WHAT IF Check report

This file was created 2017-04-26 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/pdb5k9k.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    IMMUNE SYSTEM                           31-MAY-16   5K9K
CRYSTAL STRUCTURE OF MULTIDONOR HV6-1-CLASS BROADLY NEUTRALIZING
 INFLUENZA A ANTIBODY 56.A.09 IN COMPLEX WITH HEMAGGLUTININ HONG KONG
 1968.
INFLUENZA, MULTIDONOR, H5, UNIVERSAL INFLUENZA VACCINE, IMMUNE SYSTEM
JRNL        M.G.JOYCE,A.K.WHEATLEY,P.V.THOMAS,G.Y.CHUANG,C.SOTO,
JRNL        R.T.BAILER,A.DRUZ,I.S.GEORGIEV,R.A.GILLESPIE,M.KANEKIYO,
JRNL        W.P.KONG,K.LEUNG,S.N.NARPALA,M.S.PRABHAKARAN,E.S.YANG,
JRNL        B.ZHANG,Y.ZHANG,M.ASOKAN,J.C.BOYINGTON,T.BYLUND,S.DARKO,
JRNL        C.R.LEES,A.RANSIER,C.H.SHEN,L.WANG,J.R.WHITTLE,X.WU,
JRNL        H.M.YASSINE,C.SANTOS,Y.MATSUOKA,Y.TSYBOVSKY,U.BAXA,
JRNL        J.C.MULLIKIN,K.SUBBARAO,D.C.DOUEK,B.S.GRAHAM,R.A.KOUP,
JRNL        J.E.LEDGERWOOD,M.ROEDERER,L.SHAPIRO,P.D.KWONG,J.R.MASCOLA,
JRNL        A.B.MCDERMOTT
JRNL        VACCINE-INDUCED ANTIBODIES THAT NEUTRALIZE GROUP 1 AND GROUP
JRNL        2 INFLUENZA A VIRUSES.
JRNL        REF    CELL                          V. 166   609 2016
JRNL        REFN                   ISSN 1097-4172
JRNL        PMID   27453470
JRNL        DOI    10.1016/J.CELL.2016.06.043

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and L

All-atom RMS fit for the two chains : 0.861
CA-only RMS fit for the two chains : 0.411

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and L

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: C 2 2 21
Number of matrices in space group: 8
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: 16
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: 205800.078
Volume of the Unit Cell V= 5267543.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 3.199
BIOMT matrices observed in the PDB file: 2
Matthews coefficient read from REMARK 280 Vm= 3.180
Vm by authors and this calculated Vm agree remarkably 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.

 1896 BMA  ( 605-) I  -
 1897 MAN  ( 606-) I  -
 1898 MAN  ( 607-) I  -
 1899 BMA  ( 610-) I  -
 1900 BMA  ( 615-) I  -
 1901 MAN  ( 616-) I  -
 1902 MAN  ( 617-) I  -
 1903 BMA  ( 620-) I  -
 1904 MAN  ( 621-) I  -
 1905 MAN  ( 622-) I  -
 1906 BMA  ( 604-) F  -
 1907 MAN  ( 605-) F  -
 1908 MAN  ( 606-) F  -
 1909 BMA  ( 609-) F  -
 1910 MAN  ( 610-) F  -
 1911 MAN  ( 611-) F  -
 1912 MAN  ( 612-) F  -
 1913 BMA  ( 615-) F  -
 1914 BMA  ( 618-) F  -
 1915 MAN  ( 619-) F  -
 1916 MAN  ( 620-) F  -
 1917 BMA  ( 624-) F  -
 1918 MAN  ( 625-) F  -
 1919 MAN  ( 626-) F  -

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.

 1896 BMA  ( 605-) I  -          Other ligand
 1897 MAN  ( 606-) I  -          Other ligand
 1898 MAN  ( 607-) I  -          Other ligand
 1899 BMA  ( 610-) I  -
 1900 BMA  ( 615-) I  -          Other ligand
 1901 MAN  ( 616-) I  -          Other ligand
 1902 MAN  ( 617-) I  -          Other ligand
 1903 BMA  ( 620-) I  -          Other ligand
 1904 MAN  ( 621-) I  -          Other ligand
 1905 MAN  ( 622-) I  -          Other ligand
 1906 BMA  ( 604-) F  -          Other ligand
 1907 MAN  ( 605-) F  -          Other ligand
 1908 MAN  ( 606-) F  -          Other ligand
 1909 BMA  ( 609-) F  -          Other ligand
 1910 MAN  ( 610-) F  -          Other ligand
 1911 MAN  ( 611-) F  -          Other ligand
 1912 MAN  ( 612-) F  -          Other ligand
 1913 BMA  ( 615-) F  -
 1914 BMA  ( 618-) F  -          Other ligand
 1915 MAN  ( 619-) F  -          Other ligand
 1916 MAN  ( 620-) F  -          Other ligand
 1917 BMA  ( 624-) F  -          Other ligand
 1918 MAN  ( 625-) F  -          Other ligand
 1919 MAN  ( 626-) F  -          Other ligand

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.

 1871 NAG  ( 604-) I  -    O4  bound to  1896 BMA  ( 605-) I  -    C1
 1873 NAG  ( 609-) I  -    O4  bound to  1899 BMA  ( 610-) I  -    C1
 1877 NAG  ( 614-) I  -    O4  bound to  1900 BMA  ( 615-) I  -    C1
 1879 NAG  ( 619-) I  -    O4  bound to  1903 BMA  ( 620-) I  -    C1
 1882 NAG  ( 603-) F  -    O4  bound to  1906 BMA  ( 604-) F  -    C1
 1884 NAG  ( 608-) F  -    O4  bound to  1909 BMA  ( 609-) F  -    C1
 1886 NAG  ( 614-) F  -    O4  bound to  1913 BMA  ( 615-) F  -    C1
 1888 NAG  ( 617-) F  -    O4  bound to  1914 BMA  ( 618-) F  -    C1
 1891 NAG  ( 623-) F  -    O4  bound to  1917 BMA  ( 624-) F  -    C1

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)   226 (  216) A Protein             /srv/data/pdb/fla...
     2   227 (    1)   441 (  214) B Protein             /srv/data/pdb/fla...
     3   442 (    6)   931 (  501) I Protein             /srv/data/pdb/fla...
     4   932 (    1)  1155 (  216) H Protein             /srv/data/pdb/fla...
     5  1156 (    1)  1370 (  214) L Protein             /srv/data/pdb/fla...
     6  1371 (    4)  1867 (  501) F Protein             /srv/data/pdb/fla...
     7  1868 (  601)  1868 (  601) I Sugar               /srv/data/pdb/fla...
     8  1869 (  602)  1869 (  602) I Sugar               /srv/data/pdb/fla...
     9  1870 (  603)  1870 (  603) I Sugar               /srv/data/pdb/fla...
    10  1871 (  604)  1871 (  604) I Sugar<-             /srv/data/pdb/fla...
    11  1872 (  608)  1872 (  608) I Sugar               /srv/data/pdb/fla...
    12  1873 (  609)  1873 (  609) I Sugar<-             /srv/data/pdb/fla...
    13  1874 (  611)  1874 (  611) I Sugar               /srv/data/pdb/fla...
    14  1875 (  612)  1875 (  612) I Sugar               /srv/data/pdb/fla...
    15  1876 (  613)  1876 (  613) I Sugar               /srv/data/pdb/fla...
And so on for a total of 58 lines.

Some numbers...

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: F

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



Warning: Occupancy atoms do not add up to 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

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: F

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

Warning: Arginine nomenclature problem


Warning: Tyrosine convention problem


Note: Phenylalanine torsion conventions OK

Note: Aspartic acid torsion conventions OK

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

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


Error: Nomenclature error(s)


Warning: Chirality deviations detected


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


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: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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

Note: Quality value plot

Chain identifier: B

Note: Quality value plot

Chain identifier: I

Note: Quality value plot

Chain identifier: H

Note: Quality value plot

Chain identifier: L

Note: Quality value plot

Chain identifier: F

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

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogen bond related checks

Note: Crystallisation conditions from REMARK 280


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

Note: Cell parameter anomaly

Error: Bumps in your structure

Note: His, Asn, Gln side chain flips.

Residues in need of attention

Warning: Troublesome residues