WHAT IF Check report

This file was created 2013-12-09 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 pdb2mb3.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 241 L2H   (  25-)  A  1
 242 L2H   (  25-)  A  2
 243 L2H   (  25-)  A  3
 244 L2H   (  25-)  A  4
 245 L2H   (  25-)  A  5
 246 L2H   (  25-)  A  6
 247 L2H   (  25-)  A  7
 248 L2H   (  25-)  A  8
 249 L2H   (  25-)  A  9
 250 L2H   (  25-)  A 10

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.

   1 DTHY  (   1-)  A  1   Zero
   2 DTHY  (   2-)  A  1   Zero
   3 DGUA  (   3-)  A  1   Zero
   4 DGUA  (   4-)  A  1   Zero
   5 DGUA  (   5-)  A  1   Zero
   6 DTHY  (   6-)  A  1   Zero
   7 DTHY  (   7-)  A  1   Zero
   8 DADE  (   8-)  A  1   Zero
   9 DGUA  (   9-)  A  1   Zero
  10 DGUA  (  10-)  A  1   Zero
  11 DGUA  (  11-)  A  1   Zero
  12 DTHY  (  12-)  A  1   Zero
  13 DTHY  (  13-)  A  1   Zero
  14 DADE  (  14-)  A  1   Zero
  15 DGUA  (  15-)  A  1   Zero
  16 DGUA  (  16-)  A  1   Zero
  17 DGUA  (  17-)  A  1   Zero
  18 DTHY  (  18-)  A  1   Zero
  19 DTHY  (  19-)  A  1   Zero
  20 DADE  (  20-)  A  1   Zero
  21 DGUA  (  21-)  A  1   Zero
  22 DGUA  (  22-)  A  1   Zero
  23 DGUA  (  23-)  A  1   Zero
  24 DADE  (  24-)  A  1   Zero
  25 DTHY  (   1-)  A  2   Zero
And so on for a total of 240 lines.

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.

   1 DTHY  (   1-)  A  1   C5   C7    1.53    5.5
   2 DTHY  (   2-)  A  1   C5   C7    1.53    5.1
   6 DTHY  (   6-)  A  1   C5   C7    1.53    4.9
   7 DTHY  (   7-)  A  1   C5   C7    1.53    5.2
  12 DTHY  (  12-)  A  1   C5   C7    1.53    5.2
  13 DTHY  (  13-)  A  1   C5   C7    1.53    5.2
  18 DTHY  (  18-)  A  1   C5   C7    1.53    4.9
  19 DTHY  (  19-)  A  1   C5   C7    1.53    5.2
  25 DTHY  (   1-)  A  2   C5   C7    1.53    5.1
  26 DTHY  (   2-)  A  2   C5   C7    1.53    5.3
  30 DTHY  (   6-)  A  2   C5   C7    1.53    5.1
  31 DTHY  (   7-)  A  2   C5   C7    1.53    5.2
  36 DTHY  (  12-)  A  2   C5   C7    1.53    5.3
  37 DTHY  (  13-)  A  2   C5   C7    1.53    5.1
  42 DTHY  (  18-)  A  2   C5   C7    1.53    5.1
  43 DTHY  (  19-)  A  2   C5   C7    1.53    5.3
  49 DTHY  (   1-)  A  3   C5   C7    1.53    5.2
  50 DTHY  (   2-)  A  3   C5   C7    1.53    5.1
  54 DTHY  (   6-)  A  3   C5   C7    1.53    5.0
  55 DTHY  (   7-)  A  3   C5   C7    1.53    5.2
  60 DTHY  (  12-)  A  3   C5   C7    1.53    5.3
  61 DTHY  (  13-)  A  3   C5   C7    1.53    5.4
  66 DTHY  (  18-)  A  3   C5   C7    1.52    4.8
  67 DTHY  (  19-)  A  3   C5   C7    1.53    5.4
  73 DTHY  (   1-)  A  4   C5   C7    1.53    5.1
And so on for a total of 80 lines.

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 1.203
Model 2 : 1.220
Model 3 : 1.218
Model 4 : 1.195
Model 5 : 1.201
Model 6 : 1.198
Model 7 : 1.206
Model 8 : 1.214
Model 9 : 1.195
Model 10 : 1.228

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 DTHY  (   1-)  A  1   N1   C6   C5  121.30   -4.0
   1 DTHY  (   1-)  A  1   C6   C5   C4  120.97    5.0
   1 DTHY  (   1-)  A  1   C6   C5   C7  119.44   -5.8
   2 DTHY  (   2-)  A  1   C6   C5   C4  121.08    5.1
   2 DTHY  (   2-)  A  1   C6   C5   C7  119.29   -6.0
   3 DGUA  (   3-)  A  1   N9   C8   N7  114.14    6.1
   4 DGUA  (   4-)  A  1   N9   C8   N7  113.95    5.7
   5 DGUA  (   5-)  A  1   N9   C8   N7  113.92    5.6
   6 DTHY  (   6-)  A  1   C6   C5   C4  121.02    5.0
   6 DTHY  (   6-)  A  1   C6   C5   C7  119.27   -6.0
   7 DTHY  (   7-)  A  1   N1   C6   C5  121.24   -4.1
   7 DTHY  (   7-)  A  1   C6   C5   C4  120.93    4.9
   7 DTHY  (   7-)  A  1   C6   C5   C7  119.44   -5.8
   9 DGUA  (   9-)  A  1   N9   C8   N7  114.05    5.9
  10 DGUA  (  10-)  A  1   N9   C8   N7  113.81    5.4
  11 DGUA  (  11-)  A  1   N9   C8   N7  113.98    5.8
  12 DTHY  (  12-)  A  1   N1   C6   C5  121.28   -4.0
  12 DTHY  (  12-)  A  1   C6   C5   C4  120.96    4.9
  12 DTHY  (  12-)  A  1   C6   C5   C7  119.48   -5.7
  13 DTHY  (  13-)  A  1   C6   C5   C4  120.99    5.0
  13 DTHY  (  13-)  A  1   C6   C5   C7  119.47   -5.7
  15 DGUA  (  15-)  A  1   N9   C8   N7  113.92    5.6
  16 DGUA  (  16-)  A  1   N9   C8   N7  114.10    6.0
  17 DGUA  (  17-)  A  1   N9   C8   N7  113.74    5.3
  18 DTHY  (  18-)  A  1   N1   C6   C5  121.21   -4.2
And so on for a total of 313 lines.

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 1.405
Model 2 : 1.388
Model 3 : 1.409
Model 4 : 1.403
Model 5 : 1.400
Model 6 : 1.398
Model 7 : 1.394
Model 8 : 1.399
Model 9 : 1.400
Model 10 : 1.419

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

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).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 229 DTHY  (  13-)  A 10   N3  <->  240 DADE  (  24-)  A 10   N1     0.39    2.61
  85 DTHY  (  13-)  A  4   N3  <->   96 DADE  (  24-)  A  4   N1     0.36    2.64
 109 DTHY  (  13-)  A  5   N3  <->  120 DADE  (  24-)  A  5   N1     0.36    2.64
  57 DGUA  (   9-)  A  3   N7  <->   65 DGUA  (  17-)  A  3   N2     0.35    2.65
 105 DGUA  (   9-)  A  5   N7  <->  113 DGUA  (  17-)  A  5   N2     0.34    2.66
  81 DGUA  (   9-)  A  4   N7  <->   89 DGUA  (  17-)  A  4   N2     0.33    2.67
  15 DGUA  (  15-)  A  1   N2  <->   23 DGUA  (  23-)  A  1   N7     0.33    2.67
 181 DTHY  (  13-)  A  8   N3  <->  192 DADE  (  24-)  A  8   N1     0.33    2.67
 129 DGUA  (   9-)  A  6   N7  <->  137 DGUA  (  17-)  A  6   N2     0.32    2.68
 201 DGUA  (   9-)  A  9   N7  <->  209 DGUA  (  17-)  A  9   N2     0.32    2.68
  39 DGUA  (  15-)  A  2   N2  <->   47 DGUA  (  23-)  A  2   N7     0.32    2.68
 226 DGUA  (  10-)  A 10   N2  <->  232 DGUA  (  16-)  A 10   N7     0.32    2.68
  34 DGUA  (  10-)  A  2   N2  <->   40 DGUA  (  16-)  A  2   N7     0.31    2.69
 178 DGUA  (  10-)  A  8   N2  <->  184 DGUA  (  16-)  A  8   N7     0.31    2.69
 135 DGUA  (  15-)  A  6   N2  <->  143 DGUA  (  23-)  A  6   N7     0.30    2.70
  32 DADE  (   8-)  A  2   N3  <->  242 L2H   (  25-)  A  2   N9     0.30    2.70
 153 DGUA  (   9-)  A  7   N7  <->  161 DGUA  (  17-)  A  7   N2     0.30    2.70
  87 DGUA  (  15-)  A  4   N2  <->   95 DGUA  (  23-)  A  4   N7     0.30    2.70
 104 DADE  (   8-)  A  5   N3  <->  245 L2H   (  25-)  A  5   N9     0.30    2.70
 213 DGUA  (  21-)  A  9   C5' <->  249 L2H   (  25-)  A  9   N10    0.29    2.81
  33 DGUA  (   9-)  A  2   N7  <->   41 DGUA  (  17-)  A  2   N2     0.29    2.71
   9 DGUA  (   9-)  A  1   N7  <->   17 DGUA  (  17-)  A  1   N2     0.29    2.71
  10 DGUA  (  10-)  A  1   N2  <->   16 DGUA  (  16-)  A  1   N7     0.28    2.72
 231 DGUA  (  15-)  A 10   N2  <->  239 DGUA  (  23-)  A 10   N7     0.28    2.72
  37 DTHY  (  13-)  A  2   N3  <->   48 DADE  (  24-)  A  2   N1     0.28    2.72
And so on for a total of 230 lines.

Water, ion, and hydrogenbond related checks

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.

  24 DADE  (  24-)  A  1   N6
  33 DGUA  (   9-)  A  2   N2
  49 DTHY  (   1-)  A  3   N3
  52 DGUA  (   4-)  A  3   N2
 153 DGUA  (   9-)  A  7   N2
 196 DGUA  (   4-)  A  9   N2
 208 DGUA  (  16-)  A  9   N2
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

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.

Final summary