WHAT IF Check report

This file was created 2017-09-22 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/pdb2m3s.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: Cell is 1 Angstrom cube

The unit cell in the CRYST1 card of the PDB file is given as a cube with vertices of 1 Angstrom. This is the convention for structures obtained using a method other than crystallography.

Note: Header records from PDB file

Header records from PDB file.

HEADER    METAL BINDING PROTEIN                   25-JAN-13   2M3S
CALMODULIN, I85L, F92E, H107I, L112R, A128T, M144R MUTANT
CALMODULIN, METAL BINDING PROTEIN
JRNL        O.V.MOROZ,Y.S.MOROZ,Y.WU,A.B.OLSEN,H.CHENG,K.L.MACK,
JRNL        J.M.MCLAUGHLIN,E.A.RAYMOND,K.ZHEZHERYA,H.RODER,
JRNL        I.V.KORENDOVYCH
JRNL        A SINGLE MUTATION IN A REGULATORY PROTEIN PRODUCES EVOLVABLE
JRNL        ALLOSTERICALLY REGULATED CATALYST OF NONNATURAL REACTION.
JRNL        REF    ANGEW.CHEM.INT.ED.ENGL.       V.  52  6246 2013
JRNL        REFN                   ISSN 1433-7851
JRNL        PMID   23630096
JRNL        DOI    10.1002/ANIE.201302339
SYMMETRY will be unavailable for this molecule.

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: No alternate atoms detected in NMR file

This PDB file does not contain alternate atoms. That is good, because it should not contain alternate atoms.

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.

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 (    1)   151 (  151) A Protein   Mod  1    /srv/data/pdb/fla...
     2   152 (    1)   302 (  151) A Protein   Mod  2    /srv/data/pdb/fla...
     3   303 (    1)   453 (  151) A Protein   Mod  3    /srv/data/pdb/fla...
     4   454 (    1)   604 (  151) A Protein   Mod  4    /srv/data/pdb/fla...
     5   605 (    1)   755 (  151) A Protein   Mod  5    /srv/data/pdb/fla...
     6   756 (    1)   906 (  151) A Protein   Mod  6    /srv/data/pdb/fla...
     7   907 (    1)  1057 (  151) A Protein   Mod  7    /srv/data/pdb/fla...
     8  1058 (    1)  1208 (  151) A Protein   Mod  8    /srv/data/pdb/fla...
     9  1209 (    1)  1359 (  151) A Protein   Mod  9    /srv/data/pdb/fla...
    10  1360 (    1)  1510 (  151) A Protein   Mod 10    /srv/data/pdb/fla...
    11  1511 (    1)  1661 (  151) A Protein   Mod 11    /srv/data/pdb/fla...
    12  1662 (    1)  1812 (  151) A Protein   Mod 12    /srv/data/pdb/fla...
    13  1813 (    1)  1963 (  151) A Protein   Mod 13    /srv/data/pdb/fla...
    14  1964 (    1)  2114 (  151) A Protein   Mod 14    /srv/data/pdb/fla...
    15  2115 (    1)  2265 (  151) A Protein   Mod 15    /srv/data/pdb/fla...
And so on for a total of 100 lines.

Some numbers...

Note: Chain identifiers seem OK

Note: Ramachandran plot

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

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

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.

Note: B-factors irrelevant in NMR structures

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: Per-model averages for bond-length check




















Warning: Directionality in bond lengths

Warning: Unusual bond angles


Note: Normal bond angle variability


Note: Per-model averages for bond-angle check




















Note: Residue hand check OK

Note: Chirality OK

Note: Improper dihedral angle distribution OK

Note: Per-model averages for chirality check




















Note: Tau angles OK

Note: Normal tau angle deviations

Error: Side chain planarity problems


Note: Atoms connected to aromatic rings OK

Torsion-related checks

Error: Ramachandran Z-score very low

Note: Per-model averages for Ramachandran check




















Note: Ramachandran check

Warning: Torsion angle evaluation shows unusual residues


Warning: Backbone evaluation reveals unusual conformations


Error: Chi-1/chi-2 rotamer problems


Error: chi-1/chi-2 angle correlation Z-score very low

Note: Per-model averages for chi-1/chi-2 angle check




















Warning: Unusual rotamers


Warning: Unusual backbone conformations


Note: Backbone conformation Z-score OK

Note: Omega angle restraint OK

Note: Per-model averages for omega angle check




















Note: PRO puckering amplitude OK

Warning: Unusual PRO puckering phases


Warning: Backbone oxygen evaluation


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: Per-model averages for inside/outside residue distributi ...heck




















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

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; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Warning: Low packing Z-score for some residues


Note: No series of residues with abnormal new packing environment

Note: Per-model averages for NQA




















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogen bond related checks

Warning: No crystallisation information

Error: His, Asn, Gln side chain flips


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