WHAT IF Check report

This file was created 2011-12-13 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 pdb1c2w.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-)  B  -   Zero
   2 OGUA  (   2-)  B  -   Zero
   3 OURA  (   3-)  B  -   Zero
   4 OURA  (   4-)  B  -   Zero
   5 OADE  (   5-)  B  -   Zero
   6 OADE  (   6-)  B  -   Zero
   7 OGUA  (   7-)  B  -   Zero
   8 OCYT  (   8-)  B  -   Zero
   9 OGUA  (   9-)  B  -   Zero
  10 OADE  (  10-)  B  -   Zero
  11 OCYT  (  11-)  B  -   Zero
  12 OURA  (  12-)  B  -   Zero
  13 OADE  (  13-)  B  -   Zero
  14 OADE  (  14-)  B  -   Zero
  15 OGUA  (  15-)  B  -   Zero
  16 OCYT  (  16-)  B  -   Zero
  17 OGUA  (  17-)  B  -   Zero
  18 OURA  (  18-)  B  -   Zero
  19 OADE  (  19-)  B  -   Zero
  20 OCYT  (  20-)  B  -   Zero
  21 OADE  (  21-)  B  -   Zero
  22 OCYT  (  22-)  B  -   Zero
  23 OGUA  (  23-)  B  -   Zero
  24 OGUA  (  24-)  B  -   Zero
  25 OURA  (  25-)  B  -   Zero
And so on for a total of 2891 lines.

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

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 OGUA  (   1-)  B  -   P    O5'   1.53   -6.6
   9 OGUA  (   9-)  B  -   C3'  O3'   1.64   15.7
   9 OGUA  (   9-)  B  -   P    O5'   1.88   28.3
   9 OGUA  (   9-)  B  -   O5'  C5'   1.51    4.2
   9 OGUA  (   9-)  B  -   C5'  C4'   1.69   14.0
   9 OGUA  (   9-)  B  -   C1'  N9    1.79   36.6
  10 OADE  (  10-)  B  -   C3'  O3'   1.52    6.8
  10 OADE  (  10-)  B  -   P    O5'   1.89   29.8
  10 OADE  (  10-)  B  -   C5'  C4'   1.68   12.7
  10 OADE  (  10-)  B  -   C1'  N9    1.71   25.2
  11 OCYT  (  11-)  B  -   C3'  O3'   1.76   24.3
  11 OCYT  (  11-)  B  -   P    O5'   1.84   24.6
  11 OCYT  (  11-)  B  -   C5'  C4'   1.62    8.3
  11 OCYT  (  11-)  B  -   C1'  N1    1.75   23.6
  12 OURA  (  12-)  B  -   C3'  O3'   1.49    4.8
  12 OURA  (  12-)  B  -   P    O5'   1.89   30.1
  12 OURA  (  12-)  B  -   C5'  C4'   1.66   11.6
  12 OURA  (  12-)  B  -   C1'  N1    1.72   27.8
  13 OADE  (  13-)  B  -   C3'  O3'   1.51    6.5
  13 OADE  (  13-)  B  -   P    O5'   1.81   22.1
  13 OADE  (  13-)  B  -   C5'  C4'   1.63    9.3
  13 OADE  (  13-)  B  -   C1'  N9    1.68   21.9
  14 OADE  (  14-)  B  -   C3'  O3'   1.73   21.7
  14 OADE  (  14-)  B  -   P    O5'   1.87   28.2
  14 OADE  (  14-)  B  -   O5'  C5'   1.51    4.1
And so on for a total of 5116 lines.

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: 1.603
RMS-deviation in bond distances: 0.020

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-)  B  -   N9   C8   N7  113.96    5.7
   2 OGUA  (   2-)  B  -   N9   C8   N7  113.95    5.7
   7 OGUA  (   7-)  B  -   N9   C8   N7  114.12    6.0
   9 OGUA  (   9-)  B  -   P   -C3* -O3* 113.67   -5.0
   9 OGUA  (   9-)  B  -   P    O5'  C5' 143.27   14.0
   9 OGUA  (   9-)  B  -   O3'  C3'  C2' 126.89    5.7
   9 OGUA  (   9-)  B  -   O5'  C5'  C4' 122.72    8.9
   9 OGUA  (   9-)  B  -   N9   C8   N7  113.87    5.5
  10 OADE  (  10-)  B  -   O5*  P   -O3* 114.19    5.4
  10 OADE  (  10-)  B  -   P   -C3* -O3* 129.70    8.3
  10 OADE  (  10-)  B  -   C3'  C4'  C5' 130.48   10.0
  10 OADE  (  10-)  B  -   O3'  C3'  C4' 125.41    5.7
  10 OADE  (  10-)  B  -   O5'  C5'  C4' 118.28    5.8
  10 OADE  (  10-)  B  -   C5'  C4'  O4' 114.84    4.0
  11 OCYT  (  11-)  B  -   P   -C3* -O3* 113.26   -5.4
  11 OCYT  (  11-)  B  -   P    O5'  C5' 137.03   10.1
  11 OCYT  (  11-)  B  -   C3'  C4'  C5' 136.67   14.1
  12 OURA  (  12-)  B  -   O5*  P   -O3* 111.72    4.1
  12 OURA  (  12-)  B  -   P   -C3* -O3* 147.89   23.5
  12 OURA  (  12-)  B  -   P    O5'  C5' 131.81    6.8
  12 OURA  (  12-)  B  -   C3'  C4'  C5' 130.72   10.1
  12 OURA  (  12-)  B  -   O3'  C3'  C4' 129.82    7.4
  12 OURA  (  12-)  B  -   O3'  C3'  C2' 124.63    4.9
  12 OURA  (  12-)  B  -   OP2  P    O5'  88.71   -7.3
  12 OURA  (  12-)  B  -   O5'  C5'  C4' 123.11    9.2
And so on for a total of 7599 lines.

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

2643 OURA  (2653-)  B  -   0.12
1063 OADE  (1069-)  B  -   0.11
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no torsion angle evaluation was performed.
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no rotamer check was performed.
Since there is no protein, no backbone conformation check was performed.
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no backbone oxygen evaluation was performed.

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.

 595 OURA  ( 598-)  B  -   C4' <->  932 OCYT  ( 937-)  B  -   C4'    1.44    1.76  INTRA BL
 595 OURA  ( 598-)  B  -   C5' <->  932 OCYT  ( 937-)  B  -   C5'    1.38    1.82  INTRA BL
 261 OADE  ( 262-)  B  -   C5' <->  428 OADE  ( 429-)  B  -   C4'    1.32    1.88  INTRA BL
 317 OCYT  ( 318-)  B  -   C5' <->  318 OGUA  ( 319-)  B  -   C8     1.32    1.88  INTRA BL
2048 OADE  (2058-)  B  -   C6  <-> 2059 7MG   (2069-)  B  -   CM7    1.25    1.95  INTRA BL
1934 OURA  (1944-)  B  -   C2' <-> 1935 OGUA  (1945-)  B  -   C4'    1.24    1.96  INTRA BL
1934 OURA  (1944-)  B  -   C2' <-> 1935 OGUA  (1945-)  B  -   C5'    1.24    1.96  INTRA BL
  15 OGUA  (  15-)  B  -   C5' <-> 1191 OGUA  (1197-)  B  -   N3     1.24    1.86  INTRA BL
2048 OADE  (2058-)  B  -   N6  <-> 2059 7MG   (2069-)  B  -   CM7    1.23    1.87  INTRA BL
 481 OADE  ( 483-)  B  -   C2' <->  482 OCYT  ( 484-)  B  -   C5'    1.23    1.97  INTRA BL
1474 OCYT  (1480-)  B  -   C2' <-> 1475 OURA  (1481-)  B  -   C5'    1.23    1.97  INTRA BL
 854 OGUA  ( 859-)  B  -   C5' <->  855 OURA  ( 860-)  B  -   C5     1.20    2.00  INTRA BL
1845 OADE  (1854-)  B  -   C5' <-> 1878 OGUA  (1888-)  B  -   C1'    1.20    2.00  INTRA BL
2048 OADE  (2058-)  B  -   N6  <-> 2058 OURA  (2068-)  B  -   C2     1.20    1.90  INTRA BL
1782 OADE  (1791-)  B  -   C8  <-> 1932 OCYT  (1942-)  B  -   C5'    1.20    2.00  INTRA BL
1895 OCYT  (1905-)  B  -   C4' <-> 1917 OADE  (1927-)  B  -   C4'    1.18    2.02  INTRA BL
  73 OADE  (  73-)  B  -   C4' <->  113 OURA  ( 113-)  B  -   C1'    1.18    2.02  INTRA BL
1844 OADE  (1853-)  B  -   C2' <-> 1878 OGUA  (1888-)  B  -   C8     1.17    2.03  INTRA BL
  73 OADE  (  73-)  B  -   C5' <->  113 OURA  ( 113-)  B  -   C6     1.17    2.03  INTRA BL
 854 OGUA  ( 859-)  B  -   N2  <->  907 OCYT  ( 912-)  B  -   C5     1.15    1.95  INTRA BL
1962 OGUA  (1972-)  B  -   P   <-> 2433 OCYT  (2443-)  B  -   OP2    1.14    1.86  INTRA BL
 896 OCYT  ( 901-)  B  -   C5' <->  897 OCYT  ( 902-)  B  -   C5     1.14    2.06  INTRA BL
1781 OCYT  (1790-)  B  -   C5' <-> 2433 OCYT  (2443-)  B  -   C5'    1.14    2.06  INTRA BL
  19 OADE  (  19-)  B  -   P   <->  664 OURA  ( 667-)  B  -   OP1    1.12    1.88  INTRA BL
  64 OADE  (  64-)  B  -   C8  <->   66 OCYT  (  66-)  B  -   N4     1.11    1.99  INTRA BL
And so on for a total of 10000 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.

  16 OCYT  (  16-)  B  -   O2'
  27 OGUA  (  27-)  B  -   N2
  29 OURA  (  29-)  B  -   N3
  64 OADE  (  64-)  B  -   N6
  66 OCYT  (  66-)  B  -   N4
  68 OGUA  (  68-)  B  -   N2
  78 OURA  (  78-)  B  -   N3
  79 OCYT  (  79-)  B  -   N4
  86 OGUA  (  86-)  B  -   N2
  88 OGUA  (  88-)  B  -   N2
  92 OURA  (  92-)  B  -   N3
  94 OADE  (  94-)  B  -   N6
  98 OGUA  (  98-)  B  -   N1
  99 OURA  (  99-)  B  -   N3
 101 OADE  ( 101-)  B  -   N6
 105 OCYT  ( 105-)  B  -   N4
 108 OGUA  ( 108-)  B  -   N1
 109 OCYT  ( 109-)  B  -   N4
 113 OURA  ( 113-)  B  -   N3
 115 OCYT  ( 115-)  B  -   N4
 128 OCYT  ( 128-)  B  -   N4
 159 OGUA  ( 159-)  B  -   N1
 160 OADE  ( 160-)  B  -   N6
 166 OURA  ( 166-)  B  -   N3
 194 OGUA  ( 194-)  B  -   N2
And so on for a total of 374 lines.

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