WHAT IF Check report

This file was created 2017-08-24 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/pdb1e6j.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    = 193.080  B   =  45.600  C    = 132.470
    Alpha=  90.000  Beta= 132.410  Gamma=  90.000

Dimensions of a reduced cell

    A    =  45.600  B   =  99.196  C    = 100.688
    Alpha=  83.014  Beta=  76.912  Gamma=  76.712

Dimensions of the conventional cell

    A    =  45.600  B   = 132.470  C    = 142.576
    Alpha=  89.095  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000  1.000000|
 |  1.000000  0.000000  1.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional cell: ORTHORHOMBIC

Space group name: C 1 2 1

Bravais type of conventional cell is: I

Note: Header records from PDB file

Header records from PDB file.

HEADER    VIRAL PROTEIN                           18-AUG-00   1E6J
JRNL        REF    STRUCTURE                     V.   8  1069 2000
JRNL        REFN                   ISSN 0969-2126
JRNL        PMID   11080628
JRNL        DOI    10.1016/S0969-2126(00)00507-4

Warning: New symmetry found

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

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 4

Warning: Matthews Coefficient (Vm) high

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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 69958.227
Volume of the Unit Cell V= 861181.375
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z is high: Vm= 6.155
A few residues have missing atoms that did not enter the Vm calculation
One BIOMT matrix observed in the PDB file, but that is the unitary one
Matthews coefficient read from REMARK 280 Vm= 3.070
Vm by authors and this calculated Vm do not agree very well
SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 4
which would result in the much more normal Vm= 3.077
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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.

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.

   66 ASP  (  66-) H  -    CG
   66 ASP  (  66-) H  -    OD1
   66 ASP  (  66-) H  -    OD2
  135 SER  ( 135-) H  -    CB
  135 SER  ( 135-) H  -    OG
  136 ALA  ( 136-) H  -    CB
  137 ALA  ( 137-) H  -    CB
  138 GLN  ( 138-) H  -    CB
  138 GLN  ( 138-) H  -    CG
  138 GLN  ( 138-) H  -    CD
  138 GLN  ( 138-) H  -    OE1
  138 GLN  ( 138-) H  -    NE2
  139 THR  ( 139-) H  -    CB
  139 THR  ( 139-) H  -    OG1
  139 THR  ( 139-) H  -    CG2
And so on for a total of 96 lines.

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.

  134 GLY  ( 134-) H  -    N
  134 GLY  ( 134-) H  -    CA
  134 GLY  ( 134-) H  -    C
  134 GLY  ( 134-) H  -    O
  135 SER  ( 135-) H  -    N
  135 SER  ( 135-) H  -    CA
  135 SER  ( 135-) H  -    C
  135 SER  ( 135-) H  -    O
  136 ALA  ( 136-) H  -    N
  136 ALA  ( 136-) H  -    CA
  136 ALA  ( 136-) H  -    C
  136 ALA  ( 136-) H  -    O
  137 ALA  ( 137-) H  -    N
  137 ALA  ( 137-) H  -    CA
  137 ALA  ( 137-) H  -    C
And so on for a total of 96 lines.

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

  219 PRO  ( 219-) H  -
  429 ASN  ( 210-) L  -
  639 GLY  ( 220-) P  -

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 (    1)   219 (  219) H Protein             /srv/data/pdb/fla...
     2   220 (    1)   429 (  210) L Protein             /srv/data/pdb/fla...
     3   430 (   11)   639 (  220) P Protein             /srv/data/pdb/fla...
     4   640 (  219)   640 (  219) H P O2 <-   219       /srv/data/pdb/fla...
     5   641 (  210)   641 (  210) L N O2 <-   429       /srv/data/pdb/fla...
     6   642 (  220)   642 (  220) P G O2 <-   639       /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 639
of which 52 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
No water observed in input file
Residue numbers increase monotonously OK

Some numbers...

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: P

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

Warning: Missing atoms

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

Note: All occupancies seem to add up to 0.0 - 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: L

Note: B-factor plot

Chain identifier: P

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

Note: Arginine nomenclature OK

Note: Tyrosine torsion conventions OK

Note: Phenylalanine torsion conventions OK

Note: Aspartic acid torsion conventions OK

Note: Glutamic acid torsion conventions OK

Note: Phosphate group names OK in DNA/RNA

Note: Heavy atom naming OK

Note: No decreasing residue numbers

Geometric checks

Note: All bond lengths OK

Note: Normal 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

Note: Normal bond angle variability

Note: Residue hand check OK

Note: Chirality OK

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

Note: PRO puckering amplitude OK

Note: PRO puckering phases OK

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: P

Warning: Abnormal packing environment for some residues

Warning: Abnormal packing environment for sequential residues

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: P

Warning: Low packing Z-score for some residues

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: P

Water, ion, and hydrogen bond related checks

Note: Crystallisation conditions from REMARK 280

Error: His, Asn, Gln side chain flips

Note: Histidine type assignments

Warning: Buried unsatisfied hydrogen bond donors

Warning: Buried unsatisfied hydrogen bond acceptors

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: Matthews coefficient problem

Note: Cell parameter anomaly

Error: Bumps in your structure

Note: His, Asn, Gln side chain flips.

Residues in need of attention

Warning: Troublesome residues