WHAT IF Check report

This file was created 2013-07-12 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 pdb2lv0.ent

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 OGUA  (   1-)  A  1   Zero
   2 OGUA  (   2-)  A  1   Zero
   3 OGUA  (   3-)  A  1   Zero
   4 OCYT  (   4-)  A  1   Zero
   5 OURA  (   5-)  A  1   Zero
   6 OADE  (   6-)  A  1   Zero
   7 OADE  (   7-)  A  1   Zero
   8 OURA  (   8-)  A  1   Zero
   9 OGUA  (   9-)  A  1   Zero
  10 OURA  (  10-)  A  1   Zero
  11 OURA  (  11-)  A  1   Zero
  12 OGUA  (  12-)  A  1   Zero
  13 OADE  (  13-)  A  1   Zero
  14 OADE  (  14-)  A  1   Zero
  15 OADE  (  15-)  A  1   Zero
  16 OADE  (  16-)  A  1   Zero
  17 OADE  (  17-)  A  1   Zero
  18 OURA  (  18-)  A  1   Zero
  19 OURA  (  19-)  A  1   Zero
  20 OADE  (  20-)  A  1   Zero
  21 OGUA  (  21-)  A  1   Zero
  22 OCYT  (  22-)  A  1   Zero
  23 OCYT  (  23-)  A  1   Zero
  24 OCYT  (  24-)  A  1   Zero
  25 OGUA  (   1-)  A  2   Zero
And so on for a total of 264 lines.

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 1.331
Model 2 : 1.325
Model 3 : 1.332
Model 4 : 1.324
Model 5 : 1.323
Model 6 : 1.333
Model 7 : 1.326
Model 8 : 1.336
Model 9 : 1.331
Model 10 : 1.328
Model 11 : 1.327

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 OGUA  (   1-)  A  1   N9   C8   N7  117.62   13.0
   1 OGUA  (   1-)  A  1   C8   N7   C5  101.97   -4.7
   1 OGUA  (   1-)  A  1   C8   N9   C4  103.47   -7.3
   2 OGUA  (   2-)  A  1   N9   C8   N7  117.68   13.2
   2 OGUA  (   2-)  A  1   C8   N7   C5  101.96   -4.7
   2 OGUA  (   2-)  A  1   C8   N9   C4  103.49   -7.3
   3 OGUA  (   3-)  A  1   N9   C8   N7  117.62   13.0
   3 OGUA  (   3-)  A  1   C8   N7   C5  101.92   -4.8
   3 OGUA  (   3-)  A  1   C8   N9   C4  103.52   -7.2
   6 OADE  (   6-)  A  1   N9   C8   N7  117.61    7.6
   6 OADE  (   6-)  A  1   C8   N7   C5  101.76   -4.3
   6 OADE  (   6-)  A  1   C8   N9   C4  103.33   -6.2
   6 OADE  (   6-)  A  1   N1   C2   N3  127.20   -4.2
   7 OADE  (   7-)  A  1   N9   C8   N7  117.62    7.6
   7 OADE  (   7-)  A  1   C8   N7   C5  101.72   -4.4
   7 OADE  (   7-)  A  1   C8   N9   C4  103.28   -6.3
   7 OADE  (   7-)  A  1   N1   C2   N3  127.17   -4.3
   8 OURA  (   8-)  A  1   O4'  C1'  N1  112.59    4.4
   9 OGUA  (   9-)  A  1   C3'  C2'  C1' 105.14    4.0
   9 OGUA  (   9-)  A  1   O4'  C1'  N9  114.00    5.8
   9 OGUA  (   9-)  A  1   N9   C8   N7  117.56   12.9
   9 OGUA  (   9-)  A  1   C8   N7   C5  101.93   -4.7
   9 OGUA  (   9-)  A  1   C8   N9   C4  103.34   -7.7
  10 OURA  (  10-)  A  1   C3'  C2'  C1' 105.36    4.3
  11 OURA  (  11-)  A  1   C3'  C2'  C1' 106.34    5.4
And so on for a total of 627 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.911
Model 2 : 1.909
Model 3 : 1.903
Model 4 : 1.918
Model 5 : 1.904
Model 6 : 1.904
Model 7 : 1.908
Model 8 : 1.920
Model 9 : 1.912
Model 10 : 1.900
Model 11 : 1.901

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.

 178 OURA  (  10-)  A  8   O2' <->  179 OURA  (  11-)  A  8   P      0.38    2.52
  86 OADE  (  14-)  A  4   O2' <->   87 OADE  (  15-)  A  4   C8     0.32    2.48
  63 OADE  (  15-)  A  3   O2' <->   64 OADE  (  16-)  A  3   O4'    0.29    2.11
 183 OADE  (  15-)  A  8   O2' <->  184 OADE  (  16-)  A  8   O4'    0.26    2.14
 158 OADE  (  14-)  A  7   O2' <->  159 OADE  (  15-)  A  7   C8     0.26    2.54
 134 OADE  (  14-)  A  6   O2' <->  135 OADE  (  15-)  A  6   C5'    0.23    2.57
 111 OADE  (  15-)  A  5   O2' <->  112 OADE  (  16-)  A  5   C8     0.20    2.60
 255 OADE  (  15-)  A 11   O2' <->  256 OADE  (  16-)  A 11   C8     0.20    2.60
  14 OADE  (  14-)  A  1   O2' <->   15 OADE  (  15-)  A  1   C5'    0.19    2.61
 203 OURA  (  11-)  A  9   O2  <->  206 OADE  (  14-)  A  9   N6     0.19    2.51
 159 OADE  (  15-)  A  7   O2' <->  160 OADE  (  16-)  A  7   O5'    0.18    2.22
 135 OADE  (  15-)  A  6   O2' <->  136 OADE  (  16-)  A  6   C8     0.17    2.63
 182 OADE  (  14-)  A  8   O2' <->  183 OADE  (  15-)  A  8   C5'    0.17    2.63
 107 OURA  (  11-)  A  5   O2  <->  110 OADE  (  14-)  A  5   N6     0.15    2.55
  63 OADE  (  15-)  A  3   O2' <->   64 OADE  (  16-)  A  3   C8     0.15    2.65
  86 OADE  (  14-)  A  4   O2' <->   87 OADE  (  15-)  A  4   O5'    0.15    2.25
  87 OADE  (  15-)  A  4   O2' <->   88 OADE  (  16-)  A  4   O5'    0.15    2.25
 108 OGUA  (  12-)  A  5   C4' <->  109 OADE  (  13-)  A  5   OP1    0.15    2.55
  15 OADE  (  15-)  A  1   O2' <->   16 OADE  (  16-)  A  1   C8     0.15    2.65
 230 OADE  (  14-)  A 10   O2' <->  231 OADE  (  15-)  A 10   C5'    0.15    2.65
 206 OADE  (  14-)  A  9   O2' <->  207 OADE  (  15-)  A  9   C5'    0.14    2.66
  86 OADE  (  14-)  A  4   O2' <->   87 OADE  (  15-)  A  4   P      0.14    2.76
 231 OADE  (  15-)  A 10   O2' <->  232 OADE  (  16-)  A 10   C8     0.14    2.66
 183 OADE  (  15-)  A  8   O2' <->  184 OADE  (  16-)  A  8   C8     0.14    2.66
  15 OADE  (  15-)  A  1   O2' <->   16 OADE  (  16-)  A  1   O4'    0.13    2.27
And so on for a total of 61 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.

  33 OGUA  (   9-)  A  2   N1
  58 OURA  (  10-)  A  3   N3
 178 OURA  (  10-)  A  8   N3
 201 OGUA  (   9-)  A  9   N1
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