WHAT IF Check report

This file was created 2017-09-27 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/pdb5j17.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    PROTEIN BINDING                         29-MAR-16   5J17
SOLUTION STRUCTURE OF RAS BINDING DOMAIN (RBD) OF B-RAF
MAPK, PI3K, PROTEIN BINDING
JRNL        S.K.ATHULURI-DIVAKAR,R.VASQUEZ-DEL CARPIO,K.DUTTA,S.J.BAKER,
JRNL        S.C.COSENZA,I.BASU,Y.K.GUPTA,M.V.REDDY,L.UENO,J.R.HART,
JRNL        P.K.VOGT,D.MULHOLLAND,C.GUHA,A.K.AGGARWAL,E.P.REDDY
JRNL        A SMALL MOLECULE RAS-MIMETIC DISRUPTS RAS ASSOCIATION WITH
JRNL        EFFECTOR PROTEINS TO BLOCK SIGNALING.
JRNL        REF    CELL                          V. 165   643 2016
JRNL        REFN                   ISSN 1097-4172
JRNL        PMID   27104980
JRNL        DOI    10.1016/J.CELL.2016.03.045
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 (  151)    80 (  230) A Protein   Mod  1    To check
     2    81 (  151)   160 (  230) A Protein   Mod  2    To check
     3   161 (  151)   240 (  230) A Protein   Mod  3    To check
     4   241 (  151)   320 (  230) A Protein   Mod  4    To check
     5   321 (  151)   400 (  230) A Protein   Mod  5    To check
     6   401 (  151)   480 (  230) A Protein   Mod  6    To check
     7   481 (  151)   560 (  230) A Protein   Mod  7    To check
     8   561 (  151)   640 (  230) A Protein   Mod  8    To check
     9   641 (  151)   720 (  230) A Protein   Mod  9    To check
    10   721 (  151)   800 (  230) A Protein   Mod 10    To check
MODELs skipped upon reading PDB file: 0
This NMR ensemble consists of 10 MODELs.
The MODEL numbers start at 1.
The total number of amino acids found is 800
of which 10 have poor or (essentially) missing atoms
Amino acids per NMR MODEL: 80.
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: 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: 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

Warning: Tyrosine convention problem



Note: Phenylalanine torsion conventions OK

Warning: Aspartic acid convention problem



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

Note: All bond lengths OK

Note: Normal bond length variability



Note: Per-model averages for bond-length check










Note: No bond length directionality

Note: All bond angles OK

Note: Normal bond angle variability


Note: Per-model averages for bond-angle check










Error: Nomenclature error(s)


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

Note: Side chain planarity OK

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










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: 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

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

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

Water, ion, and hydrogen bond related checks

Warning: No crystallisation information

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