WHAT IF Check report

This file was created 2011-12-21 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 pdb1cng.ent

Administrative problems that can generate validation failures

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 IF 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 IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 HIS   (   4-)  A  -   CG
   1 HIS   (   4-)  A  -   ND1
   1 HIS   (   4-)  A  -   CD2
   1 HIS   (   4-)  A  -   CE1
   1 HIS   (   4-)  A  -   NE2
 257 LYS   ( 261-)  A  -   CB
 257 LYS   ( 261-)  A  -   CG
 257 LYS   ( 261-)  A  -   CD
 257 LYS   ( 261-)  A  -   CE
 257 LYS   ( 261-)  A  -   NZ

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 cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.410
RMS-deviation in bond distances: 0.009

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.

  65 VAL   (  68-)  A      N    CA   C    99.39   -4.2
  93 HIS   (  96-)  A      N    CA   C    99.99   -4.0

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 203 VAL   ( 207-)  A    4.45
  65 VAL   (  68-)  A    4.25
  93 HIS   (  96-)  A    4.16
 194 LEU   ( 198-)  A    4.06

Torsion-related checks

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.

  80 PRO   (  83-)  A    -2.4
  57 LEU   (  60-)  A    -2.4
 172 PHE   ( 176-)  A    -2.2
  19 ILE   (  22-)  A    -2.1
  27 PRO   (  30-)  A    -2.1
 159 VAL   ( 163-)  A    -2.1
  55 ARG   (  58-)  A    -2.1
  76 LEU   (  79-)  A    -2.1
 189 THR   ( 193-)  A    -2.1
  89 GLN   (  92-)  A    -2.0

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.

  26 SER   (  29-)  A  PRO omega poor
  61 HIS   (  64-)  A  Poor phi/psi
  72 ASP   (  75-)  A  Poor phi/psi
 107 ASP   ( 110-)  A  Poor phi/psi
 108 LYS   ( 111-)  A  Poor phi/psi
 174 ASN   ( 178-)  A  Poor phi/psi
 197 PRO   ( 201-)  A  PRO omega poor
 239 ASP   ( 243-)  A  Poor phi/psi
 248 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.418

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!

   4 TYR   (   7-)  A      0
   7 HIS   (  10-)  A      0
  16 ASP   (  19-)  A      0
  17 PHE   (  20-)  A      0
  21 LYS   (  24-)  A      0
  24 ARG   (  27-)  A      0
  26 SER   (  29-)  A      0
  47 SER   (  50-)  A      0
  49 ASP   (  52-)  A      0
  51 ALA   (  54-)  A      0
  55 ARG   (  58-)  A      0
  59 ASN   (  62-)  A      0
  61 HIS   (  64-)  A      0
  62 ALA   (  65-)  A      0
  69 ASP   (  72-)  A      0
  70 SER   (  73-)  A      0
  72 ASP   (  75-)  A      0
  74 ALA   (  77-)  A      0
  77 LYS   (  80-)  A      0
  80 PRO   (  83-)  A      0
  82 ASP   (  85-)  A      0
  89 GLN   (  92-)  A      0
  93 HIS   (  96-)  A      0
 100 GLN   ( 103-)  A      0
 104 HIS   ( 107-)  A      0
And so on for a total of 109 lines.

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 : 1.823

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.

  12 HIS   (  15-)  A      ND1 <->   15 LYS   (  18-)  A      NZ     0.22    2.78  INTRA BL
 257 LYS   ( 261-)  A      CB  <->  260 HOH   ( 464 )  A      O      0.13    2.67  INTRA
  48 TYR   (  51-)  A      OH  <->  119 HIS   ( 122-)  A      NE2    0.13    2.57  INTRA BL
 259  CL   ( 262-)  A     CL   <->  260 HOH   ( 376 )  A      O      0.09    2.61  INTRA
  27 PRO   (  30-)  A      O   <->  245 GLN   ( 249-)  A      N      0.07    2.63  INTRA BL
  69 ASP   (  72-)  A      OD2 <->  120 TRP   ( 123-)  A      NE1    0.04    2.66  INTRA
   5 GLY   (   8-)  A      O   <->    9 GLY   (  12-)  A      N      0.02    2.68  INTRA
  18 PRO   (  21-)  A      C   <->   20 ALA   (  23-)  A      N      0.02    2.88  INTRA BL
 257 LYS   ( 261-)  A      CG  <->  260 HOH   ( 464 )  A      O      0.02    2.78  INTRA
 104 HIS   ( 107-)  A      NE2 <->  190 TYR   ( 194-)  A      OH     0.01    2.69  INTRA BL

Packing, accessibility and threading

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.

   7 HIS   (  10-)  A      -5.86
  97 LEU   ( 100-)  A      -5.05

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: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 260 HOH   ( 424 )  A      O     11.22   -6.72   22.85

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 260 HOH   ( 456 )  A      O
 260 HOH   ( 464 )  A      O
Marked this atom as acceptor  259  CL  ( 262-) A     CL
Metal-coordinating Histidine residue  91 fixed to   1
Metal-coordinating Histidine residue  93 fixed to   1
Metal-coordinating Histidine residue 116 fixed to   1

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 133 GLN   ( 137-)  A
 174 ASN   ( 178-)  A

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.

  21 LYS   (  24-)  A      NZ
  28 VAL   (  31-)  A      N
  71 GLN   (  74-)  A      N
  73 LYS   (  76-)  A      NZ
  97 LEU   ( 100-)  A      N
 196 THR   ( 200-)  A      N
 200 LEU   ( 204-)  A      N
 241 TRP   ( 245-)  A      N
 256 PHE   ( 260-)  A      N
Only metal coordination for   93 HIS  (  96-) A      NE2
Only metal coordination for  116 HIS  ( 119-) A      ND1

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.

  29 ASP   (  32-)  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 :  -0.296
  2nd generation packing quality :   0.337
  Ramachandran plot appearance   :  -1.165
  chi-1/chi-2 rotamer normality  :  -1.418
  Backbone conformation          :  -0.616

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.410 (tight)
  Bond angles                    :   0.720
  Omega angle restraints         :   0.331 (tight)
  Side chain planarity           :   0.521 (tight)
  Improper dihedral distribution :   0.934
  B-factor distribution          :   0.526
  Inside/Outside distribution    :   0.947

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

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, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.410 (tight)
  Bond angles                    :   0.720
  Omega angle restraints         :   0.331 (tight)
  Side chain planarity           :   0.521 (tight)
  Improper dihedral distribution :   0.934
  B-factor distribution          :   0.526
  Inside/Outside distribution    :   0.947
==============

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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      protein structures
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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
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
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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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