WHAT IF Check report

This file was created 2012-01-25 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 pdb2gwe.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.

 155   K   ( 151-)  F  E
 156   K   ( 153-)  F  E
 169   K   ( 158-)  I  J
 173   K   ( 173-)  K  L

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.

 145   K   ( 161-)  A  -
 156   K   ( 153-)  F  E
 171   K   ( 171-)  K  -

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 DGUA  (   1-)  A  -   Zero
   4 DGUA  (   4-)  A  -   Zero
  20 DTHY  (  20-)  B  -   Zero
  21 DGUA  (  21-)  B  -   Zero
  23 DGUA  (  23-)  B  -   Zero
  24 DGUA  (  24-)  B  -   Zero
  32 DTHY  (  32-)  C  -   Zero
  35 DGUA  (  35-)  C  -   Zero
  37 DGUA  (  37-)  D  -   Zero
  49 DGUA  (  49-)  E  -   Zero
  50 DGUA  (  50-)  E  -   Zero
  54 DTHY  (  54-)  E  -   Zero
  60 DGUA  (  60-)  E  -   Zero
  62 DGUA  (  62-)  F  -   Zero
  68 DTHY  (  68-)  F  -   Zero
  70 DGUA  (  70-)  F  -   Zero
  71 DGUA  (  71-)  F  -   Zero
  73 DGUA  (  73-)  G  -   Zero
  78 DTHY  (  78-)  G  -   Zero
  94 DGUA  (  94-)  H  -   Zero
  96 DGUA  (  96-)  H  -   Zero
 105 DGUA  ( 105-)  I  -   Zero
 106 DGUA  ( 106-)  I  -   Zero
 107 DGUA  ( 107-)  I  -   Zero
 109 DGUA  ( 109-)  J  -   Zero
 110 DGUA  ( 110-)  J  -   Zero
 116 DTHY  ( 116-)  J  -   Zero
 128 DTHY  ( 128-)  K  -   Zero
 129 DGUA  ( 129-)  K  -   Zero
 130 DGUA  ( 130-)  K  -   Zero
 133 DGUA  ( 133-)  L  -   Zero
 142 DGUA  ( 142-)  L  -   Zero

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:

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 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 DGUA  (   1-)  A  -   N9   C8   N7  113.21    4.2
   2 DGUA  (   2-)  A  -   N9   C8   N7  113.30    4.4
   3 DGUA  (   3-)  A  -   N9   C8   N7  113.23    4.3
   4 DGUA  (   4-)  A  -   N9   C8   N7  113.33    4.5
   9 DGUA  (   9-)  A  -   N9   C8   N7  113.25    4.3
  10 DGUA  (  10-)  A  -   N9   C8   N7  113.28    4.4
  11 DGUA  (  11-)  A  -   N9   C8   N7  113.21    4.2
  12 DGUA  (  12-)  A  -   N9   C8   N7  113.19    4.2
  13 DGUA  (  13-)  B  -   N9   C8   N7  113.19    4.2
  14 DGUA  (  14-)  B  -   N9   C8   N7  113.22    4.2
  15 DGUA  (  15-)  B  -   N9   C8   N7  113.19    4.2
  16 DGUA  (  16-)  B  -   N9   C8   N7  113.36    4.5
  21 DGUA  (  21-)  B  -   N9   C8   N7  113.29    4.4
  22 DGUA  (  22-)  B  -   N9   C8   N7  113.32    4.4
  23 DGUA  (  23-)  B  -   N9   C8   N7  113.28    4.4
  24 DGUA  (  24-)  B  -   N9   C8   N7  113.26    4.3
  25 DGUA  (  25-)  C  -   N9   C8   N7  113.27    4.3
  26 DGUA  (  26-)  C  -   N9   C8   N7  113.34    4.5
  27 DGUA  (  27-)  C  -   N9   C8   N7  113.22    4.2
  28 DGUA  (  28-)  C  -   N9   C8   N7  113.25    4.3
  33 DGUA  (  33-)  C  -   N9   C8   N7  113.20    4.2
  34 DGUA  (  34-)  C  -   N9   C8   N7  113.32    4.4
  35 DGUA  (  35-)  C  -   N9   C8   N7  113.22    4.2
  36 DGUA  (  36-)  C  -   N9   C8   N7  113.21    4.2
  37 DGUA  (  37-)  D  -   N9   C8   N7  113.20    4.2
And so on for a total of 96 lines.

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.

   2 DGUA  (   2-)  A  -   N2  <->   15 DGUA  (  15-)  B  -   N7     0.33    2.67  INTRA BL
  50 DGUA  (  50-)  E  -   N2  <->   63 DGUA  (  63-)  F  -   N7     0.32    2.68  INTRA BL
 108 DGUA  ( 108-)  I  -   N2  <->  112 DGUA  ( 112-)  J  -   N7     0.31    2.69  INTRA BL
  74 DGUA  (  74-)  G  -   N7  <->   94 DGUA  (  94-)  H  -   N2     0.30    2.70  INTRA BL
 121 DGUA  ( 121-)  K  -   N2  <->  141 DGUA  ( 141-)  L  -   N7     0.30    2.70  INTRA BL
  49 DGUA  (  49-)  E  -   N7  <->   64 DGUA  (  64-)  F  -   N2     0.30    2.70  INTRA BL
 123 DGUA  ( 123-)  K  -   N7  <->  134 DGUA  ( 134-)  L  -   N2     0.30    2.70  INTRA
  34 DGUA  (  34-)  C  -   N2  <->   38 DGUA  (  38-)  D  -   N7     0.30    2.70  INTRA BL
  26 DGUA  (  26-)  C  -   N2  <->   39 DGUA  (  39-)  D  -   N7     0.30    2.70  INTRA BL
 122 DGUA  ( 122-)  K  -   N2  <->  135 DGUA  ( 135-)  L  -   N7     0.30    2.70  INTRA BL
 121 DGUA  ( 121-)  K  -   N7  <->  136 DGUA  ( 136-)  L  -   N2     0.30    2.70  INTRA BL
 124 DGUA  ( 124-)  K  -   N2  <->  133 DGUA  ( 133-)  L  -   N7     0.30    2.70  INTRA
  81 DGUA  (  81-)  G  -   N7  <->   85 DGUA  (  85-)  H  -   N2     0.30    2.70  INTRA BL
  97 DGUA  (  97-)  I  -   N7  <->  112 DGUA  ( 112-)  J  -   N2     0.30    2.70  INTRA BL
  99 DGUA  (  99-)  I  -   N7  <->  110 DGUA  ( 110-)  J  -   N2     0.30    2.70  INTRA BL
  98 DGUA  (  98-)  I  -   N2  <->  111 DGUA  ( 111-)  J  -   N7     0.30    2.70  INTRA BL
   1 DGUA  (   1-)  A  -   N7  <->   16 DGUA  (  16-)  B  -   N2     0.30    2.70  INTRA BL
  28 DGUA  (  28-)  C  -   N2  <->   37 DGUA  (  37-)  D  -   N7     0.30    2.70  INTRA BL
 106 DGUA  ( 106-)  I  -   N2  <->  110 DGUA  ( 110-)  J  -   N7     0.30    2.70  INTRA BL
  76 DGUA  (  76-)  G  -   N2  <->   85 DGUA  (  85-)  H  -   N7     0.30    2.70  INTRA
  73 DGUA  (  73-)  G  -   N7  <->   88 DGUA  (  88-)  H  -   N2     0.30    2.70  INTRA
  25 DGUA  (  25-)  C  -   N2  <->   45 DGUA  (  45-)  D  -   N7     0.29    2.71  INTRA BL
  58 DGUA  (  58-)  E  -   N2  <->   62 DGUA  (  62-)  F  -   N7     0.28    2.72  INTRA BL
  76 DGUA  (  76-)  G  -   N7  <->   96 DGUA  (  96-)  H  -   N2     0.28    2.72  INTRA BL
  57 DGUA  (  57-)  E  -   N7  <->   61 DGUA  (  61-)  F  -   N2     0.27    2.73  INTRA BL
And so on for a total of 121 lines.

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.

 175 HOH   ( 243 )  A      O     13.11   13.44   50.99
 177 HOH   ( 300 )  C      O     13.34   38.98   43.87
 185 HOH   ( 234 )  K      O     35.98   50.40   21.60

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 183 HOH   ( 297 )  I      O
Since there are no HIS GLN or ASN residues in the soup, no hydrogen-bond
flip check will be performed.

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.

 123 DGUA  ( 123-)  K  -   N2
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 145   K   ( 161-)  A  -  -.-  -.-  Part of ionic cluster
 146   K   ( 162-)  A  -  -.-  -.-  Part of ionic cluster
 147   K   ( 163-)  A  -  -.-  -.-  Part of ionic cluster
 148   K   ( 164-)  A  -  -.-  -.-  Part of ionic cluster
 149   K   ( 160-)  B  -  -.-  -.-  Part of ionic cluster
 150   K   ( 145-)  C  -  -.-  -.-  Part of ionic cluster
 151   K   ( 146-)  C  -  -.-  -.-  Part of ionic cluster
 152   K   ( 147-)  C  -  -.-  -.-  Part of ionic cluster
 153   K   ( 148-)  C  -  -.-  -.-  Part of ionic cluster
 154   K   ( 149-)  D  -  -.-  -.-  Part of ionic cluster
 155   K   ( 151-)  F  E  -.-  -.-  Part of ionic cluster
 156   K   ( 153-)  F  E  -.-  -.-  Part of ionic cluster
 157   K   ( 154-)  E  -  -.-  -.-  Part of ionic cluster
 158   K   ( 150-)  F  -  -.-  -.-  Part of ionic cluster
 159   K   ( 152-)  F  -  -.-  -.-  Part of ionic cluster
 160   K   ( 166-)  G  -  -.-  -.-  Part of ionic cluster
 161   K   ( 167-)  G  -  -.-  -.-  Part of ionic cluster
 162   K   ( 168-)  G  -  -.-  -.-  Part of ionic cluster
 163   K   ( 169-)  G  -  -.-  -.-  Part of ionic cluster
 164   K   ( 165-)  H  -  -.-  -.-  Part of ionic cluster
 165   K   ( 156-)  I  -  -.-  -.-  Part of ionic cluster
 166   K   ( 159-)  I  -  -.-  -.-  Part of ionic cluster
 167   K   ( 155-)  J  -  -.-  -.-  Part of ionic cluster
 168   K   ( 157-)  J  -  -.-  -.-  Part of ionic cluster
 169   K   ( 158-)  I  J  -.-  -.-  Part of ionic cluster
 170   K   ( 170-)  K  -  -.-  -.-  Part of ionic cluster
 171   K   ( 171-)  K  -  -.-  -.-  Part of ionic cluster
 172   K   ( 172-)  K  -  -.-  -.-  Part of ionic cluster
 173   K   ( 173-)  K  L  -.-  -.-  Part of ionic cluster
 174   K   ( 174-)  L  -  -.-  -.-  Part of ionic cluster

Final summary