287 (    8) P Protein             /srv/data/pdb/fla...
     3   288 (    1)   386 (   99) L Protein             /srv/data/pdb/fla...
     4   387 (    1)   664 (  278) I Protein             /srv/data/pdb/fla...
     5   665 (    1)   672 (    8) Q Protein             /srv/data/pdb/fla...
     6   673 (    1)   771 (   99) M Protein             /srv/data/pdb/fla...
     7   772 (    8)   772 (    8) P L O2 <-   287       /srv/data/pdb/fla...
     8   773 (   99)   773 (   99) L M O2 <-   386       /srv/data/pdb/fla...
     9   774 (    8)   774 (    8) Q L O2 <-   672       /srv/data/pdb/fla...
    10   775 (   99)   775 (   99) M M O2 <-   771       /srv/data/pdb/fla...
    11   776 ( HOH )   776 ( HOH ) H water   (  127)     /srv/data/pdb/fla...
    12   777 ( HOH )   777 ( HOH ) P water   (    7)     /srv/data/pdb/fla...
    13   778 ( HOH )   778 ( HOH ) L water   (   62)     /srv/data/pdb/fla...
    14   779 ( HOH )   779 ( HOH ) I water   (  121)     /srv/data/pdb/fla...
    15   780 ( HOH )   780 ( HOH ) Q water   (    6)     /srv/data/pdb/fla...
    16   781 ( HOH )   781 ( HOH ) M water   (   53)     /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 771
 of which one has poor or (essentially) missing atoms')

Some numbers...

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: M

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



Warning: Occupancy atoms do not add up to 1.0.





Warning: What type of B-factor?


Note: Number of buried atoms with low B-factor is OK

Note: B-factor distribution normal



Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: M

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

Warning: Arginine nomenclature problem


Warning: Tyrosine convention problem


Warning: Phenylalanine convention problem


Warning: Aspartic acid convention problem


Warning: Glutamic acid convention problem


Note: Phosphate group names OK in DNA/RNA

Note: Heavy atom naming OK

Note: No decreasing residue numbers

Geometric checks

Warning: Unusual bond lengths


Note: Normal bond length variability


Note: No bond length directionality

Warning: Unusual bond angles


Note: Normal bond angle variability


Error: Nomenclature error(s)


Warning: Chirality deviations detected


Note: Improper dihedral angle distribution OK

Error: Tau angle problems


Note: Normal tau angle deviations

Note: Side chain planarity OK

Note: Atoms connected to aromatic rings OK

Torsion-related checks

Note: Ramachandran Z-score OK

Note: Ramachandran check

Warning: Torsion angle evaluation shows unusual residues


Warning: Backbone evaluation reveals unusual conformations


Error: Chi-1/chi-2 rotamer problems


Warning: chi-1/chi-2 angle correlation Z-score 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


Warning: Unusual PRO puckering phases


Warning: Backbone oxygen evaluation


Warning: Possible peptide flips


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: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

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: H

Note: Quality value plot

Chain identifier: L

Note: Quality value plot

Chain identifier: I

Note: Quality value plot

Chain identifier: M

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: H

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: M

Water, ion, and hydrogen bond related checks

Note: Crystallisation conditions from REMARK 280


Error: Water clusters without contacts with non-water atoms


Note: No waters need moving

Error: Water molecules without hydrogen bonds


Error: His, Asn, Gln side chain flips


Note: Histidine type assignments


Warning: Buried unsatisfied hydrogen bond donors


Note: Buried hydrogen bond acceptors OK

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

Error: Bumps in your structure

Note: Bond length variabilty Z-score low

Note: Bond angle variabilty Z-score high

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues