WHAT IF Check report

This file was created 2011-12-15 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 pdb2ke8.ent

Checks that need to be done early-on in validation

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

 699  AG   (  35-)  B  A
 728  AG   (  37-)  B 1A

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

 681  AG   (  35-)  A  1
 684  AG   (  35-)  A  2
 689  AG   (  37-)  A  3
 690  AG   (  35-)  A  4
 695  AG   (  37-)  A  5
 696  AG   (  35-)  A  6
 702  AG   (  35-)  A  8
 707  AG   (  37-)  A  9
 708  AG   (  35-)  A 10
 713  AG   (  37-)  A 11
 716  AG   (  37-)  A 12
 719  AG   (  37-)  A 13
 722  AG   (  37-)  A 14
 723  AG   (  35-)  A 15
 729  AG   (  35-)  A 17
 734  AG   (  37-)  A 18
 735  AG   (  35-)  A 19
 738  AG   (  35-)  A 20

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 DADE  (   3-)  A  1   Zero
   4 DADE  (   4-)  A  1   Zero
   5 DTHY  (   5-)  A  1   Zero
   6 DTHY  (   6-)  A  1   Zero
   7 DTHY  (   7-)  A  1   Zero
   8 D33   (   8-)  A  1   Zero
   9 D33   (   9-)  A  1   Zero
  10 D33   (  10-)  A  1   Zero
  11 DADE  (  11-)  A  1   Zero
  12 DADE  (  12-)  A  1   Zero
  13 DADE  (  13-)  A  1   Zero
  14 DTHY  (  14-)  A  1   Zero
  15 DTHY  (  15-)  A  1   Zero
  16 DADE  (  16-)  A  1   Zero
  17 DADE  (  17-)  A  1   Zero
  18 DTHY  (  18-)  B  1   Zero
  19 DTHY  (  19-)  B  1   Zero
  20 DADE  (  20-)  B  1   Zero
  21 DADE  (  21-)  B  1   Zero
  22 DTHY  (  22-)  B  1   Zero
  23 DTHY  (  23-)  B  1   Zero
  24 DTHY  (  24-)  B  1   Zero
  25 D33   (  25-)  B  1   Zero
And so on for a total of 680 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 : 0.974
Model 2 : 0.987
Model 3 : 1.032
Model 4 : 0.965
Model 5 : 0.978
Model 6 : 1.022
Model 7 : 0.968
Model 8 : 0.963
Model 9 : 0.949
Model 10 : 1.024
Model 11 : 0.990
Model 12 : 0.972
Model 13 : 0.990
Model 14 : 0.988
Model 15 : 0.988
Model 16 : 0.942
Model 17 : 0.961
Model 18 : 0.950
Model 19 : 0.988
Model 20 : 0.988

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.

   3 DADE  (   3-)  A  1   N1   C2   N3  127.07   -4.5
   4 DADE  (   4-)  A  1   N1   C2   N3  127.04   -4.5
  11 DADE  (  11-)  A  1   N1   C2   N3  126.96   -4.7
  12 DADE  (  12-)  A  1   N1   C2   N3  126.92   -4.8
  13 DADE  (  13-)  A  1   N1   C2   N3  127.23   -4.1
  16 DADE  (  16-)  A  1   N1   C2   N3  126.83   -4.9
  17 DADE  (  17-)  A  1   N1   C2   N3  127.25   -4.1
  20 DADE  (  20-)  B  1   N1   C2   N3  126.92   -4.8
  21 DADE  (  21-)  B  1   N1   C2   N3  127.12   -4.4
  28 DADE  (  28-)  B  1   N1   C2   N3  126.89   -4.8
  29 DADE  (  29-)  B  1   N1   C2   N3  127.02   -4.6
  30 DADE  (  30-)  B  1   N1   C2   N3  127.20   -4.2
  33 DADE  (  33-)  B  1   N1   C2   N3  126.91   -4.8
  34 DADE  (  34-)  B  1   N1   C2   N3  127.11   -4.4
  37 DADE  (   3-)  A  2   N1   C2   N3  126.91   -4.8
  38 DADE  (   4-)  A  2   N1   C2   N3  127.06   -4.5
  45 DADE  (  11-)  A  2   N1   C2   N3  127.08   -4.4
  46 DADE  (  12-)  A  2   N1   C2   N3  127.05   -4.5
  47 DADE  (  13-)  A  2   N1   C2   N3  127.15   -4.3
  50 DADE  (  16-)  A  2   N1   C2   N3  127.07   -4.5
  51 DADE  (  17-)  A  2   N1   C2   N3  127.03   -4.5
  54 DADE  (  20-)  B  2   N1   C2   N3  127.12   -4.4
  55 DADE  (  21-)  B  2   N1   C2   N3  127.09   -4.4
  62 DADE  (  28-)  B  2   N1   C2   N3  127.14   -4.3
  63 DADE  (  29-)  B  2   N1   C2   N3  126.94   -4.7
And so on for a total of 276 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.290
Model 2 : 1.311
Model 3 : 1.308
Model 4 : 1.311
Model 5 : 1.283
Model 6 : 1.301
Model 7 : 1.311
Model 8 : 1.315
Model 9 : 1.302
Model 10 : 1.289
Model 11 : 1.324
Model 12 : 1.288
Model 13 : 1.329
Model 14 : 1.321
Model 15 : 1.294
Model 16 : 1.310
Model 17 : 1.316
Model 18 : 1.331
Model 19 : 1.323
Model 20 : 1.314

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.

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).

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

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.

  16 DADE  (  16-)  A  1   C2   <->    20 DADE  (  20-)  B  1   C2   0.44    2.76
 186 DADE  (  16-)  A  6   C2   <->   190 DADE  (  20-)  B  6   C2   0.43    2.77
   3 DADE  (   3-)  A  1   C2   <->    33 DADE  (  33-)  B  1   C2   0.43    2.77
 173 DADE  (   3-)  A  6   C2   <->   203 DADE  (  33-)  B  6   C2   0.43    2.77
 322 DADE  (  16-)  A 10   C2   <->   326 DADE  (  20-)  B 10   C2   0.43    2.77
 309 DADE  (   3-)  A 10   C2   <->   339 DADE  (  33-)  B 10   C2   0.43    2.77
 547 DADE  (   3-)  A 17   C2   <->   577 DADE  (  33-)  B 17   C2   0.42    2.78
 560 DADE  (  16-)  A 17   C2   <->   564 DADE  (  20-)  B 17   C2   0.42    2.78
 377 DADE  (   3-)  A 12   C2   <->   407 DADE  (  33-)  B 12   C2   0.35    2.85
 390 DADE  (  16-)  A 12   C2   <->   394 DADE  (  20-)  B 12   C2   0.34    2.86
  71 DADE  (   3-)  A  3   C2   <->   101 DADE  (  33-)  B  3   C2   0.32    2.88
 118 DADE  (  16-)  A  4   C2   <->   122 DADE  (  20-)  B  4   C2   0.31    2.89
 105 DADE  (   3-)  A  4   C2   <->   135 DADE  (  33-)  B  4   C2   0.31    2.89
 254 DADE  (  16-)  A  8   C2   <->   258 DADE  (  20-)  B  8   C2   0.29    2.91
 241 DADE  (   3-)  A  8   C2   <->   271 DADE  (  33-)  B  8   C2   0.29    2.91
 207 DADE  (   3-)  A  7   C2   <->   237 DADE  (  33-)  B  7   C2   0.28    2.92
 220 DADE  (  16-)  A  7   C2   <->   224 DADE  (  20-)  B  7   C2   0.28    2.92
  37 DADE  (   3-)  A  2   C2   <->    67 DADE  (  33-)  B  2   C2   0.28    2.92
 139 DADE  (   3-)  A  5   C2   <->   169 DADE  (  33-)  B  5   C2   0.27    2.93
 513 DADE  (   3-)  A 16   C2   <->   543 DADE  (  33-)  B 16   C2   0.27    2.93
 152 DADE  (  16-)  A  5   C2   <->   156 DADE  (  20-)  B  5   C2   0.27    2.93
  84 DADE  (  16-)  A  3   C2   <->    88 DADE  (  20-)  B  3   C2   0.27    2.93
  40 DTHY  (   6-)  A  2   N3   <->    63 DADE  (  29-)  B  2   N1   0.26    2.74
  50 DADE  (  16-)  A  2   C2   <->    54 DADE  (  20-)  B  2   C2   0.26    2.94
 526 DADE  (  16-)  A 16   C2   <->   530 DADE  (  20-)  B 16   C2   0.26    2.94
And so on for a total of 372 lines.

Water, ion, and hydrogenbond related checks

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