WHAT IF Check report

This file was created 2017-08-31 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/pdb1nma.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    COMPLEX (HYDROLASE/IMMUNOGLOBULIN)      06-MAY-94   1NMA
N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL
 FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH
 MUTANT BINDING DATA
COMPLEX (HYDROLASE-IMMUNOGLOBULIN), COMPLEX (HYDROLASE-
 IMMUNOGLOBULIN) COMPLEX
JRNL        W.R.TULIP,V.R.HARLEY,R.G.WEBSTER,J.NOVOTNY
JRNL        N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10:
JRNL        EMPIRICAL FREE ENERGY CALCULATIONS CAPTURE SPECIFICITY
JRNL        TRENDS OBSERVED WITH MUTANT BINDING DATA.
JRNL        REF    BIOCHEMISTRY                  V.  33  7986 1994
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   7517697
JRNL        DOI    10.1021/BI00192A002

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 4 2 2
Number of matrices in space group: 16
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: 16
Z, spacegroup, and NCS seem to agree administratively

Warning: Matthews Coefficient (Vm) high

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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 67932.875
Volume of the Unit Cell V= 4711836.0
Space group multiplicity: 16
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z is high: Vm= 4.335
BIOMT matrices observed in the PDB file: 4
Matthews coefficient read from REMARK 280 Vm= 4.250
Vm by authors and this calculated Vm agree well

Note: All atoms are sufficiently far away from symmetry axes

None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis.

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.

  615 BMA  ( 471C) N  -
  616 MAN  ( 472D) N  -
  617 MAN  ( 473E) N  -
  618 MAN  ( 474F) N  -

Warning: Covalently bound ligands

The ligands in this table are covalently bound to something else. It is already difficult to automatically generate topologies for ligands, but when they are covalently bound to something it becomes even more complicated to do everything right. So, if you get weird error messages that seem related to this covalent bond, then please feel free to ignore those, or even better, make a topology entry by hand.

The comment `Other ligand` indicates that the covalent bond is to another ligand. In that case you might want to convert the two ligands into one bigger ligand.

  615 BMA  ( 471C) N  -

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).

Warning: Groups attached to potentially hydrogen-bonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogen-bonding related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

  611 NAG  ( 470B) N  -    O4  bound to   615 BMA  ( 471C) N  -    C1

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.

    1 ARG  (  82-) N  -    CB
    1 ARG  (  82-) N  -    CG
    1 ARG  (  82-) N  -    CD
    1 ARG  (  82-) N  -    NE
    1 ARG  (  82-) N  -    CZ
    1 ARG  (  82-) N  -    NH1
    1 ARG  (  82-) N  -    NH2
    2 GLU  (  83-) N  -    CB
    2 GLU  (  83-) N  -    CG
    2 GLU  (  83-) N  -    CD
    2 GLU  (  83-) N  -    OE1
    2 GLU  (  83-) N  -    OE2
  129 ARG  ( 209-) N  -    CB
  129 ARG  ( 209-) N  -    CG
  129 ARG  ( 209-) N  -    CD
And so on for a total of 115 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.

  385 THR  (   7-) L  -    N
  385 THR  (   7-) L  -    CA
  385 THR  (   7-) L  -    C
  385 THR  (   7-) L  -    O
  386 THR  (   8-) L  -    N
  386 THR  (   8-) L  -    CA
  386 THR  (   8-) L  -    C
  386 THR  (   8-) L  -    O
  392 SER  (  14-) L  -    N
  392 SER  (  14-) L  -    CA
  392 SER  (  14-) L  -    C
  392 SER  (  14-) L  -    O
  434 SER  (  56-) L  -    N
  434 SER  (  56-) L  -    CA
  434 SER  (  56-) L  -    C
And so on for a total of 44 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 (   82)   378 (  458) N Protein             /srv/data/pdb/fla...
     2   379 (    1)   487 (  109) L Protein             /srv/data/pdb/fla...
     3   488 (    1)   609 (  113) H Protein             /srv/data/pdb/fla...
     4   610 (  469)   610 (  469) N Sugar               /srv/data/pdb/fla...
     5   611 (  470)   611 (  470) N Sugar<-             /srv/data/pdb/fla...
     6   612 (  475)   612 (  475) N Sugar               /srv/data/pdb/fla...
     7   613 (  109)   613 (  109) L A O2 <-   487       /srv/data/pdb/fla...
     8   614 (  113)   614 (  113) H S O2 <-   609       /srv/data/pdb/fla...
     9   615 (  471)   615 (  471) N BMA  <-             /srv/data/pdb/fla...
    10   616 (  472)   616 (  472) N MAN                 /srv/data/pdb/fla...
    11   617 (  473)   617 (  473) N MAN                 /srv/data/pdb/fla...
    12   618 (  474)   618 (  474) N MAN                 /srv/data/pdb/fla...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 609
 of which one has poor or (essentially) missing atoms')

Some numbers...

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: H

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?


Warning: Low M-factor

Note: Number of buried atoms with low B-factor is OK

Note: B-factor distribution normal



Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: H

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


Note: No bond length directionality

Warning: Unusual bond angles


Warning: High bond angle deviations


Note: Residue hand check OK

Warning: Chirality deviations detected


Note: Improper dihedral angle distribution OK

Error: Tau angle problems


Warning: High tau angle deviations

Error: Side chain planarity problems


Note: Atoms connected to aromatic rings OK

Torsion-related checks

Warning: Ramachandran Z-score low

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

Warning: Unusual rotamers


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


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: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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: N

Note: Quality value plot

Chain identifier: L

Note: Quality value plot

Chain identifier: H

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: N

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: H

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


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: Matthews coefficient problem

Error: Bumps in your structure

Note: Bond length variabilty Z-score high

Note: Bond angle variabilty Z-score high

Note: His, Asn, Gln side chain flips.

Residues in need of attention

Warning: Troublesome residues