WHAT IF Check report

This file was created 2017-09-29 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/pdb2ydf.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: 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    =  55.072  B   =  55.440  C    = 119.845
    Alpha=  81.000  Beta=  90.830  Gamma=  64.520

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    =  55.072  B   =  55.440  C    = 119.845
    Alpha=  81.000  Beta=  90.830  Gamma=  64.520

Dimensions of a reduced cell

    A    =  55.072  B   =  55.440  C    = 119.845
    Alpha=  99.000  Beta=  90.830  Gamma= 115.480

Dimensions of the conventional cell

    A    =  55.072  B   =  55.440  C    = 119.845
    Alpha=  99.000  Beta=  90.830  Gamma= 115.480

Transformation to conventional cell

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

Note: Header records from PDB file

Header records from PDB file.

HEADER    TRANSPORT PROTEIN                       18-MAR-11   2YDF
JRNL        REF    BMC STRUCT.BIOL.              V.  11    18 2011
JRNL        REFN                   ISSN 1472-6807
JRNL        PMID   21501503
JRNL        DOI    10.1186/1472-6807-11-18

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
Number of matrices in space group: 1
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: 2
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: 128899.258
Volume of the Unit Cell V= 324873.312
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.520
Be aware though that the number of residues with missing atoms is: 206
BIOMT matrices observed in the PDB file: 2
Matthews coefficient read from REMARK 280 Vm= 2.600
Vm by authors and this calculated Vm agree well

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.

 1136 IO3  (2001-) A  -
 1137 IO3  (2002-) A  -
 1138 IO3  (2003-) A  -
 1139 IO3  (2004-) A  -
 1140 IO3  (2001-) B  -
 1141 IO3  (2002-) B  -
 1142 IO3  (2003-) B  -
 1143 IO3  (2004-) B  -

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.

  569 ALA  ( 582-) A  -
 1135 ALA  ( 582-) B  -

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 (    5)   569 (  582) A Protein             To check
     2   570 (    5)  1135 (  582) B Protein             To check
     3  1136 ( 2001)  1136 ( 2001) A IO3                 To check
     4  1137 ( 2002)  1137 ( 2002) A IO3                 To check
     5  1138 ( 2003)  1138 ( 2003) A IO3                 To check
     6  1139 ( 2004)  1139 ( 2004) A IO3                 To check
     7  1140 ( 2001)  1140 ( 2001) B IO3                 To check
     8  1141 ( 2002)  1141 ( 2002) B IO3                 To check
     9  1142 ( 2003)  1142 ( 2003) B IO3                 To check
    10  1143 ( 2004)  1143 ( 2004) B IO3                 To check
    11  1144 ( HOH )  1144 ( HOH ) A water   (   12)     To check
    12  1145 ( HOH )  1145 ( HOH ) B water   (   11)     To check
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 1135
of which 270 have poor or (essentially) missing atoms
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 23
Residue numbers increase monotonously OK

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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?

Warning: More than 5 percent of buried atoms has low B-factor

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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

Note: No bond length directionality

Warning: Unusual bond angles

Note: Normal bond angle variability

Note: Residue hand check OK

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

Error: Ramachandran Z-score very low

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: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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

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: No crippling problems detected

Error: Bumps in your structure

Note: His, Asn, Gln side chain flips.

Note: Free floating waters

Residues in need of attention

Warning: Troublesome residues