WHAT IF Check report

This file was created 2013-12-10 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 pdb4k31.ent

Checks that need to be done early-on in validation

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

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.

  45 AM2   ( 101-)  B  -
  46 AM2   ( 102-)  B  -
  47 AM2   ( 101-)  C  -
  48 AM2   ( 102-)  C  -

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Warning: Average B-factor problem

The average B-factor for all buried protein atoms normally lies between 10-30. Values around 3-10 are expected for X-ray studies performed at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed.

Average B-factor for buried atoms : 0.000

Geometric checks

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.

   2 OGUA  (   3-)  B  -   N9   C8   N7  114.47    6.7
   7 OGUA  (   8-)  B  -   N9   C8   N7  113.49    4.8
   7 OGUA  (   8-)  B  -   N2   C2   N3  116.41   -5.0
  12 OGUA  (  13-)  B  -   N9   C8   N7  113.24    4.3
  18 OGUA  (  19-)  B  -   N9   C8   N7  114.67    7.1
  24 OGUA  (   3-)  C  -   N9   C8   N7  114.14    6.1
  29 OGUA  (   8-)  C  -   N9   C8   N7  113.34    4.5
  34 OGUA  (  13-)  C  -   N9   C8   N7  113.17    4.1
  40 OGUA  (  19-)  C  -   N9   C8   N7  114.13    6.1

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.

  35 OGUA  (  14-)  C  -   C4  <->   36 OADE  (  15-)  C  -   C8     0.21    2.99  INTRA
  37 OADE  (  16-)  C  -   N6  <->   38 OADE  (  17-)  C  -   N6     0.20    2.65  INTRA
  12 OGUA  (  13-)  B  -   N1  <->   33 OCYT  (  12-)  C  -   N3     0.16    2.84  INTRA
  11 OCYT  (  12-)  B  -   N3  <->   34 OGUA  (  13-)  C  -   N1     0.16    2.84  INTRA
  16 OADE  (  17-)  B  -   C2' <->   17 OADE  (  18-)  B  -   O5'    0.15    2.65  INTRA BF
  20 OCYT  (  21-)  B  -   N3  <->   26 OGUA  (   5-)  C  -   N1     0.15    2.85  INTRA BL
  37 OADE  (  16-)  C  -   N6  <->   38 OADE  (  17-)  C  -   C6     0.14    2.96  INTRA
  15 OADE  (  16-)  B  -   N6  <->   16 OADE  (  17-)  B  -   N6     0.14    2.71  INTRA
  17 OADE  (  18-)  B  -   C2' <->   18 OGUA  (  19-)  B  -   OP1    0.13    2.57  INTRA BF
   4 OGUA  (   5-)  B  -   N1  <->   42 OCYT  (  21-)  C  -   N3     0.13    2.87  INTRA BL
   2 OGUA  (   3-)  B  -   N1  <->   44 OCYT  (  23-)  C  -   N3     0.13    2.87  INTRA BL
  15 OADE  (  16-)  B  -   N1  <->   30 OURA  (   9-)  C  -   N3     0.13    2.87  INTRA
  10 OCYT  (  11-)  B  -   N3  <->   35 OGUA  (  14-)  C  -   N1     0.12    2.88  INTRA
  14 OADE  (  15-)  B  -   N1  <->   31 OURA  (  10-)  C  -   N3     0.12    2.88  INTRA
  22 OCYT  (  23-)  B  -   N3  <->   24 OGUA  (   3-)  C  -   N1     0.12    2.88  INTRA BL
  35 OGUA  (  14-)  C  -   C5  <->   36 OADE  (  15-)  C  -   N7     0.12    2.98  INTRA
  35 OGUA  (  14-)  C  -   C6  <->   36 OADE  (  15-)  C  -   C5     0.11    3.09  INTRA
  47 AM2   ( 101-)  C  -   NB4 <->   50 HOH   ( 236 )  C      O      0.11    2.59  INTRA
  37 OADE  (  16-)  C  -   C6  <->   38 OADE  (  17-)  C  -   C5     0.11    3.09  INTRA
   6 OCYT  (   7-)  B  -   N3  <->   40 OGUA  (  19-)  C  -   N1     0.10    2.90  INTRA BL
  31 OURA  (  10-)  C  -   P   <->   47 AM2   ( 101-)  C  -   OB6    0.10    2.90  INTRA
  15 OADE  (  16-)  B  -   C2' <->   16 OADE  (  17-)  B  -   C5'    0.09    3.11  INTRA BF
   3 OCYT  (   4-)  B  -   N3  <->   43 OGUA  (  22-)  C  -   N1     0.09    2.91  INTRA BL
  46 AM2   ( 102-)  B  -   NB4 <->   49 HOH   ( 232 )  B      O      0.09    2.61  INTRA
  21 OGUA  (  22-)  B  -   N1  <->   25 OCYT  (   4-)  C  -   N3     0.09    2.91  INTRA BL
  18 OGUA  (  19-)  B  -   N1  <->   28 OCYT  (   7-)  C  -   N3     0.08    2.92  INTRA BL
  12 OGUA  (  13-)  B  -   N2  <->   33 OCYT  (  12-)  C  -   O2     0.08    2.62  INTRA
  17 OADE  (  18-)  B  -   C2' <->   18 OGUA  (  19-)  B  -   P      0.08    2.92  INTRA BF
  16 OADE  (  17-)  B  -   N1  <->   29 OGUA  (   8-)  C  -   N1     0.07    2.93  INTRA
  37 OADE  (  16-)  C  -   C6  <->   38 OADE  (  17-)  C  -   C6     0.06    3.14  INTRA
  38 OADE  (  17-)  C  -   N6  <->   45 AM2   ( 101-)  B  -   NA2    0.05    2.95  INTRA
  37 OADE  (  16-)  C  -   C2' <->   38 OADE  (  17-)  C  -   C5'    0.05    3.15  INTRA BF
   9 OURA  (  10-)  B  -   N3  <->   36 OADE  (  15-)  C  -   N1     0.04    2.96  INTRA
  13 OGUA  (  14-)  B  -   N1  <->   32 OCYT  (  11-)  C  -   N3     0.04    2.96  INTRA
  35 OGUA  (  14-)  C  -   C2  <->   36 OADE  (  15-)  C  -   C4     0.04    3.16  INTRA
  48 AM2   ( 102-)  C  -   NC6 <->   50 HOH   ( 284 )  C      O      0.03    2.67  INTRA
  35 OGUA  (  14-)  C  -   C2  <->   36 OADE  (  15-)  C  -   N9     0.03    3.07  INTRA
   8 OURA  (   9-)  B  -   N3  <->   37 OADE  (  16-)  C  -   N1     0.03    2.97  INTRA
  34 OGUA  (  13-)  C  -   C2' <->   35 OGUA  (  14-)  C  -   C5'    0.03    3.17  INTRA BF
  11 OCYT  (  12-)  B  -   O2  <->   34 OGUA  (  13-)  C  -   N2     0.03    2.67  INTRA
  35 OGUA  (  14-)  C  -   N1  <->   36 OADE  (  15-)  C  -   C5     0.02    3.08  INTRA
  15 OADE  (  16-)  B  -   N1  <->   16 OADE  (  17-)  B  -   C6     0.02    3.08  INTRA
  18 OGUA  (  19-)  B  -   O6  <->   48 AM2   ( 102-)  C  -   NA2    0.01    2.69  INTRA BL
  40 OGUA  (  19-)  C  -   OP1 <->   50 HOH   ( 281 )  C      O      0.01    2.39  INTRA BF
  13 OGUA  (  14-)  B  -   C5  <->   14 OADE  (  15-)  B  -   N7     0.01    3.09  INTRA
  13 OGUA  (  14-)  B  -   C4  <->   14 OADE  (  15-)  B  -   C8     0.01    3.19  INTRA BF
   9 OURA  (  10-)  B  -   OP1 <->   46 AM2   ( 102-)  B  -   NA7    0.01    2.69  INTRA BL

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.

  49 HOH   ( 280 )  B      O     25.18   -6.96  -23.42
  49 HOH   ( 293 )  B      O      1.58   -7.62   20.11
  50 HOH   ( 285 )  C      O      0.24  -17.16   -2.76
  50 HOH   ( 301 )  C      O     21.30  -13.07  -18.83

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.

  50 HOH   ( 282 )  C      O
  50 HOH   ( 291 )  C      O
Since there are no HIS GLN or ASN residues in the soup, no hydrogen-bond
flip check will be performed.

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.

  23 OURA  (   2-)  C  -   O2'
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

Final summary