WHAT IF Check report

This file was created 2012-01-19 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 pdb244d.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.

 100  CA   ( 177-)  D  A
 101  CA   ( 179-)  D  A
 102  NA   ( 164-)  A  B
 103  CA   ( 178-)  A  B
 104  CA   ( 176-)  B  C
 105  CA   ( 175-)  C  D
 108  NA   ( 169-)  G  E
 109  NA   ( 158-)  L  I
 111  NA   ( 167-)  J  I
 112  NA   ( 162-)  K  L
 116  NA   ( 168-)  N  M
 117  CA   ( 171-)  P  M
 118  CA   ( 173-)  M  N
 119  CA   ( 172-)  O  P

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.

  97  NA   ( 159-)  A  -
  98  NA   ( 160-)  A  -
  99  NA   ( 170-)  A  -
 106  NA   ( 161-)  E  -
 107  NA   ( 165-)  E  -
 108  NA   ( 169-)  G  E
 109  NA   ( 158-)  L  I
 110  NA   ( 166-)  I  -
 111  NA   ( 167-)  J  I
 112  NA   ( 162-)  K  L
 114  NA   ( 157-)  M  -
 115  NA   ( 163-)  M  -
 116  NA   ( 168-)  N  M

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  12 DTHY  (  16-)  B  -   C3'
  12 DTHY  (  16-)  B  -   O3'
  12 DTHY  (  16-)  B  -   O5'
  12 DTHY  (  16-)  B  -   C5'
  12 DTHY  (  16-)  B  -   C4'
  12 DTHY  (  16-)  B  -   O4'
  12 DTHY  (  16-)  B  -   C1'
  12 DTHY  (  16-)  B  -   C2'
  12 DTHY  (  16-)  B  -   N1
  12 DTHY  (  16-)  B  -   C6
  12 DTHY  (  16-)  B  -   C5
  12 DTHY  (  16-)  B  -   C4
  12 DTHY  (  16-)  B  -   O4
  12 DTHY  (  16-)  B  -   N3
  12 DTHY  (  16-)  B  -   C2
  12 DTHY  (  16-)  B  -   O2
  12 DTHY  (  16-)  B  -   C7
  13 DTHY  (  21-)  C  -   C3'
  13 DTHY  (  21-)  C  -   O5'
  13 DTHY  (  21-)  C  -   C5'
  13 DTHY  (  21-)  C  -   C4'
  13 DTHY  (  21-)  C  -   O4'
  13 DTHY  (  21-)  C  -   C1'
  13 DTHY  (  21-)  C  -   C2'
  13 DTHY  (  21-)  C  -   N1
And so on for a total of 84 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:

Crystal temperature (K) :277.000

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 DTHY  (   1-)  A  -   C5   C7    1.53    4.9
   2 DGUA  (   2-)  A  -   C5   C4    1.41    5.0
   2 DGUA  (   2-)  A  -   N1   C2    1.43    6.6
   3 DGUA  (   3-)  A  -   N9   C8    1.40    4.2
   4 DGUA  (   4-)  A  -   O4'  C1'   1.47    4.0
   6 DTHY  (   6-)  A  -   O4'  C1'   1.50    5.9
   6 DTHY  (   6-)  A  -   C1'  C2'   1.46   -4.4
   7 DTHY  (  11-)  B  -   C2   O2    1.25    4.3
   7 DTHY  (  11-)  B  -   C5   C7    1.52    4.5
  11 DGUA  (  15-)  B  -   C4'  O4'   1.49    4.2
  15 DGUA  (  23-)  C  -   O4'  C1'   1.48    4.9
  15 DGUA  (  23-)  C  -   N9   C8    1.34   -4.2
  15 DGUA  (  23-)  C  -   C2   N3    1.37    6.2
  15 DGUA  (  23-)  C  -   C6   O6    1.28    5.1
  16 DGUA  (  24-)  C  -   O4'  C1'   1.48    4.3
  17 DGUA  (  25-)  C  -   N7   C5    1.36   -4.5
  19 DTHY  (  31-)  D  -   C4'  C3'   1.48   -4.3
  19 DTHY  (  31-)  D  -   C5   C7    1.53    5.1
  20 DGUA  (  32-)  D  -   C1'  C2'   1.58    4.0
  20 DGUA  (  32-)  D  -   N3   C4    1.39    5.7
  21 DGUA  (  33-)  D  -   N1   C2    1.41    4.6
  21 DGUA  (  33-)  D  -   C6   O6    1.28    4.4
  22 DGUA  (  34-)  D  -   O4'  C1'   1.49    5.2
  23 DGUA  (  35-)  D  -   O4'  C1'   1.48    4.6
  24 DTHY  (  36-)  D  -   C5   C7    1.53    5.4
And so on for a total of 113 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: 2.064
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 DTHY  (   1-)  A  -   O4'  C1'  N1  103.33   -5.6
   1 DTHY  (   1-)  A  -   N1   C6   C5  120.04   -6.1
   1 DTHY  (   1-)  A  -   C5   C4   O4  122.07   -4.0
   1 DTHY  (   1-)  A  -   C5   C4   N3  117.85    4.4
   1 DTHY  (   1-)  A  -   C4   N3   C2  123.38   -6.4
   2 DGUA  (   2-)  A  -   P   -C3* -O3* 125.38    4.7
   2 DGUA  (   2-)  A  -   O4'  C1'  N9  111.18    4.2
   2 DGUA  (   2-)  A  -   N9   C8   N7  113.36    4.5
   2 DGUA  (   2-)  A  -   N7   C5   C4  109.06   -4.4
   2 DGUA  (   2-)  A  -   C5   C6   O6  124.80   -6.3
   2 DGUA  (   2-)  A  -   O6   C6   N1  123.41    5.8
   2 DGUA  (   2-)  A  -   C2   N3   C4  114.18    4.6
   3 DGUA  (   3-)  A  -   P   -C3* -O3* 125.42    4.8
   3 DGUA  (   3-)  A  -   C5   C6   N1  114.35    5.7
   4 DGUA  (   4-)  A  -   O4'  C1'  N9  102.16   -7.1
   4 DGUA  (   4-)  A  -   N9   C8   N7  114.88    7.6
   4 DGUA  (   4-)  A  -   C8   N9   C4  103.27   -7.8
   5 DGUA  (   5-)  A  -   C8   N9   C4  108.02    4.0
   5 DGUA  (   5-)  A  -   C5   C6   O6  126.14   -4.1
   5 DGUA  (   5-)  A  -   C5   C6   N1  114.72    6.4
   5 DGUA  (   5-)  A  -   N1   C2   N3  121.01   -4.8
   5 DGUA  (   5-)  A  -   C2   N3   C4  116.27    8.7
   6 DTHY  (   6-)  A  -   P   -C3* -O3* 124.70    4.2
   6 DTHY  (   6-)  A  -   O4'  C1'  N1  100.31   -9.4
   6 DTHY  (   6-)  A  -   N1   C6   C5  119.62   -6.8
And so on for a total of 399 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.547
RMS-deviation in bond angles: 2.492

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.

  52 DGUA  (  84-)  I  -   N2  <->   70 DGUA  ( 114-)  L  -   N7     0.22    2.78  INTRA BL
  27 DGUA  (  43-)  E  -   N7  <->   33 DGUA  (  53-)  F  -   N2     0.20    2.80  INTRA BL
  32 DGUA  (  52-)  F  -   N7  <->   38 DGUA  (  62-)  G  -   N2     0.19    2.81  INTRA BL
  88 DGUA  ( 144-)  O  -   N7  <->   94 DGUA  ( 154-)  P  -   N2     0.19    2.81  INTRA BL
   2 DGUA  (   2-)  A  -   N7  <->    8 DGUA  (  12-)  B  -   N2     0.19    2.81  INTRA BL
  63 DGUA  ( 103-)  K  -   N7  <->   69 DGUA  ( 113-)  L  -   N2     0.18    2.82  INTRA BL
  89 DGUA  ( 145-)  O  -   N7  <->   95 DGUA  ( 155-)  P  -   N2     0.18    2.82  INTRA BL
  10 DGUA  (  14-)  B  -   N7  <->   16 DGUA  (  24-)  C  -   N2     0.17    2.83  INTRA BL
  35 DGUA  (  55-)  F  -   N7  <->   41 DGUA  (  65-)  G  -   N2     0.17    2.83  INTRA BL
  74 DGUA  ( 122-)  M  -   N2  <->   92 DGUA  ( 152-)  P  -   N7     0.17    2.83  INTRA BL
  50 DGUA  (  82-)  I  -   N2  <->   68 DGUA  ( 112-)  L  -   N7     0.17    2.83  INTRA BL
  86 DGUA  ( 142-)  O  -   N7  <->   92 DGUA  ( 152-)  P  -   N2     0.17    2.83  INTRA BL
   3 DGUA  (   3-)  A  -   P   <->  120 HOH   ( 384 )  A      O      0.16    2.84  INTRA
  77 DGUA  ( 125-)  M  -   N7  <->   83 DGUA  ( 135-)  N  -   N2     0.16    2.84  INTRA BL
  40 DGUA  (  64-)  G  -   N7  <->   46 DGUA  (  74-)  H  -   N2     0.16    2.84  INTRA BL
  53 DGUA  (  85-)  I  -   N2  <->   71 DGUA  ( 115-)  L  -   N7     0.16    2.84  INTRA BL
  76 DGUA  ( 124-)  M  -   N2  <->   94 DGUA  ( 154-)  P  -   N7     0.16    2.84  INTRA BL
  64 DGUA  ( 104-)  K  -   N7  <->   70 DGUA  ( 114-)  L  -   N2     0.16    2.84  INTRA BL
  16 DGUA  (  24-)  C  -   N7  <->   22 DGUA  (  34-)  D  -   N2     0.16    2.84  INTRA BL
  26 DGUA  (  42-)  E  -   N7  <->   32 DGUA  (  52-)  F  -   N2     0.15    2.85  INTRA BL
   4 DGUA  (   4-)  A  -   N2  <->   22 DGUA  (  34-)  D  -   N7     0.15    2.85  INTRA BL
  56 DGUA  (  92-)  J  -   N7  <->   62 DGUA  ( 102-)  K  -   N2     0.15    2.85  INTRA BL
  27 DGUA  (  43-)  E  -   N2  <->   45 DGUA  (  73-)  H  -   N7     0.15    2.85  INTRA BL
  50 DGUA  (  82-)  I  -   N7  <->   56 DGUA  (  92-)  J  -   N2     0.15    2.85  INTRA BL
  58 DGUA  (  94-)  J  -   N7  <->   64 DGUA  ( 104-)  K  -   N2     0.15    2.85  INTRA BL
And so on for a total of 80 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.

 120 HOH   ( 478 )  A      O     15.26   -4.50  -10.65
 122 HOH   ( 547 )  C      O    -10.33   15.55   39.82
 123 HOH   ( 574 )  D      O     -8.12   13.42   42.76
 123 HOH   ( 676 )  D      O     17.01    6.37   40.36
 124 HOH   ( 662 )  E      O     16.86   34.05   33.11
 127 HOH   ( 683 )  H      O     14.36   -0.45   39.35
 130 HOH   ( 593 )  K      O      8.66   -7.83   12.80
 132 HOH   ( 652 )  M      O     23.52   13.55   16.79
 135 HOH   ( 491 )  P      O     -6.66    5.05   27.75

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+.

  97  NA   ( 159-)  A  -  -.-  -.-  Part of ionic cluster
  97  NA   ( 159-)  A  -    0.58   0.98 Is perhaps  K
  98  NA   ( 160-)  A  -  -.-  -.-  Part of ionic cluster
  98  NA   ( 160-)  A  -    0.64   1.14 Is perhaps  K
  99  NA   ( 170-)  A  -  -.-  -.-  Part of ionic cluster
  99  NA   ( 170-)  A  -    1.20   0.95 Scores about as good as CA *1
 100  CA   ( 177-)  D  A    0.84   1.09 Scores about as good as NA *1
 101  CA   ( 179-)  D  A    0.79   1.03 Scores about as good as NA *1
 102  NA   ( 164-)  A  B  -.-  -.-  Part of ionic cluster
 102  NA   ( 164-)  A  B   0.73  -.-   Poor packing
 103  CA   ( 178-)  A  B    0.80   1.04 Scores about as good as NA *1
 104  CA   ( 176-)  B  C    0.79   1.03 Scores about as good as NA *1
 105  CA   ( 175-)  C  D    0.83   1.07 Scores about as good as NA *1
 106  NA   ( 161-)  E  -  -.-  -.-  Part of ionic cluster
 106  NA   ( 161-)  E  -    0.72   1.53 Scores about as good as  K
 107  NA   ( 165-)  E  -  -.-  -.-  Part of ionic cluster
 107  NA   ( 165-)  E  -   0.67  -.-   Poor packing
 108  NA   ( 169-)  G  E  -.-  -.-  Part of ionic cluster
 108  NA   ( 169-)  G  E    1.20   0.95 Scores about as good as CA *1
 109  NA   ( 158-)  L  I  -.-  -.-  Part of ionic cluster
 109  NA   ( 158-)  L  I    0.63   1.11 Is perhaps  K
 110  NA   ( 166-)  I  -  -.-  -.-  Part of ionic cluster
 110  NA   ( 166-)  I  -    1.20   0.96 Scores about as good as CA *1
 111  NA   ( 167-)  J  I  -.-  -.-  Part of ionic cluster
 111  NA   ( 167-)  J  I   0.66  -.-   Poor packing
 112  NA   ( 162-)  K  L  -.-  -.-  Part of ionic cluster
 112  NA   ( 162-)  K  L   0.72  -.-   Poor packing
 113  CA   ( 174-)  L  -    0.85   1.10 Scores about as good as NA *1
 114  NA   ( 157-)  M  -  -.-  -.-  Part of ionic cluster
 114  NA   ( 157-)  M  -    0.59   1.01 Is perhaps  K
 115  NA   ( 163-)  M  -  -.-  -.-  Part of ionic cluster
 115  NA   ( 163-)  M  -   0.67  -.-   Poor packing
 116  NA   ( 168-)  N  M  -.-  -.-  Part of ionic cluster
 116  NA   ( 168-)  N  M    1.18   0.93 Scores about as good as CA *1
 117  CA   ( 171-)  P  M    0.85   1.09 Scores about as good as NA *1
 118  CA   ( 173-)  M  N    0.79   1.03 Scores about as good as NA *1
 119  CA   ( 172-)  O  P    0.78   1.03 Scores about as good as NA *1

Final summary