WHAT IF Check report

This file was created 2012-01-19 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.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1xq8.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

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

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 72.97

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Geometric checks

Warning: Directionality in bond lengths and no X-ray cell

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes.

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   4 PHE   (   4-)  A      CA   CB   CG  109.54   -4.3
  50 HIS   (  50-)  A      CA   CB   CG  109.51   -4.3
  94 PHE   (  94-)  A      CA   CB   CG  109.28   -4.5

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.852

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 127 MET   ( 127-)  A    -2.3
  97 LYS   (  97-)  A    -2.3
 112 ILE   ( 112-)  A    -2.2
 133 TYR   ( 133-)  A    -2.2
  95 VAL   (  95-)  A    -2.1
  40 VAL   (  40-)  A    -2.1

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  99 GLN   (  99-)  A  Poor phi/psi
 105 GLU   ( 105-)  A  Poor phi/psi
 108 PRO   ( 108-)  A  Poor phi/psi
 109 GLN   ( 109-)  A  Poor phi/psi
 110 GLU   ( 110-)  A  Poor phi/psi
 114 GLU   ( 114-)  A  Poor phi/psi
 115 ASP   ( 115-)  A  Poor phi/psi
 123 GLU   ( 123-)  A  Poor phi/psi
 124 ALA   ( 124-)  A  Poor phi/psi
 127 MET   ( 127-)  A  Poor phi/psi
 130 GLU   ( 130-)  A  Poor phi/psi
 133 TYR   ( 133-)  A  Poor phi/psi
 135 ASP   ( 135-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.757

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  38 LEU   (  38-)  A      0
  43 LYS   (  43-)  A      0
  94 PHE   (  94-)  A      0
  95 VAL   (  95-)  A      0
  96 LYS   (  96-)  A      0
  98 ASP   (  98-)  A      0
  99 GLN   (  99-)  A      0
 100 LEU   ( 100-)  A      0
 102 LYS   ( 102-)  A      0
 104 GLU   ( 104-)  A      0
 105 GLU   ( 105-)  A      0
 108 PRO   ( 108-)  A      0
 109 GLN   ( 109-)  A      0
 110 GLU   ( 110-)  A      0
 112 ILE   ( 112-)  A      0
 113 LEU   ( 113-)  A      0
 114 GLU   ( 114-)  A      0
 115 ASP   ( 115-)  A      0
 116 MET   ( 116-)  A      0
 117 PRO   ( 117-)  A      0
 121 ASP   ( 121-)  A      0
 122 ASN   ( 122-)  A      0
 123 GLU   ( 123-)  A      0
 124 ALA   ( 124-)  A      0
 125 TYR   ( 125-)  A      0
 126 GLU   ( 126-)  A      0
 127 MET   ( 127-)  A      0
 128 PRO   ( 128-)  A      0
 129 SER   ( 129-)  A      0
 130 GLU   ( 130-)  A      0
 131 GLU   ( 131-)  A      0
 133 TYR   ( 133-)  A      0
 134 GLN   ( 134-)  A      0
 135 ASP   ( 135-)  A      0
 137 GLU   ( 137-)  A      0
 138 PRO   ( 138-)  A      0
  37 VAL   (  37-)  A      1
 103 ASN   ( 103-)  A      1
 106 GLY   ( 106-)  A      1
 107 ALA   ( 107-)  A      1
  39 TYR   (  39-)  A      2
  42 SER   (  42-)  A      2
  44 THR   (  44-)  A      2
 118 VAL   ( 118-)  A      2

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.335

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 116 MET   ( 116-)  A      N   <->  117 PRO   ( 117-)  A      CD     0.37    2.63  INTRA BL
 132 GLY   ( 132-)  A      O   <->  134 GLN   ( 134-)  A      N      0.33    2.37  INTRA BL
 122 ASN   ( 122-)  A      O   <->  124 ALA   ( 124-)  A      N      0.29    2.41  INTRA BL
  40 VAL   (  40-)  A      O   <->   42 SER   (  42-)  A      N      0.28    2.42  INTRA BL
  63 VAL   (  63-)  A      O   <->   67 GLY   (  67-)  A      N      0.28    2.42  INTRA BL
 122 ASN   ( 122-)  A      ND2 <->  124 ALA   ( 124-)  A      O      0.27    2.43  INTRA BL
 121 ASP   ( 121-)  A      OD1 <->  122 ASN   ( 122-)  A      ND2    0.25    2.45  INTRA BL
  40 VAL   (  40-)  A      C   <->   42 SER   (  42-)  A      N      0.22    2.68  INTRA BL
 113 LEU   ( 113-)  A      C   <->  115 ASP   ( 115-)  A      N      0.22    2.68  INTRA BL
 113 LEU   ( 113-)  A      O   <->  115 ASP   ( 115-)  A      N      0.22    2.48  INTRA BL
 121 ASP   ( 121-)  A      OD1 <->  122 ASN   ( 122-)  A      N      0.19    2.41  INTRA BL
  66 VAL   (  66-)  A      O   <->   69 ALA   (  69-)  A      N      0.19    2.51  INTRA BL
 121 ASP   ( 121-)  A      CG  <->  122 ASN   ( 122-)  A      ND2    0.18    2.92  INTRA BL
 122 ASN   ( 122-)  A      CG  <->  124 ALA   ( 124-)  A      O      0.18    2.62  INTRA BL
   2 ASP   (   2-)  A      C   <->    4 PHE   (   4-)  A      N      0.17    2.73  INTRA BL
 127 MET   ( 127-)  A      CB  <->  128 PRO   ( 128-)  A      CD     0.16    2.94  INTRA BL
  44 THR   (  44-)  A      CG2 <->   45 LYS   (  45-)  A      N      0.16    2.84  INTRA BL
 107 ALA   ( 107-)  A      N   <->  108 PRO   ( 108-)  A      CD     0.15    2.85  INTRA BL
   2 ASP   (   2-)  A      O   <->    4 PHE   (   4-)  A      N      0.14    2.56  INTRA BL
 131 GLU   ( 131-)  A      O   <->  133 TYR   ( 133-)  A      N      0.13    2.57  INTRA BL
 137 GLU   ( 137-)  A      CB  <->  138 PRO   ( 138-)  A      CD     0.12    2.98  INTRA BL
  19 ALA   (  19-)  A      O   <->   23 LYS   (  23-)  A      N      0.12    2.58  INTRA BL
 104 GLU   ( 104-)  A      CG  <->  105 GLU   ( 105-)  A      N      0.10    2.90  INTRA BL
 115 ASP   ( 115-)  A      C   <->  117 PRO   ( 117-)  A      CD     0.10    3.10  INTRA BL
  39 TYR   (  39-)  A      C   <->   40 VAL   (  40-)  A      CG2    0.09    3.01  INTRA BL
  94 PHE   (  94-)  A      O   <->   96 LYS   (  96-)  A      N      0.09    2.61  INTRA BL
  82 VAL   (  82-)  A      CG2 <->   83 GLU   (  83-)  A      N      0.07    2.93  INTRA BL
  89 ALA   (  89-)  A      O   <->   93 GLY   (  93-)  A      N      0.07    2.63  INTRA BL
 126 GLU   ( 126-)  A      C   <->  127 MET   ( 127-)  A      CG     0.06    3.04  INTRA BL
 129 SER   ( 129-)  A      O   <->  130 GLU   ( 130-)  A      C      0.06    2.54  INTRA BL
  58 LYS   (  58-)  A      C   <->   60 LYS   (  60-)  A      N      0.05    2.85  INTRA BL
 122 ASN   ( 122-)  A      C   <->  124 ALA   ( 124-)  A      N      0.04    2.86  INTRA BL
 109 GLN   ( 109-)  A      CB  <->  110 GLU   ( 110-)  A      N      0.03    2.67  INTRA BL
  18 ALA   (  18-)  A      O   <->   22 THR   (  22-)  A      N      0.01    2.69  INTRA BL

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.287

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 133 TYR   ( 133-)  A      -8.28
  39 TYR   (  39-)  A      -7.88
 125 TYR   ( 125-)  A      -7.02
 136 TYR   ( 136-)  A      -7.01
 109 GLN   ( 109-)  A      -6.97
 127 MET   ( 127-)  A      -6.61
 134 GLN   ( 134-)  A      -6.51
  99 GLN   (  99-)  A      -6.41
 110 GLU   ( 110-)  A      -6.08
 104 GLU   ( 104-)  A      -6.07
 100 LEU   ( 100-)  A      -5.89
 139 GLU   ( 139-)  A      -5.87
 130 GLU   ( 130-)  A      -5.72
 102 LYS   ( 102-)  A      -5.39
  96 LYS   (  96-)  A      -5.33
  65 ASN   (  65-)  A      -5.11
 126 GLU   ( 126-)  A      -5.03

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  98 ASP   (  98-)  A       100 - LEU    100- ( A)         -5.51
 112 ILE   ( 112-)  A       114 - GLU    114- ( A)         -4.67
 125 TYR   ( 125-)  A       127 - MET    127- ( A)         -6.22

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 140 : -2.020

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   4 PHE   (   4-)  A      N
  38 LEU   (  38-)  A      N
  99 GLN   (  99-)  A      N
 107 ALA   ( 107-)  A      N
 115 ASP   ( 115-)  A      N

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 104 GLU   ( 104-)  A   H-bonding suggests Gln
 119 ASP   ( 119-)  A   H-bonding suggests Asn; but Alt-Rotamer
 121 ASP   ( 121-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -3.800 (poor)
  2nd generation packing quality :  -1.814
  Ramachandran plot appearance   :  -4.852 (bad)
  chi-1/chi-2 rotamer normality  :  -0.757
  Backbone conformation          :   0.440

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.990
  Bond angles                    :   0.909
  Omega angle restraints         :   0.061 (tight)
  Side chain planarity           :   0.093 (tight)
  Improper dihedral distribution :   0.784
  Inside/Outside distribution    :   1.287 (unusual)
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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      Who checks the checkers
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