WHAT IF Check report

This file was created 2014-02-06 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 pdb4j2i.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  72.400  B   =  27.945  C    = 159.715
    Alpha=  90.000  Beta= 103.100  Gamma=  90.000

Dimensions of a reduced cell

    A    =  27.945  B   =  38.803  C    = 159.715
    Alpha=  77.793  Beta=  90.000  Gamma= 111.106

Dimensions of the conventional cell

    A    =  27.945  B   =  72.400  C    = 311.117
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|
 | -1.000000  0.000000 -2.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: C 1 2 1

Bravais type of conventional cell is: F

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   2 DADE  (   2-)  A  -   High
  24 DTHY  (  24-)  B  -   High
  31 DTHY  (   7-)  C  -   High
  32 DTHY  (   8-)  C  -   High
  33 DTHY  (   9-)  C  -   High
  34 DADE  (  10-)  C  -   High
  35 DTHY  (  11-)  C  -   High
  40 DADE  (  16-)  D  -   High
  41 DADE  (  17-)  D  -   High
  43 DTHY  (  19-)  D  -   High
  44 DTHY  (  20-)  D  -   High
  47 DTHY  (  23-)  D  -   High
  49 DADE  (   1-)  E  -   High
  50 DADE  (   2-)  E  -   High
  51 DTHY  (   3-)  E  -   High
  52 DADE  (   4-)  E  -   High
  53 DADE  (   5-)  E  -   High
  55 DTHY  (   7-)  E  -   High
  57 DTHY  (   9-)  E  -   High
  61 DADE  (  13-)  F  -   High
  62 DADE  (  14-)  F  -   High
  63 DTHY  (  15-)  F  -   High
  64 DADE  (  16-)  F  -   High
  67 DTHY  (  19-)  F  -   High

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

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 DTHY  (  11-)  C  -   N3  <->   38 DADE  (  14-)  D  -   N1     0.42    2.58  INTRA BF
  34 DADE  (  10-)  C  -   N1  <->   39 DTHY  (  15-)  D  -   N3     0.38    2.62  INTRA BF
  33 DTHY  (   9-)  C  -   N3  <->   40 DADE  (  16-)  D  -   N1     0.31    2.69  INTRA BF
  84 DTHY  (  12-)  G  -   N3  <->   85 DADE  (  13-)  H  -   N1     0.31    2.69  INTRA BF
  42 DADE  (  18-)  D  -   C5' <->  100 HOH   ( 104 )  D      O      0.29    2.51  INTRA BF
  57 DTHY  (   9-)  E  -   N3  <->   64 DADE  (  16-)  F  -   N1     0.26    2.74  INTRA BF
  56 DTHY  (   8-)  E  -   N3  <->   65 DADE  (  17-)  F  -   N1     0.25    2.75  INTRA BL
  36 DTHY  (  12-)  C  -   N3  <->   37 DADE  (  13-)  D  -   N1     0.25    2.75  INTRA BL
   1 DADE  (   1-)  A  -   N1  <->   24 DTHY  (  24-)  B  -   N3     0.24    2.76  INTRA BL
  34 DADE  (  10-)  C  -   N6  <->   38 DADE  (  14-)  D  -   N6     0.24    2.61  INTRA BF
  58 DADE  (  10-)  E  -   N1  <->   63 DTHY  (  15-)  F  -   N3     0.23    2.77  INTRA BF
  83 DTHY  (  11-)  G  -   N3  <->   86 DADE  (  14-)  H  -   N1     0.23    2.77  INTRA BL
  50 DADE  (   2-)  E  -   N1  <->   71 DTHY  (  23-)  F  -   N3     0.20    2.80  INTRA BF
  24 DTHY  (  24-)  B  -   OP1 <->   98 HOH   ( 101 )  B      O      0.20    2.20  INTRA BF
  55 DTHY  (   7-)  E  -   N3  <->   66 DADE  (  18-)  F  -   N1     0.20    2.80  INTRA BF
  11 DTHY  (  11-)  A  -   N3  <->   14 DADE  (  14-)  B  -   N1     0.18    2.82  INTRA BL
   9 DTHY  (   9-)  A  -   N3  <->   16 DADE  (  16-)  B  -   N1     0.18    2.82  INTRA BL
  51 DTHY  (   3-)  E  -   N3  <->   70 DADE  (  22-)  F  -   N1     0.18    2.82  INTRA BF
  54 DADE  (   6-)  E  -   N1  <->   67 DTHY  (  19-)  F  -   N3     0.18    2.82  INTRA BF
  12 DTHY  (  12-)  A  -   N3  <->   13 DADE  (  13-)  B  -   N1     0.17    2.83  INTRA BL
  32 DTHY  (   8-)  C  -   N3  <->   41 DADE  (  17-)  D  -   N1     0.17    2.83  INTRA BF
  49 DADE  (   1-)  E  -   N1  <->   72 DTHY  (  24-)  F  -   N3     0.17    2.83  INTRA BF
  26 DADE  (   2-)  C  -   N1  <->   47 DTHY  (  23-)  D  -   N3     0.17    2.83  INTRA BF
  82 DADE  (  10-)  G  -   N1  <->   87 DTHY  (  15-)  H  -   N3     0.17    2.83  INTRA BL
  59 DTHY  (  11-)  E  -   N3  <->   62 DADE  (  14-)  F  -   N1     0.16    2.84  INTRA BF
And so on for a total of 83 lines.

Final summary