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 pdb1a42.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but 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 first.

 259 BZU   ( 555-)  A  -

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 256 PHE   ( 260-)  A  -

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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 256 PHE   ( 260-)  A      O

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:

Crystal temperature (K) :295.000

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 : 10.50

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: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.003553  0.000142 -0.000126|
 |  0.000142  1.002377 -0.000173|
 | -0.000126 -0.000173  0.999782|
Proposed new scale matrix

 |  0.023337 -0.000002  0.006104|
 | -0.000003  0.023924  0.000004|
 |  0.000002  0.000002  0.014159|
With corresponding cell

    A    =  42.852  B   =  41.799  C    =  73.005
    Alpha=  90.023  Beta= 104.666  Gamma=  89.984

The CRYST1 cell dimensions

    A    =  42.700  B   =  41.700  C    =  73.000
    Alpha=  90.000  Beta= 104.600  Gamma=  90.000

Variance: 41.231
(Under-)estimated Z-score: 4.732

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.

   1 HIS   (   4-)  A      CB   CG   ND1 132.62    7.3
   1 HIS   (   4-)  A      CB   CG   CD2 121.62   -5.8
   2 TRP   (   5-)  A      CD1  CG   CD2 113.16    4.3
   2 TRP   (   5-)  A      CG   CD1  NE1 104.75   -4.2
   2 TRP   (   5-)  A      CG   CD2  CE2 101.49   -4.8
   7 HIS   (  10-)  A      CA   CB   CG  109.19   -4.6
   7 HIS   (  10-)  A      CB   CG   ND1 129.15    5.0
   7 HIS   (  10-)  A      CB   CG   CD2 123.85   -4.0
   8 ASN   (  11-)  A      ND2  CG   OD1 118.18   -4.4
  12 HIS   (  15-)  A      CB   CG   ND1 129.47    5.2
  12 HIS   (  15-)  A      CB   CG   CD2 122.70   -4.9
  13 TRP   (  16-)  A      CG   CD2  CE2 102.05   -4.3
  14 HIS   (  17-)  A      CB   CG   ND1 127.64    4.0
  55 ARG   (  58-)  A      CB   CG   CD  104.84   -4.6
  59 ASN   (  62-)  A      ND2  CG   OD1 118.46   -4.1
  63 PHE   (  66-)  A      CA   CB   CG  118.62    4.8
  64 ASN   (  67-)  A      ND2  CG   OD1 116.53   -6.1
  77 LYS   (  80-)  A      CA   CB   CG  123.23    4.6
  89 GLN   (  92-)  A      NE2  CD   OE1 116.50   -6.1
  90 PHE   (  93-)  A      CA   CB   CG  123.52    9.7
  92 PHE   (  95-)  A      CA   CB   CG  118.05    4.2
  93 HIS   (  96-)  A      CB   CG   ND1 127.76    4.1
  94 TRP   (  97-)  A      CD1  CG   CD2 113.44    4.5
  94 TRP   (  97-)  A      CG   CD1  NE1 104.26   -4.6
  94 TRP   (  97-)  A      CE3  CD2  CG  138.24    4.3
And so on for a total of 66 lines.

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    4.52
  74 ALA   (  77-)  A    4.07

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.

  55 ARG   (  58-)  A    -2.4
  39 PRO   (  42-)  A    -2.4
 163 ILE   ( 167-)  A    -2.2
 235 GLU   ( 239-)  A    -2.2
  77 LYS   (  80-)  A    -2.1
  89 GLN   (  92-)  A    -2.1
  45 SER   (  48-)  A    -2.1
  19 ILE   (  22-)  A    -2.0
 147 GLY   ( 151-)  A    -2.0
  10 PRO   (  13-)  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
  54 LEU   (  57-)  A  omega poor
 108 LYS   ( 111-)  A  Poor phi/psi
 174 ASN   ( 178-)  A  Poor phi/psi
 197 PRO   ( 201-)  A  PRO omega poor
 199 LEU   ( 203-)  A  Poor phi/psi
 202 CYS   ( 206-)  A  omega poor
 249 ASN   ( 253-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.483

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
  17 PHE   (  20-)  A      0
  23 GLU   (  26-)  A      0
  24 ARG   (  27-)  A      0
  26 SER   (  29-)  A      0
  47 SER   (  50-)  A      0
  49 ASP   (  52-)  A      0
  50 GLN   (  53-)  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
  73 LYS   (  76-)  A      0
  74 ALA   (  77-)  A      0
  77 LYS   (  80-)  A      0
  80 PRO   (  83-)  A      0
  81 LEU   (  84-)  A      0
  82 ASP   (  85-)  A      0
  89 GLN   (  92-)  A      0
 100 GLN   ( 103-)  A      0
 103 GLU   ( 106-)  A      0
 104 HIS   ( 107-)  A      0
And so on for a total of 107 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  27 PRO   (  30-)  A    0.47 HIGH
  80 PRO   (  83-)  A    0.46 HIGH
 151 PRO   ( 155-)  A    0.48 HIGH
 182 PRO   ( 186-)  A    0.46 HIGH
 197 PRO   ( 201-)  A    0.50 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 243 PRO   ( 247-)  A    49.1 half-chair C-delta/C-gamma (54 degrees)

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.

  93 HIS   (  96-)  A      NE2 <->  116 HIS   ( 119-)  A      ND1    0.16    2.84  INTRA BL
  47 SER   (  50-)  A      OG  <->   77 LYS   (  80-)  A      NZ     0.13    2.57  INTRA
 104 HIS   ( 107-)  A      NE2 <->  190 TYR   ( 194-)  A      OH     0.10    2.60  INTRA BL
  12 HIS   (  15-)  A      ND1 <->   15 LYS   (  18-)  A      NZ     0.06    2.94  INTRA BL
 132 GLN   ( 136-)  A      N   <->  133 GLN   ( 137-)  A      N      0.04    2.56  INTRA BL
 243 PRO   ( 247-)  A      O   <->  245 GLN   ( 249-)  A      NE2    0.04    2.66  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      -5.93
  97 LEU   ( 100-)  A      -5.31

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   ( 295 )  A      O     -0.05   -0.81   -4.76
 260 HOH   ( 427 )  A      O     12.97   -5.67   25.15

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   ( 285 )  A      O
 260 HOH   ( 289 )  A      O
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.

   7 HIS   (  10-)  A
  61 HIS   (  64-)  A
 132 GLN   ( 136-)  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.

  28 VAL   (  31-)  A      N
  42 LYS   (  45-)  A      N
  50 GLN   (  53-)  A      N
  70 SER   (  73-)  A      N
  71 GLN   (  74-)  A      N
  97 LEU   ( 100-)  A      N
  98 ASP   ( 101-)  A      N
 164 LYS   ( 168-)  A      N
 165 THR   ( 169-)  A      N
 169 SER   ( 173-)  A      N
 200 LEU   ( 204-)  A      N
 228 ASN   ( 232-)  A      N
 241 TRP   ( 245-)  A      N
 250 ARG   ( 254-)  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: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  11 GLU   (  14-)  A      OE1

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.

 235 GLU   ( 239-)  A   H-bonding suggests Gln

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 :  -0.284
  2nd generation packing quality :   0.233
  Ramachandran plot appearance   :  -2.108
  chi-1/chi-2 rotamer normality  :  -2.483
  Backbone conformation          :  -0.854

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.800
  Bond angles                    :   1.529
  Omega angle restraints         :   0.947
  Side chain planarity           :   0.613 (tight)
  Improper dihedral distribution :   1.132
  Inside/Outside distribution    :   0.963

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 : 2.25


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.800
  Bond angles                    :   1.529
  Omega angle restraints         :   0.947
  Side chain planarity           :   0.613 (tight)
  Improper dihedral distribution :   1.132
  Inside/Outside distribution    :   0.963
==============

WHAT IF
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Matthews' Coefficient
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Protein side chain planarity
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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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,
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Checking checks
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      Who checks the checkers
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