WHAT IF Check report

This file was created 2014-02-13 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 pdb4c5x.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.

  23 5HC   (   9-)  A  -
  25 5HC   (  21-)  B  -

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 lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   2 DGUA  (   2-)  A  -   C5   C4    1.35   -4.6
   3 DCYT  (   3-)  A  -   N1   C6    1.34   -4.8
   4 DGUA  (   4-)  A  -   C5   C6    1.38   -4.1
   5 DADE  (   5-)  A  -   P    OP1   1.41   -4.4
   5 DADE  (   5-)  A  -   C3'  C2'   1.47   -4.5
   6 DADE  (   6-)  A  -   P    OP1   1.41   -4.2
   6 DADE  (   6-)  A  -   O5'  C5'   1.34   -6.3
   7 DTHY  (   7-)  A  -   C5   C7    1.46   -5.2
  11 DGUA  (  12-)  A  -   C1'  N9    1.40   -6.4
  12 DCYT  (  13-)  B  -   C3'  C2'   1.47   -4.8
  12 DCYT  (  13-)  B  -   C2   O2    1.15  -10.5
  12 DCYT  (  13-)  B  -   N3   C2    1.32   -4.5
  13 DGUA  (  14-)  B  -   C3'  O3'   1.36   -5.1
  13 DGUA  (  14-)  B  -   P    O5'   1.64    4.5
  14 DCYT  (  15-)  B  -   C6   C5    1.38    4.6
  14 DCYT  (  15-)  B  -   C2   O2    1.20   -4.5
  16 DADE  (  17-)  B  -   N3   C4    1.32   -4.8
  17 DADE  (  18-)  B  -   C2   N3    1.37    4.1
  19 DTHY  (  20-)  B  -   P    O5'   1.65    5.9
  20 DGUA  (  22-)  B  -   N3   C4    1.32   -4.4

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 1.958
RMS-deviation in bond distances: 0.021

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 DCYT  (   1-)  A  -   C6   N1   C2  118.65   -4.1
   2 DGUA  (   2-)  A  -   O4'  C1'  N9  104.57   -4.0
   4 DGUA  (   4-)  A  -   C3'  C2'  C1'  96.18   -4.7
   4 DGUA  (   4-)  A  -   N9   C8   N7  113.68    5.2
   4 DGUA  (   4-)  A  -   C8   N7   C5  101.93   -4.7
   4 DGUA  (   4-)  A  -   C5   C4   N3  131.51    5.8
   4 DGUA  (   4-)  A  -   C2   N3   C4  109.48   -4.8
   6 DADE  (   6-)  A  -   P    O5'  C5' 113.77   -4.5
   6 DADE  (   6-)  A  -   N9   C4   C5  108.18    6.0
   6 DADE  (   6-)  A  -   C6   C5   C4  119.06    4.1
   7 DTHY  (   7-)  A  -   O4'  C1'  C2' 101.63   -4.1
   8 DTHY  (   8-)  A  -   C6   C5   C7  120.43   -4.1
   8 DTHY  (   8-)  A  -   C4   C5   C7  122.01    5.0
   9 DGUA  (  10-)  A  -   OP1  P    OP2 127.99    5.6
   9 DGUA  (  10-)  A  -   OP2  P    O5'  95.01   -4.9
   9 DGUA  (  10-)  A  -   N7   C5   C4  108.85   -4.9
  10 DCYT  (  11-)  A  -   O4'  C1'  N1  104.37   -4.3
  11 DGUA  (  12-)  A  -   O4'  C1'  N9  100.54   -9.1
  11 DGUA  (  12-)  A  -   N9   C8   N7  113.59    5.0
  11 DGUA  (  12-)  A  -   N9   C4   C5  108.46    7.6
  11 DGUA  (  12-)  A  -   C8   N9   C4  104.22   -5.4
  11 DGUA  (  12-)  A  -   N7   C5   C6  133.03    4.4
  11 DGUA  (  12-)  A  -   N7   C5   C4  108.28   -6.3
  11 DGUA  (  12-)  A  -   O6   C6   N1  117.25   -4.4
  12 DCYT  (  13-)  B  -   O4'  C1'  N1  101.57   -7.8
  12 DCYT  (  13-)  B  -   C6   N1   C2  118.39   -4.8
  13 DGUA  (  14-)  B  -   P    O5'  C5' 109.56   -7.1
  13 DGUA  (  14-)  B  -   OP1  P    OP2 129.58    6.7
  13 DGUA  (  14-)  B  -   OP2  P    O5'  94.49   -5.1
  13 DGUA  (  14-)  B  -   C4'  O4'  C1' 102.00   -5.5
  13 DGUA  (  14-)  B  -   C4'  C3'  C2' 107.36    4.2
  13 DGUA  (  14-)  B  -   O4'  C1'  N9  102.35   -6.8
  14 DCYT  (  15-)  B  -   C2'  C1'  N1  121.33    4.5
  14 DCYT  (  15-)  B  -   N1   C2   O2  116.13   -4.6
  15 DGUA  (  16-)  B  -   O4'  C1'  N9  113.66    7.3
  16 DADE  (  17-)  B  -   C5   C6   N1  115.59   -4.2
  16 DADE  (  17-)  B  -   C6   N1   C2  121.17    4.3
  16 DADE  (  17-)  B  -   N1   C2   N3  125.89   -6.8
  17 DADE  (  18-)  B  -   C5   C6   N1  115.43   -4.5
  18 DTHY  (  19-)  B  -   C4   C5   C7  121.43    4.1
  20 DGUA  (  22-)  B  -   N9   C8   N7  113.70    5.2
  20 DGUA  (  22-)  B  -   C2   N3   C4  113.96    4.1
  21 DCYT  (  23-)  B  -   C3'  C4'  O4' 101.13   -4.5
  22 DGUA  (  24-)  B  -   N9   C8   N7  113.76    5.3

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.038
RMS-deviation in bond angles: 2.362

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.

  19 DTHY  (  20-)  B  -   O3' <->   25 5HC   (  21-)  B  -   P      1.01    1.59  INTRA B3
   8 DTHY  (   8-)  A  -   O3' <->   23 5HC   (   9-)  A  -   P      0.96    1.64  INTRA B3
  19 DTHY  (  20-)  B  -   C3' <->   25 5HC   (  21-)  B  -   P      0.75    2.65  INTRA
   8 DTHY  (   8-)  A  -   C3' <->   23 5HC   (   9-)  A  -   P      0.70    2.70  INTRA
   8 DTHY  (   8-)  A  -   N3  <->   16 DADE  (  17-)  B  -   N1     0.22    2.78  INTRA BL
   5 DADE  (   5-)  A  -   N3  <->   26 HOH   (2038 )  A      O      0.20    2.50  INTRA
   7 DTHY  (   7-)  A  -   N3  <->   17 DADE  (  18-)  B  -   N1     0.18    2.82  INTRA BL
  26 HOH   (2009 )  A      O   <->   26 HOH   (2038 )  A      O      0.17    2.03  INTRA
   6 DADE  (   6-)  A  -   N1  <->   18 DTHY  (  19-)  B  -   N3     0.14    2.86  INTRA BL
   5 DADE  (   5-)  A  -   N1  <->   19 DTHY  (  20-)  B  -   N3     0.14    2.86  INTRA BL
  10 DCYT  (  11-)  A  -   N3  <->   13 DGUA  (  14-)  B  -   N1     0.13    2.87  INTRA BL
   3 DCYT  (   3-)  A  -   N3  <->   20 DGUA  (  22-)  B  -   N1     0.11    2.89  INTRA BL
   9 DGUA  (  10-)  A  -   N1  <->   14 DCYT  (  15-)  B  -   N3     0.09    2.91  INTRA BL
   4 DGUA  (   4-)  A  -   N1  <->   25 5HC   (  21-)  B  -   N3     0.08    2.92  INTRA
   1 DCYT  (   1-)  A  -   N3  <->   22 DGUA  (  24-)  B  -   N1     0.07    2.93  INTRA BL
   2 DGUA  (   2-)  A  -   N1  <->   21 DCYT  (  23-)  B  -   N3     0.06    2.94  INTRA BL
  15 DGUA  (  16-)  B  -   N1  <->   23 5HC   (   9-)  A  -   N3     0.06    2.94  INTRA BL
  26 HOH   (2009 )  A      O   <->   26 HOH   (2034 )  A      O      0.05    2.15  INTRA
  11 DGUA  (  12-)  A  -   N1  <->   12 DCYT  (  13-)  B  -   N3     0.04    2.96  INTRA
  13 DGUA  (  14-)  B  -   OP1 <->   27 HOH   (2013 )  B      O      0.02    2.38  INTRA

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.

  26 HOH   (2027 )  A      O      0.08   -3.86   21.26

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 DGUA  (   4-)  A  -   N1
  15 DGUA  (  16-)  B  -   N1
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

Final summary