WHAT IF Check report

This file was created 2011-12-17 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 pdb2qs6.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 13
Highest polymer chain multiplicity according to SEQRES: 14
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 56
Polymer chain multiplicity and SEQRES multiplicity disagree 13 14
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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'.

  71 DTHY  (   8-)  I  -   C3'
  71 DTHY  (   8-)  I  -   O3'
  71 DTHY  (   8-)  I  -   O5'
  71 DTHY  (   8-)  I  -   C5'
  71 DTHY  (   8-)  I  -   C4'
  71 DTHY  (   8-)  I  -   O4'
  71 DTHY  (   8-)  I  -   C1'
  71 DTHY  (   8-)  I  -   C2'
  71 DTHY  (   8-)  I  -   N1
  71 DTHY  (   8-)  I  -   C6
  71 DTHY  (   8-)  I  -   C5
  71 DTHY  (   8-)  I  -   C4
  71 DTHY  (   8-)  I  -   O4
  71 DTHY  (   8-)  I  -   N3
  71 DTHY  (   8-)  I  -   C2
  71 DTHY  (   8-)  I  -   O2
  71 DTHY  (   8-)  I  -   C7
 102 DCYT  (   7-)  M  -   N1
 102 DCYT  (   7-)  M  -   C6
 102 DCYT  (   7-)  M  -   C5
 102 DCYT  (   7-)  M  -   C4
 102 DCYT  (   7-)  M  -   N4
 102 DCYT  (   7-)  M  -   N3
 102 DCYT  (   7-)  M  -   C2
 102 DCYT  (   7-)  M  -   O2

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.

  31 DCYT  (   7-)  D  -   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: 1

Crystal temperature (K) :113.150

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.

  23 DCYT  (   7-)  C  -   C1'  N1    1.52    4.1
  31 DCYT  (   7-)  D  -   C1'  N1    1.57    8.0
  39 DCYT  (   7-)  E  -   C3'  O3'   1.49    4.3
  39 DCYT  (   7-)  E  -   C1'  N1    1.57    7.9
  47 DCYT  (   7-)  F  -   C1'  N1    1.54    6.2
  49 DTHY  (   2-)  G  -   O5'  C5'   1.37   -4.4
  53 DTHY  (   6-)  G  -   C1'  N1    1.53    4.1
  54 DCYT  (   7-)  G  -   C1'  N1    1.55    7.0
  55 DTHY  (   8-)  G  -   C5'  C4'   1.54    4.1
  55 DTHY  (   8-)  G  -   C1'  N1    1.54    4.9
  60 DADE  (   5-)  H  -   C3'  O3'   1.37   -4.8
  60 DADE  (   5-)  H  -   O5'  C5'   1.35   -5.5
  60 DADE  (   5-)  H  -   C4'  C3'   1.49   -4.1
  62 DCYT  (   7-)  H  -   N1   C6    1.34   -4.7
  70 DCYT  (   7-)  I  -   C1'  N1    1.56    7.5
  73 DTHY  (   2-)  J  -   C3'  C2'   1.56    4.2
  77 DTHY  (   6-)  J  -   C3'  O3'   1.37   -4.4
  79 DTHY  (   8-)  J  -   C1'  N1    1.53    4.2
  86 DCYT  (   7-)  K  -   C1'  N1    1.55    7.0
  91 DTHY  (   4-)  L  -   C1'  N1    1.53    4.2
  92 DADE  (   5-)  L  -   C3'  O3'   1.37   -4.7
  93 DTHY  (   6-)  L  -   C1'  N1    1.53    4.0
  94 DCYT  (   7-)  L  -   C1'  N1    1.55    6.9
  97 DTHY  (   2-)  M  -   C1'  N1    1.53    4.0
 110 DCYT  (   7-)  N  -   C1'  N1    1.53    5.0

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.

   2 DTHY  (   2-)  A  -   O4   C4   N3  122.33    4.0
   4 DTHY  (   4-)  A  -   O4   C4   N3  122.41    4.2
  10 DTHY  (   2-)  B  -   O4   C4   N3  122.33    4.1
  12 DTHY  (   4-)  B  -   O4'  C1'  N1  112.93    6.4
  12 DTHY  (   4-)  B  -   C5   C4   O4  122.10   -4.0
  12 DTHY  (   4-)  B  -   O4   C4   N3  122.42    4.2
  24 DTHY  (   8-)  C  -   C5   C4   O4  122.06   -4.1
  24 DTHY  (   8-)  C  -   O4   C4   N3  122.65    4.6
  32 DTHY  (   8-)  D  -   C5   C4   O4  122.06   -4.1
  32 DTHY  (   8-)  D  -   O4   C4   N3  122.42    4.2
  34 DTHY  (   2-)  E  -   C5   C4   O4  121.86   -4.3
  34 DTHY  (   2-)  E  -   O4   C4   N3  122.50    4.3
  38 DTHY  (   6-)  E  -   O4'  C1'  N1  112.63    6.0
  38 DTHY  (   6-)  E  -   O4   C4   N3  122.52    4.4
  44 DTHY  (   4-)  F  -   P   -C3* -O3* 124.95    4.4
  55 DTHY  (   8-)  G  -   P   -C3* -O3* 126.31    5.5
  55 DTHY  (   8-)  G  -   C4'  O4'  C1' 103.59   -4.4
  55 DTHY  (   8-)  G  -   O4'  C1'  N1  113.68    7.3
  57 DTHY  (   2-)  H  -   O4   C4   N3  122.34    4.1
  59 DTHY  (   4-)  H  -   O4   C4   N3  122.33    4.0
  67 DTHY  (   4-)  I  -   O4   C4   N3  122.62    4.5
  69 DTHY  (   6-)  I  -   O4   C4   N3  122.34    4.1
  76 DADE  (   5-)  J  -   O4'  C1'  N9  111.11    4.1
  77 DTHY  (   6-)  J  -   O4   C4   N3  122.62    4.5
  78 DCYT  (   7-)  J  -   O4'  C1'  N1  112.20    5.5
  85 DTHY  (   6-)  K  -   C5   C4   O4  121.91   -4.3
  85 DTHY  (   6-)  K  -   O4   C4   N3  122.79    4.8
  89 DTHY  (   2-)  L  -   O4   C4   N3  122.31    4.0
  91 DTHY  (   4-)  L  -   O4'  C1'  N1  111.01    4.0
  91 DTHY  (   4-)  L  -   C5   C4   O4  121.99   -4.2
  91 DTHY  (   4-)  L  -   O4   C4   N3  122.52    4.4
  93 DTHY  (   6-)  L  -   O4'  C1'  N1  111.27    4.3
  93 DTHY  (   6-)  L  -   C5   C4   O4  121.88   -4.3
  93 DTHY  (   6-)  L  -   O4   C4   N3  122.50    4.3
 107 DTHY  (   4-)  N  -   O4'  C1'  N1  112.02    5.3

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.

  37 DADE  (   5-)  E  -   N7  <->   42 DTHY  (   2-)  F  -   N3     0.59    2.41  INTRA BL
  68 DADE  (   5-)  I  -   N7  <->   73 DTHY  (   2-)  J  -   N3     0.55    2.45  INTRA BF
  80 DADE  (   1-)  K  -   N7  <->   93 DTHY  (   6-)  L  -   N3     0.53    2.47  INTRA BF
  84 DADE  (   5-)  K  -   N7  <->   89 DTHY  (   2-)  L  -   N3     0.51    2.49  INTRA BF
  96 DADE  (   1-)  M  -   N7  <->  109 DTHY  (   6-)  N  -   N3     0.50    2.50  INTRA BL
  22 DTHY  (   6-)  C  -   N3  <->   25 DADE  (   1-)  D  -   N7     0.47    2.53  INTRA BF
  33 DADE  (   1-)  E  -   N7  <->   46 DTHY  (   6-)  F  -   N3     0.42    2.58  INTRA BF
  20 DTHY  (   4-)  C  -   N3  <->   27 DADE  (   3-)  D  -   N7     0.42    2.58  INTRA BL
   5 DADE  (   5-)  A  -   OP2 <->  112 HOH   (  10 )  A      O      0.39    2.01  INTRA BL
  81 DTHY  (   2-)  K  -   N3  <->   92 DADE  (   5-)  L  -   N7     0.39    2.61  INTRA BF
  38 DTHY  (   6-)  E  -   N3  <->   41 DADE  (   1-)  F  -   N7     0.39    2.61  INTRA BL
  53 DTHY  (   6-)  G  -   N3  <->   56 DADE  (   1-)  H  -   N7     0.39    2.61  INTRA BL
  69 DTHY  (   6-)  I  -   C2  <->   80 DADE  (   1-)  K  -   C2     0.38    2.82  INTRA BL
  35 DADE  (   3-)  E  -   N7  <->   44 DTHY  (   4-)  F  -   N3     0.38    2.62  INTRA BL
  19 DADE  (   3-)  C  -   N7  <->   28 DTHY  (   4-)  D  -   N3     0.37    2.63  INTRA BF
 107 DTHY  (   4-)  N  -   O3' <->  124 HOH   (  25 )  N      O      0.36    2.04  INTRA BF
  35 DADE  (   3-)  E  -   N6  <->   44 DTHY  (   4-)  F  -   O4     0.35    2.35  INTRA BL
  83 DTHY  (   4-)  K  -   N3  <->   90 DADE  (   3-)  L  -   N7     0.35    2.65  INTRA BF
  49 DTHY  (   2-)  G  -   N3  <->   60 DADE  (   5-)  H  -   N7     0.34    2.66  INTRA BL
  97 DTHY  (   2-)  M  -   N3  <->  108 DADE  (   5-)  N  -   N7     0.34    2.66  INTRA BL
  27 DADE  (   3-)  D  -   N3  <->  115 HOH   (  50 )  D      O      0.33    2.37  INTRA BL
   6 DTHY  (   6-)  A  -   N3  <->    9 DADE  (   1-)  B  -   N7     0.32    2.68  INTRA BL
  52 DADE  (   5-)  G  -   N7  <->   57 DTHY  (   2-)  H  -   N3     0.31    2.69  INTRA BL
  51 DTHY  (   4-)  G  -   N3  <->   58 DADE  (   3-)  H  -   N7     0.31    2.69  INTRA BL
  85 DTHY  (   6-)  K  -   N3  <->   88 DADE  (   1-)  L  -   N7     0.31    2.69  INTRA BL
And so on for a total of 126 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.

 113 HOH   (  20 )  B      O    110.50  -33.67   84.20

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.

  70 DCYT  (   7-)  I  -   N4
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

Final summary