WHAT IF Check report

This file was created 2011-12-18 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 pdb1tn1.ent

Checks that need to be done early-on in validation

Warning: Non-triclinic cell with acute angle

The crystallographic unit cell does not conform to the convention that all non-orthogonal angles in a non-triclinic cell should be obtuse.

The CRYST1 cell dimensions

    A    =  56.700  B   =  33.200  C    =  63.000
    Alpha=  90.000  Beta=  89.900  Gamma=  90.000

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  56.700  B   =  33.200  C    =  63.000
    Alpha=  90.000  Beta=  89.900  Gamma=  90.000

Dimensions of a reduced cell

    A    =  33.200  B   =  56.700  C    =  63.000
    Alpha=  89.900  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  33.200  B   =  56.700  C    =  63.000
    Alpha=  90.100  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

  85 SPM   (  77-)  A  -

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. 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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 OGUA  (   1-)  A  -   N9   C8    1.41    5.0
   1 OGUA  (   1-)  A  -   C8   N7    1.42   19.4
   1 OGUA  (   1-)  A  -   C5   C4    1.41    4.0
   1 OGUA  (   1-)  A  -   N3   C4    1.39    6.4
   1 OGUA  (   1-)  A  -   C5   C6    1.38   -4.3
   1 OGUA  (   1-)  A  -   C6   N1    1.34   -7.1
   2 OCYT  (   2-)  A  -   N1   C6    1.32   -7.8
   2 OCYT  (   2-)  A  -   C6   C5    1.39    7.0
   2 OCYT  (   2-)  A  -   C4   N3    1.30   -5.5
   2 OCYT  (   2-)  A  -   C5   C4    1.39   -4.5
   3 OGUA  (   3-)  A  -   C1'  N9    1.51    5.3
   3 OGUA  (   3-)  A  -   N9   C8    1.44    9.5
   3 OGUA  (   3-)  A  -   C8   N7    1.44   22.4
   3 OGUA  (   3-)  A  -   N1   C2    1.32   -6.2
   3 OGUA  (   3-)  A  -   C5   C6    1.37   -5.1
   3 OGUA  (   3-)  A  -   C6   N1    1.31  -11.6
   4 OGUA  (   4-)  A  -   C3'  C2'   1.48   -4.5
   4 OGUA  (   4-)  A  -   N9   C8    1.42    6.4
   4 OGUA  (   4-)  A  -   C8   N7    1.44   23.2
   4 OGUA  (   4-)  A  -   C5   C4    1.41    4.2
   4 OGUA  (   4-)  A  -   C2   N3    1.29   -4.7
   4 OGUA  (   4-)  A  -   C5   C6    1.38   -4.3
   4 OGUA  (   4-)  A  -   C6   N1    1.33   -9.1
   5 OADE  (   5-)  A  -   N9   C8    1.42    5.7
   5 OADE  (   5-)  A  -   N9   C4    1.33   -7.6
And so on for a total of 346 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: 2.954
RMS-deviation in bond distances: 0.026

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  -   C2'  C1'  N9  103.46   -6.2
   1 OGUA  (   1-)  A  -   N9   C8   N7  108.81   -4.6
   1 OGUA  (   1-)  A  -   N9   C4   C5  109.54   10.4
   1 OGUA  (   1-)  A  -   N9   C4   N3  134.78   14.6
   1 OGUA  (   1-)  A  -   N7   C5   C4  108.64   -5.4
   1 OGUA  (   1-)  A  -   C5   C6   O6  118.55  -16.8
   1 OGUA  (   1-)  A  -   C5   C6   N1  117.86   12.7
   1 OGUA  (   1-)  A  -   C5   C4   N3  115.64  -25.9
   1 OGUA  (   1-)  A  -   C6   N1   C2  121.28   -6.4
   1 OGUA  (   1-)  A  -   C6   C5   C4  122.20    5.7
   1 OGUA  (   1-)  A  -   O6   C6   N1  123.59    6.2
   1 OGUA  (   1-)  A  -   N1   C2   N2  120.03    4.3
   1 OGUA  (   1-)  A  -   C2   N3   C4  120.82   17.8
   2 OCYT  (   2-)  A  -   C3'  C4'  C5' 108.23   -4.8
   2 OCYT  (   2-)  A  -   O5'  C5'  C4' 101.11   -6.5
   2 OCYT  (   2-)  A  -   C6   C5   C4  119.56    4.3
   2 OCYT  (   2-)  A  -   C5   C4   N3  119.31   -6.5
   2 OCYT  (   2-)  A  -   N3   C2   O2  118.08   -5.5
   3 OGUA  (   3-)  A  -   P    O5'  C5' 112.07   -5.5
   3 OGUA  (   3-)  A  -   N9   C8   N7  108.97   -4.3
   3 OGUA  (   3-)  A  -   N9   C4   C5  110.55   12.9
   3 OGUA  (   3-)  A  -   N9   C4   N3  135.03   15.0
   3 OGUA  (   3-)  A  -   N7   C5   C6  127.79   -4.3
   3 OGUA  (   3-)  A  -   C5   C6   O6  118.16  -17.4
   3 OGUA  (   3-)  A  -   C5   C6   N1  117.98   13.0
And so on for a total of 565 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: 3.083
RMS-deviation in bond angles: 3.132

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

  53 OGUA  (  53-)  A  -   0.12
  19 OGUA  (  19-)  A  -   0.12
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no torsion angle evaluation was performed.
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no rotamer check was performed.
Since there is no protein, no backbone conformation check was performed.
Since there is no protein, no ramachandran check was performed.
Since there is no protein, no backbone oxygen evaluation was performed.

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.

  86 HOH   (  86 )  A      O   <->   86 HOH   ( 163 )  A      O      1.85    0.35  INTRA
  23 OADE  (  23-)  A  -   P   <->   86 HOH   ( 162 )  A      O      1.63    1.37  INTRA
  85 SPM   (  77-)  A  -   N10 <->   86 HOH   ( 182 )  A      O      1.11    1.59  INTRA
   3 OGUA  (   3-)  A  -   P   <->   86 HOH   ( 152 )  A      O      0.97    2.03  INTRA
  85 SPM   (  77-)  A  -   C8  <->   86 HOH   ( 182 )  A      O      0.89    1.91  INTRA
  86 HOH   ( 181 )  A      O   <->   86 HOH   ( 190 )  A      O      0.88    1.32  INTRA
   3 OGUA  (   3-)  A  -   OP2 <->   86 HOH   ( 152 )  A      O      0.87    1.53  INTRA
  23 OADE  (  23-)  A  -   OP2 <->   86 HOH   ( 162 )  A      O      0.83    1.57  INTRA
  85 SPM   (  77-)  A  -   C9  <->   86 HOH   ( 182 )  A      O      0.81    1.99  INTRA
  83  PB   (  84-)  A  -  PB   <->   85 SPM   (  77-)  A  -   C8     0.76    2.04  INTRA B3
  79  MG   (  80-)  A  -  MG   <->   82  PB   (  83-)  A  -  PB      0.72    2.48  INTRA
  85 SPM   (  77-)  A  -   N10 <->   86 HOH   ( 181 )  A      O      0.71    1.99  INTRA
  85 SPM   (  77-)  A  -   C11 <->   86 HOH   ( 181 )  A      O      0.69    2.11  INTRA
  73 OADE  (  73-)  A  -   C8  <->   86 HOH   ( 119 )  A      O      0.68    2.12  INTRA
  65 OGUA  (  65-)  A  -   C1' <->   86 HOH   ( 115 )  A      O      0.67    2.13  INTRA
  47 OURA  (  47-)  A  -   C5  <->   86 HOH   ( 101 )  A      O      0.65    2.15  INTRA
  15 OGUA  (  15-)  A  -   C2' <->   86 HOH   ( 102 )  A      O      0.64    2.16  INTRA
  85 SPM   (  77-)  A  -   C12 <->   86 HOH   ( 181 )  A      O      0.63    2.17  INTRA
  62 OADE  (  62-)  A  -   P   <->   86 HOH   ( 169 )  A      O      0.61    2.39  INTRA
  23 OADE  (  23-)  A  -   O5' <->   86 HOH   ( 162 )  A      O      0.56    1.84  INTRA
  48 OCYT  (  48-)  A  -   P   <->   86 HOH   ( 163 )  A      O      0.54    2.46  INTRA
  48 OCYT  (  48-)  A  -   P   <->   86 HOH   (  86 )  A      O      0.50    2.50  INTRA
  22 OGUA  (  22-)  A  -   C3' <->   86 HOH   ( 162 )  A      O      0.49    2.31  INTRA
  15 OGUA  (  15-)  A  -   O2' <->   86 HOH   ( 102 )  A      O      0.48    1.92  INTRA
  67 OADE  (  67-)  A  -   O2' <->   86 HOH   (  95 )  A      O      0.45    1.95  INTRA
And so on for a total of 97 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.

  86 HOH   (  87 )  A      O     46.87   27.24   40.50
  86 HOH   (  88 )  A      O     43.37   -8.28   11.40
  86 HOH   (  92 )  A      O     45.84   25.38   35.49
  86 HOH   (  94 )  A      O     44.91   -3.38   30.29
  86 HOH   (  96 )  A      O     45.42   -9.65   15.42
  86 HOH   (  98 )  A      O     49.68   -4.79   10.69
  86 HOH   ( 100 )  A      O     43.59   -9.34    1.86
  86 HOH   ( 104 )  A      O     47.23   -7.64   12.11
  86 HOH   ( 114 )  A      O     49.14   -4.27   23.21
  86 HOH   ( 117 )  A      O     53.92   -5.00   11.21
  86 HOH   ( 120 )  A      O     26.00  -12.77   59.42
  86 HOH   ( 122 )  A      O     53.61  -12.27   -2.10
  86 HOH   ( 123 )  A      O     34.10   -4.85   -0.17
  86 HOH   ( 125 )  A      O     47.61   -2.45   11.09
  86 HOH   ( 128 )  A      O     56.36   22.71   45.81
  86 HOH   ( 132 )  A      O     40.62   -3.75    5.25
  86 HOH   ( 134 )  A      O     42.64   23.87   35.39
  86 HOH   ( 136 )  A      O     29.19   13.73   35.25
  86 HOH   ( 137 )  A      O     28.92   -1.31   24.51
  86 HOH   ( 138 )  A      O     48.03   30.49   40.56
  86 HOH   ( 141 )  A      O     48.60   -9.22   17.29
  86 HOH   ( 143 )  A      O     46.45   20.68   47.78
  86 HOH   ( 146 )  A      O     30.63   -3.95    9.59
  86 HOH   ( 147 )  A      O     48.20   10.16   54.49
  86 HOH   ( 148 )  A      O     31.91   -3.73    7.12
  86 HOH   ( 153 )  A      O     32.95   -4.54   57.85
  86 HOH   ( 154 )  A      O     20.62  -10.30   57.16
  86 HOH   ( 155 )  A      O     39.11    9.88   44.97
  86 HOH   ( 156 )  A      O     42.76   10.69   44.29
  86 HOH   ( 157 )  A      O     44.17    5.22   43.63
  86 HOH   ( 160 )  A      O     55.32   -6.80    5.68
  86 HOH   ( 161 )  A      O     41.50   -2.52    7.60
  86 HOH   ( 167 )  A      O     46.28   -0.72   10.74
  86 HOH   ( 168 )  A      O     45.78    0.09   12.76
  86 HOH   ( 174 )  A      O     30.84   -4.00   26.81
  86 HOH   ( 176 )  A      O     37.40    8.19   53.43
  86 HOH   ( 178 )  A      O     45.78   -3.07   10.65
  86 HOH   ( 180 )  A      O     41.71   -0.96   56.49
  86 HOH   ( 183 )  A      O     47.28   -6.28   22.75
  86 HOH   ( 184 )  A      O     50.41  -14.23   13.66
  86 HOH   ( 187 )  A      O     40.74   -9.66   17.18
  86 HOH   ( 188 )  A      O     43.68    8.15   42.56
  86 HOH   ( 191 )  A      O     55.28   -4.26   -8.88

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.

  86 HOH   ( 122 )  A      O
  86 HOH   ( 123 )  A      O
  86 HOH   ( 124 )  A      O
  86 HOH   ( 126 )  A      O
  86 HOH   ( 128 )  A      O
  86 HOH   ( 130 )  A      O
  86 HOH   ( 131 )  A      O
  86 HOH   ( 140 )  A      O
  86 HOH   ( 142 )  A      O
  86 HOH   ( 147 )  A      O
  86 HOH   ( 158 )  A      O
  86 HOH   ( 160 )  A      O
  86 HOH   ( 172 )  A      O
  86 HOH   ( 176 )  A      O
  86 HOH   ( 180 )  A      O
  86 HOH   ( 184 )  A      O
  86 HOH   ( 189 )  A      O
  86 HOH   ( 191 )  A      O
  86 HOH   ( 192 )  A      O
ERROR. Strange cone in HB2INI
Affected atom   10 2MG  (  10-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   16 H2U  (  16-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   17 H2U  (  17-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   26 M2G  (  26-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   32 OMC  (  32-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   34 OMG  (  34-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   37  YG  (  37-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   39 PSU  (  39-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   40 5MC  (  40-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   46 7MG  (  46-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   49 5MC  (  49-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   54 5MU  (  54-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   55 PSU  (  55-) A  -   P
ERROR. Strange cone in HB2INI
Affected atom   58 1MA  (  58-) A  -   P
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
Expected ambiguity-2 in FILL1HARR 0 1 170
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.

   9 OADE  (   9-)  A  -   N6
  11 OCYT  (  11-)  A  -   N4
  14 OADE  (  14-)  A  -   N6
  18 OGUA  (  18-)  A  -   N1
  18 OGUA  (  18-)  A  -   N2
  25 OCYT  (  25-)  A  -   N4
  30 OGUA  (  30-)  A  -   N1
  45 OGUA  (  45-)  A  -   N1
  45 OGUA  (  45-)  A  -   N2
  59 OURA  (  59-)  A  -   N3
  65 OGUA  (  65-)  A  -   N1
Since there is no protein, no check for buried unsatisfied hydrogen
bond acceptors was performed.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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+.

  77  MG   (  78-)  A  -    0.44   0.88 Is perhaps NA (Few ligands (4) )
  78  MG   (  79-)  A  -    0.73   1.40 Scores about as good as CA (Few ligands (4) )
  79  MG   (  80-)  A  -  -.-  -.-  Part of ionic cluster
  79  MG   (  80-)  A  -  -.-  -.-  Too few ligands (1)
  80  MG   (  81-)  A  -    0.67   1.34 Scores about as good as NA (Few ligands (4) )
  81  MG   (  82-)  A  -  -.-  -.-  Too few ligands (0)

Final summary