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 pdb3r1c.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    =  39.697  B   =  76.891  C    =  85.398
    Alpha=  89.980  Beta=  88.610  Gamma=  77.290

Dimensions of a reduced cell

    A    =  39.697  B   =  76.891  C    =  85.398
    Alpha=  89.980  Beta=  91.390  Gamma= 102.710

Dimensions of the conventional cell

    A    =  39.697  B   =  76.891  C    =  85.398
    Alpha=  89.980  Beta=  91.390  Gamma= 102.710

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

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: P 1
Number of matrices in space group: 1
Highest polymer chain multiplicity in structure: 36
Highest polymer chain multiplicity according to SEQRES: 16
There is also strong SEQRES evidence for a multiplicity of: 36
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 36
Polymer chain multiplicity and SEQRES multiplicity disagree 36 16
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) too low

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 94041.781
Volume of the Unit Cell V= 254209.109
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z low: Vm= 1.201
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.720 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

 289 SO4   (   9-)  S  -
 290 SO4   (   9-)  W  -
 291 SO4   (   9-)  X  -
 292 SO4   (   9-)  B  -
 293 SO4   (   9-)  C  -
 294 SO4   (   9-)  D  -
 295 SO4   (   9-)  E  -

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

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

Nomenclature related problems

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): A, B, C, D, E, F, G, H, I, J

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.

 139 OGUA  (   3-)  R  -   O5'  C5'   1.38   -4.0
 285 OCYT  (   5-)  J  -   C1'  N1    1.52    4.2

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 OGUA  (   1-)  A  -   C4'  C3'  C2'  98.45   -4.2
   1 OGUA  (   1-)  A  -   N9   C8   N7  113.43    4.7
   4 OGUA  (   4-)  A  -   N9   C8   N7  113.22    4.2
   6 OGUA  (   6-)  A  -   N9   C8   N7  113.80    5.4
   9 OGUA  (   1-)  B  -   N9   C8   N7  113.15    4.1
  11 OGUA  (   3-)  B  -   C4'  C3'  C2'  97.77   -4.9
  11 OGUA  (   3-)  B  -   N9   C8   N7  113.17    4.1
  12 OGUA  (   4-)  B  -   N9   C8   N7  113.44    4.7
  14 OGUA  (   6-)  B  -   N9   C8   N7  113.61    5.0
  17 OGUA  (   1-)  C  -   N9   C8   N7  113.30    4.4
  19 OGUA  (   3-)  C  -   C4'  C3'  C2'  98.28   -4.4
  19 OGUA  (   3-)  C  -   N9   C8   N7  113.73    5.3
  22 OGUA  (   6-)  C  -   N9   C8   N7  113.19    4.2
  25 OGUA  (   1-)  D  -   N9   C8   N7  113.23    4.3
  28 OGUA  (   4-)  D  -   N9   C8   N7  113.14    4.1
  30 OGUA  (   6-)  D  -   C4'  C3'  C2'  98.62   -4.1
  30 OGUA  (   6-)  D  -   O4'  C1'  N9  112.45    4.3
  30 OGUA  (   6-)  D  -   N9   C8   N7  113.60    5.0
  31 OGUA  (   7-)  D  -   N9   C8   N7  113.48    4.8
  33 OGUA  (   1-)  E  -   N9   C8   N7  113.50    4.8
  35 OGUA  (   3-)  E  -   C4'  C3'  C2'  98.00   -4.7
  36 OGUA  (   4-)  E  -   N9   C8   N7  113.77    5.3
  38 OGUA  (   6-)  E  -   N9   C8   N7  113.90    5.6
  39 OGUA  (   7-)  E  -   N9   C8   N7  113.32    4.4
  41 OGUA  (   1-)  F  -   N9   C8   N7  113.21    4.2
And so on for a total of 164 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.

  19 OGUA  (   3-)  C  -   N7  <->   30 OGUA  (   6-)  D  -   N2     0.39    2.61  INTRA
 246 OGUA  (   6-)  E  -   N2  <->  251 OGUA  (   3-)  F  -   N7     0.35    2.65  INTRA BL
 278 OGUA  (   6-)  I  -   N2  <->  283 OGUA  (   3-)  J  -   N7     0.32    2.68  INTRA
 134 OGUA  (   6-)  Q  -   N7  <->  139 OGUA  (   3-)  R  -   N2     0.31    2.69  INTRA BL
 150 OGUA  (   6-)  S  -   N7  <->  155 OGUA  (   3-)  Y  -   N2     0.30    2.70  INTRA BF
 259 OGUA  (   3-)  G  -   N2  <->  270 OGUA  (   6-)  H  -   N7     0.30    2.70  INTRA BL
 275 OGUA  (   3-)  I  -   N2  <->  286 OGUA  (   6-)  J  -   N7     0.30    2.70  INTRA
 179 OGUA  (   3-)  W  -   N7  <->  190 OGUA  (   6-)  X  -   N2     0.29    2.71  INTRA BL
  70 OGUA  (   6-)  I  -   N2  <->   75 OGUA  (   3-)  J  -   N7     0.29    2.71  INTRA BL
 214 OGUA  (   6-)  A  -   N7  <->  219 OGUA  (   3-)  B  -   N2     0.28    2.72  INTRA BF
  38 OGUA  (   6-)  E  -   N2  <->   43 OGUA  (   3-)  F  -   N7     0.28    2.72  INTRA BL
 102 OGUA  (   6-)  M  -   N7  <->  107 OGUA  (   3-)  N  -   N2     0.27    2.73  INTRA
 198 OGUA  (   6-)  V  -   N7  <->  203 OGUA  (   3-)  Z  -   N2     0.25    2.75  INTRA
 118 OGUA  (   6-)  O  -   N7  <->  123 OGUA  (   3-)  P  -   N2     0.25    2.75  INTRA BL
 149 OCYT  (   5-)  S  -   N3  <->  156 OGUA  (   4-)  Y  -   N1     0.24    2.76  INTRA BF
 273 OGUA  (   1-)  I  -   N1  <->  288 OCYT  (   8-)  J  -   N3     0.24    2.76  INTRA
 242 OCYT  (   2-)  E  -   N3  <->  255 OGUA  (   7-)  F  -   N1     0.24    2.76  INTRA BL
 148 OGUA  (   4-)  S  -   N2  <->  158 OGUA  (   6-)  Y  -   C8     0.23    2.87  INTRA BF
  22 OGUA  (   6-)  C  -   N2  <->   27 OGUA  (   3-)  D  -   N7     0.23    2.77  INTRA BL
  35 OGUA  (   3-)  E  -   N2  <->   46 OGUA  (   6-)  F  -   N7     0.22    2.78  INTRA BL
 103 OGUA  (   7-)  M  -   N1  <->  106 OCYT  (   2-)  N  -   N3     0.21    2.79  INTRA
 166 OGUA  (   6-)  T  -   N7  <->  171 OGUA  (   3-)  U  -   N2     0.21    2.79  INTRA BL
 213 OCYT  (   5-)  A  -   N3  <->  220 OGUA  (   4-)  B  -   N1     0.21    2.79  INTRA BF
 135 OGUA  (   7-)  Q  -   N1  <->  138 OCYT  (   2-)  R  -   N3     0.21    2.79  INTRA BL
 243 OGUA  (   3-)  E  -   N7  <->  254 OGUA  (   6-)  F  -   N2     0.21    2.79  INTRA BL
And so on for a total of 187 lines.

Water, ion, and hydrogenbond related checks

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.

 319 HOH   (  60 )  X    B 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.

  12 OGUA  (   4-)  B  -   N2
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

Final summary