WHAT IF Check report

This file was created 2017-10-19 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/pdb3zlw.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    TRANSFERASE                             04-FEB-13   3ZLW
CRYSTAL STRUCTURE OF MEK1 IN COMPLEX WITH FRAGMENT 3
TRANSFERASE
JRNL        K.AMANING,M.LOWINSKI,F.VALLEE,V.STEIER,C.MARCIREAU,
JRNL        A.UGOLINI,C.DELORME,F.FOUCALT,G.MCCORT,N.DERIMAY,C.ANDOUCHE,
JRNL        S.VOUGIER,S.LLOPART,N.HALLAND,A.RAK
JRNL        THE USE OF VIRTUAL SCREENING AND DIFFERENTIAL SCANNING
JRNL        FLUORIMETRY FOR THE RAPID IDENTIFICATION OF FRAGMENTS
JRNL        ACTIVE AGAINST MEK1.
JRNL        REF    BIOORG.MED.CHEM.LETT.         V.  23  3620 2013
JRNL        REFN                   ISSN 0960-894X
JRNL        PMID   23648182
JRNL        DOI    10.1016/J.BMCL.2013.04.003

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 61 2 2
Number of matrices in space group: 12
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: 12
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: 34945.918
Volume of the Unit Cell V= 1140482.6
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.720
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= 2.440
Vm by authors and this calculated Vm agree reasonably 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.

  314 HOH  (2070 ) A  -    O      11
  314 HOH  (2167 ) A  -    O      11
============================================================
At special position with too high occupancy   314 HOH (2081 )A  -    O
============================================================
At special position with too high occupancy   314 HOH (2167 )A  -    O

Warning: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT CHECK will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. The column 'mult' indicates how many symmetry matrices (including the unitary matrix) contributed to the problem. The column 'occupancy' lists the resulting overall occupancy at this site.

So, I suggest you first fix this problem and run WHAT CHECK again on the fixed PDB file. 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...

  314 HOH  (2081 ) A  -    O    2    1.00
  314 HOH  (2167 ) A  -    O    2    1.00

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.

  313 MT8  (1383-) 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.

Note: No probable side chain atoms with zero occupancy detected.

Either there are no side chain atoms with zero occupancy, or the side chain atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: No probable backbone atoms with zero occupancy detected.

Either there are no backbone atoms with zero occupancy, or the backbone atoms with zero occupancy were left out of the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

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.

  182 ALA  ( 220-) A  -
  236 CYS  ( 277-) A  -
  312 ASN  ( 382-) A  -

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 (   39)   312 (  382) A Protein             To check
     2   313 ( 1383)   313 ( 1383) A MT8                 To check
     3   314 ( HOH )   314 ( HOH ) A water   (  175)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 312
of which 20 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 175
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

Warning: Missing atoms



Warning: B-factors outside 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

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

Warning: Unusual bond lengths


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


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

Warning: Unusual rotamers


Warning: Unusual backbone conformations


Note: Backbone conformation Z-score OK

Warning: Omega angles too tightly restrained

Warning: Unusual PRO puckering amplitudes


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: A

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: A

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: A

Water, ion, and hydrogen bond related checks

Warning: No crystallisation information

Note: Water contacts OK

Note: No waters need moving

Note: Water hydrogen bonds OK

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: Cell parameter anomaly

Error: Bumps in your structure

Note: His, Asn, Gln side chain flips.

Residues in need of attention

Warning: Troublesome residues