WHAT IF Check report

This file was created 2017-10-11 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/pdb2a94.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.

Note: Header records from PDB file

Header records from PDB file.

HEADER    OXIDOREDUCTASE                          11-JUL-05   2A94
STRUCTURE OF PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE COMPLEXED TO
 APADH.
ROSSMANN FOLD, OXIDOREDUCTASE
JRNL        A.CHAIKUAD,V.FAIRWEATHER,R.CONNERS,T.JOSEPH-HORNE,
JRNL        D.TURGUT-BALIK,R.L.BRADY
JRNL        STRUCTURE OF LACTATE DEHYDROGENASE FROM PLASMODIUM VIVAX:
JRNL        COMPLEXES WITH NADH AND APADH.
JRNL        REF    BIOCHEMISTRY                  V.  44 16221 2005
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   16331982
JRNL        DOI    10.1021/BI051416Y

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: I 2 2 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
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: 33958.828
Volume of the Unit Cell V= 627846.438
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.311
BIOMT matrices observed in the PDB file: 4
Matthews coefficient read from REMARK 280 Vm= 2.310
Vm by authors and this calculated Vm agree remarkably well

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected. This column often shows overlap with the check for atoms at special positions.

  317 HOH  ( 546 ) A  -    O       2

Note: No atoms with high occupancy detected at special positions

Either there were no atoms at special positions, or all atoms at special positions have adequately reduced occupancies. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

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.

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.

  316 AP0  ( 336-) A  -

Note: Covalently bound ligands

No problems were detected that seem related to covalently bound ligands.

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.

   82 THR  ( 101-) A  -    CB
   82 THR  ( 101-) A  -    OG1
   82 THR  ( 101-) A  -    CG2
   83 LYS  ( 102-) A  -    CB
   83 LYS  ( 102-) A  -    CG
   83 LYS  ( 102-) A  -    CD
   83 LYS  ( 102-) A  -    CE
   83 LYS  ( 102-) A  -    NZ
   84 ALA  ( 103A) A  -    CB
   85 PRO  ( 103B) A  -    CB
   85 PRO  ( 103B) A  -    CG
   85 PRO  ( 103B) A  -    CD
   87 LYS  ( 103D) A  -    CB
   87 LYS  ( 103D) A  -    CG
   87 LYS  ( 103D) A  -    CD
And so on for a total of 62 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.

   82 THR  ( 101-) A  -    N
   82 THR  ( 101-) A  -    CA
   82 THR  ( 101-) A  -    C
   82 THR  ( 101-) A  -    O
   83 LYS  ( 102-) A  -    N
   83 LYS  ( 102-) A  -    CA
   83 LYS  ( 102-) A  -    C
   83 LYS  ( 102-) A  -    O
   84 ALA  ( 103A) A  -    N
   84 ALA  ( 103A) A  -    CA
   84 ALA  ( 103A) A  -    C
   84 ALA  ( 103A) A  -    O
   85 PRO  ( 103B) A  -    N
   85 PRO  ( 103B) A  -    CA
   85 PRO  ( 103B) A  -    C
And so on for a total of 60 lines.

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 (   18)   315 (  329) A Protein             To check
     2   316 (  336)   316 (  336) A AP0                 To check
     3   317 ( HOH )   317 ( HOH ) A water   (  214)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 315.
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 214
Residue numbers increase monotonously OK

Some numbers...

Note: Ramachandran plot

Chain identifier: A

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



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: A

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

Warning: Tyrosine convention problem


Warning: Phenylalanine convention problem


Note: Aspartic acid torsion conventions OK

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


Warning: Low 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

Note: Tau angles OK

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


Note: chi-1/chi-2 angle correlation Z-score OK

Note: Rotamers checked OK

Warning: Unusual backbone conformations


Note: Backbone conformation Z-score OK

Note: Omega angle restraint OK

Warning: Unusual PRO puckering amplitudes


Warning: Unusual PRO puckering phases


Note: Backbone oxygen evaluation OK

Note: Peptide bond conformations

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: A

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: A

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: A

Water, ion, and hydrogen bond related checks

Note: Crystallisation conditions from REMARK 280


Note: Water contacts OK

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







Note: Matrices used



  



  



  



  



  



  



  



  

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: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues