WHAT IF Check report

This file was created 2012-01-31 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 pdb2pis.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 145 FFD   (  20-)  B  -
 146 FFD   (   7-)  C  -
 147 FFD   (  20-)  D  -
 148 FFD   (   7-)  E  -
 149 FFD   (  20-)  F  -
 150 FFD   (   7-)  G  -
 151 FFD   (  20-)  H  -
 152 FFD   (   7-)  I  -
 153 FFD   (  20-)  J  -
 154 FFD   (   7-)  K  -
 155 FFD   (  20-)  L  -
 162 FFD   (   7-)  A  -

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.

  15 CBR   (  16-)  B  -   High
  27 CBR   (   3-)  C  -   High
  29 DADE  (   5-)  C  -   High
  51 CBR   (   3-)  E  -   High
  52 DGUA  (   4-)  E  -   High
  53 DADE  (   5-)  E  -   High
  85 DCYT  (  14-)  H  -   High
  86 DGUA  (  15-)  H  -   High
  87 CBR   (  16-)  H  -   High
  97 DCYT  (   1-)  I  -   High
  99 CBR   (   3-)  I  -   High
 101 DADE  (   5-)  I  -   High
 103 DTHY  (   8-)  I  -   High
 104 DTHY  (   9-)  I  -   High
 105 DCYT  (  10-)  I  -   High
 107 DCYT  (  12-)  I  -   High
 108 DGUA  (  13-)  I  -   High
 109 DCYT  (  14-)  J  -   High
 110 DGUA  (  15-)  J  -   High
 111 CBR   (  16-)  J  -   High
 112 DGUA  (  17-)  J  -   High
 113 DADE  (  18-)  J  -   High
 114 DADE  (  19-)  J  -   High
 115 DTHY  (  21-)  J  -   High
 122 DGUA  (   2-)  K  -   High
 123 CBR   (   3-)  K  -   High
 124 DGUA  (   4-)  K  -   High
 125 DADE  (   5-)  K  -   High
 126 DADE  (   6-)  K  -   High
 127 DTHY  (   8-)  K  -   High
 129 DCYT  (  10-)  K  -   High
 130 DGUA  (  11-)  K  -   High
 131 DCYT  (  12-)  K  -   High
 132 DGUA  (  13-)  K  -   High
 134 DGUA  (  15-)  L  -   High
 135 CBR   (  16-)  L  -   High
 136 DGUA  (  17-)  L  -   High
 137 DADE  (  18-)  L  -   High
 138 DADE  (  19-)  L  -   High
 139 DTHY  (  21-)  L  -   High
 140 DTHY  (  22-)  L  -   High
 141 DCYT  (  23-)  L  -   High
 142 DGUA  (  24-)  L  -   High
 143 DCYT  (  25-)  L  -   High
 144 DGUA  (  26-)  L  -   High

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  13 DCYT  (  14-)  B  -   0.50
 109 DCYT  (  14-)  J  -   0.50
 120 DGUA  (  26-)  J  -   0.50
 133 DCYT  (  14-)  L  -   0.50

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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 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 DCYT  (   1-)  A  -   C3'  O3'   1.37   -4.9
   2 DGUA  (   2-)  A  -   O5'  C5'   1.37   -4.4
   4 DGUA  (   4-)  A  -   C3'  O3'   1.35   -6.4
   7 DTHY  (   8-)  A  -   C5'  C4'   1.48   -4.4
  10 DGUA  (  11-)  A  -   N1   C2    1.41    4.9
  10 DGUA  (  11-)  A  -   C6   O6    1.28    4.5
  11 DCYT  (  12-)  A  -   O5'  C5'   1.37   -4.6
  13 DCYT  (  14-)  B  -   C1'  N1    1.52    4.1
  14 DGUA  (  15-)  B  -   C3'  O3'   1.49    4.5
  16 DGUA  (  17-)  B  -   C3'  C2'   1.56    4.0
  16 DGUA  (  17-)  B  -   N1   C2    1.41    4.0
  17 DADE  (  18-)  B  -   C8   N7    1.35    5.2
  17 DADE  (  18-)  B  -   C5   C4    1.41    4.1
  20 DTHY  (  22-)  B  -   C1'  N1    1.54    4.5
  21 DCYT  (  23-)  B  -   O5'  C5'   1.35   -5.6
  21 DCYT  (  23-)  B  -   C5'  C4'   1.47   -5.1
  21 DCYT  (  23-)  B  -   C4'  C3'   1.48   -4.3
  21 DCYT  (  23-)  B  -   C1'  N1    1.54    5.9
  22 DGUA  (  24-)  B  -   C3'  O3'   1.36   -5.3
  26 DGUA  (   2-)  C  -   C2   N3    1.36    5.1
  28 DGUA  (   4-)  C  -   C2   N3    1.37    6.5
  29 DADE  (   5-)  C  -   C3'  C2'   1.56    4.1
  31 DTHY  (   8-)  C  -   C3'  O3'   1.35   -6.0
  34 DGUA  (  11-)  C  -   C3'  O3'   1.34   -7.0
  35 DCYT  (  12-)  C  -   N1   C6    1.34   -4.0
And so on for a total of 55 lines.

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 DCYT  (   1-)  A  -   O4'  C1'  N1  111.16    4.2
   2 DGUA  (   2-)  A  -   O4'  C1'  N9  102.60   -6.5
   4 DGUA  (   4-)  A  -   N9   C8   N7  113.29    4.4
   8 DTHY  (   9-)  A  -   C5   C4   O4  121.45   -4.9
   8 DTHY  (   9-)  A  -   O4   C4   N3  122.64    4.6
  10 DGUA  (  11-)  A  -   O4'  C1'  N9  112.83    6.3
  10 DGUA  (  11-)  A  -   N9   C8   N7  113.16    4.1
  12 DGUA  (  13-)  A  -   N9   C8   N7  113.32    4.4
  14 DGUA  (  15-)  B  -   N9   C8   N7  113.27    4.3
  16 DGUA  (  17-)  B  -   N9   C8   N7  113.68    5.2
  22 DGUA  (  24-)  B  -   C4'  C3'  C2'  98.90   -4.3
  24 DGUA  (  26-)  B  -   N9   C8   N7  113.31    4.4
  26 DGUA  (   2-)  C  -   N9   C8   N7  113.40    4.6
  28 DGUA  (   4-)  C  -   N9   C8   N7  113.30    4.4
  34 DGUA  (  11-)  C  -   O4'  C1'  N9  111.93    5.2
  34 DGUA  (  11-)  C  -   N9   C8   N7  113.15    4.1
  38 DGUA  (  15-)  D  -   O4'  C1'  N9  103.90   -4.9
  38 DGUA  (  15-)  D  -   N9   C8   N7  113.33    4.5
  40 DGUA  (  17-)  D  -   N9   C8   N7  113.95    5.7
  42 DADE  (  19-)  D  -   C4'  O4'  C1' 100.28   -6.7
  42 DADE  (  19-)  D  -   O4'  C1'  N9  113.78    7.5
  43 DTHY  (  21-)  D  -   O4'  C1'  N1  104.54   -4.1
  43 DTHY  (  21-)  D  -   C5   C4   O4  121.90   -4.3
  43 DTHY  (  21-)  D  -   O4   C4   N3  123.32    5.7
  44 DTHY  (  22-)  D  -   C5   C4   O4  121.74   -4.5
And so on for a total of 83 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.

  42 DADE  (  19-)  D  -   O3' <->  147 FFD   (  20-)  D  -   P      1.02    1.58  INTRA BF
   6 DADE  (   6-)  A  -   O3' <->  162 FFD   (   7-)  A  -   P      1.01    1.59  INTRA BL
  78 DADE  (   6-)  G  -   O3' <->  150 FFD   (   7-)  G  -   P      1.01    1.59  INTRA BF
  66 DADE  (  19-)  F  -   O3' <->  149 FFD   (  20-)  F  -   P      1.01    1.59  INTRA BF
  30 DADE  (   6-)  C  -   O3' <->  146 FFD   (   7-)  C  -   P      1.01    1.59  INTRA BF
 126 DADE  (   6-)  K  -   O3' <->  154 FFD   (   7-)  K  -   P      1.00    1.60  INTRA BF
  18 DADE  (  19-)  B  -   O3' <->  145 FFD   (  20-)  B  -   P      1.00    1.60  INTRA BF
 102 DADE  (   6-)  I  -   O3' <->  152 FFD   (   7-)  I  -   P      1.00    1.60  INTRA BF
 114 DADE  (  19-)  J  -   O3' <->  153 FFD   (  20-)  J  -   P      1.00    1.60  INTRA BF
  90 DADE  (  19-)  H  -   O3' <->  151 FFD   (  20-)  H  -   P      1.00    1.60  INTRA BF
 138 DADE  (  19-)  L  -   O3' <->  155 FFD   (  20-)  L  -   P      1.00    1.60  INTRA BF
  54 DADE  (   6-)  E  -   O3' <->  148 FFD   (   7-)  E  -   P      0.99    1.61  INTRA BF
 122 DGUA  (   2-)  K  -   C2' <->  123 CBR   (   3-)  K  -  BR      0.92    2.28  INTRA BF
 130 DGUA  (  11-)  K  -   C8  <->  131 DCYT  (  12-)  K  -   C5     0.87    2.33  INTRA BF
   6 DADE  (   6-)  A  -   C3' <->  162 FFD   (   7-)  A  -   P      0.83    2.57  INTRA BL
  78 DADE  (   6-)  G  -   C3' <->  150 FFD   (   7-)  G  -   P      0.83    2.57  INTRA BF
  30 DADE  (   6-)  C  -   C3' <->  146 FFD   (   7-)  C  -   P      0.82    2.58  INTRA BF
  42 DADE  (  19-)  D  -   C3' <->  147 FFD   (  20-)  D  -   P      0.82    2.58  INTRA BF
  66 DADE  (  19-)  F  -   C3' <->  149 FFD   (  20-)  F  -   P      0.82    2.58  INTRA BF
 126 DADE  (   6-)  K  -   C3' <->  154 FFD   (   7-)  K  -   P      0.78    2.62  INTRA BF
 114 DADE  (  19-)  J  -   C3' <->  153 FFD   (  20-)  J  -   P      0.78    2.62  INTRA BF
 102 DADE  (   6-)  I  -   C3' <->  152 FFD   (   7-)  I  -   P      0.77    2.63  INTRA BF
 138 DADE  (  19-)  L  -   C3' <->  155 FFD   (  20-)  L  -   P      0.77    2.63  INTRA BF
  90 DADE  (  19-)  H  -   C3' <->  151 FFD   (  20-)  H  -   P      0.75    2.65  INTRA BF
  18 DADE  (  19-)  B  -   C3' <->  145 FFD   (  20-)  B  -   P      0.75    2.65  INTRA BF
And so on for a total of 372 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.

  10 DGUA  (  11-)  A  -   N1
  10 DGUA  (  11-)  A  -   N2
  22 DGUA  (  24-)  B  -   N1
  22 DGUA  (  24-)  B  -   N2
  31 DTHY  (   8-)  C  -   N3
  34 DGUA  (  11-)  C  -   N1
  34 DGUA  (  11-)  C  -   N2
  46 DGUA  (  24-)  D  -   N1
  46 DGUA  (  24-)  D  -   N2
  47 DCYT  (  25-)  D  -   N4
  48 DGUA  (  26-)  D  -   N2
  58 DGUA  (  11-)  E  -   N1
  58 DGUA  (  11-)  E  -   N2
  70 DGUA  (  24-)  F  -   N1
  70 DGUA  (  24-)  F  -   N2
  76 DGUA  (   4-)  G  -   N2
  82 DGUA  (  11-)  G  -   N1
  82 DGUA  (  11-)  G  -   N2
  83 DCYT  (  12-)  G  -   N4
  94 DGUA  (  24-)  H  -   N1
  94 DGUA  (  24-)  H  -   N2
  98 DGUA  (   2-)  I  -   N1
  98 DGUA  (   2-)  I  -   N2
 106 DGUA  (  11-)  I  -   N1
 108 DGUA  (  13-)  I  -   N1
 110 DGUA  (  15-)  J  -   N2
 118 DGUA  (  24-)  J  -   N1
 118 DGUA  (  24-)  J  -   N2
 142 DGUA  (  24-)  L  -   N1
 142 DGUA  (  24-)  L  -   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+.

 156  MG   (   1-)  F  -  -.-  -.-  Too few ligands (0)
 157  MG   (   2-)  C  -  -.-  -.-  Too few ligands (0)
 158  MG   (  14-)  E  -  -.-  -.-  Too few ligands (1)
 159  MG   (  14-)  G  -  -.-  -.-  Too few ligands (0)
 160  MG   (  15-)  A  -  -.-  -.-  Too few ligands (0)
 161  MG   (  16-)  H  -  -.-  -.-  Too few ligands (0)
Since there are no waters, the water check has been skipped.

Final summary