WHAT IF Check report

This file was created 2011-12-15 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 pdb3jyx.ent

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

 217 OCYT  ( 106-)  4  -              216 OADE  ( 104-)  4  -           3.7

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.

   1 OGUA  (   1-)  3  -   Zero
   2 OGUA  (   2-)  3  -   Zero
   3 OURA  (   3-)  3  -   Zero
   4 OURA  (   4-)  3  -   Zero
   5 OGUA  (   5-)  3  -   Zero
   6 OCYT  (   6-)  3  -   Zero
   7 OGUA  (   7-)  3  -   Zero
   8 OGUA  (   8-)  3  -   Zero
   9 OCYT  (   9-)  3  -   Zero
  10 OCYT  (  10-)  3  -   Zero
  11 OADE  (  11-)  3  -   Zero
  12 OURA  (  12-)  3  -   Zero
  13 OADE  (  13-)  3  -   Zero
  14 OURA  (  14-)  3  -   Zero
  15 OCYT  (  15-)  3  -   Zero
  16 OURA  (  16-)  3  -   Zero
  17 OADE  (  17-)  3  -   Zero
  18 OCYT  (  18-)  3  -   Zero
  19 OCYT  (  19-)  3  -   Zero
  20 OADE  (  20-)  3  -   Zero
  21 OGUA  (  21-)  3  -   Zero
  22 OADE  (  22-)  3  -   Zero
  23 OADE  (  23-)  3  -   Zero
  24 OADE  (  24-)  3  -   Zero
  25 OGUA  (  25-)  3  -   Zero
And so on for a total of 3439 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:

Temperature not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

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.

  11 OADE  (  11-)  3  -   C6   N6    1.37    4.1
  21 OGUA  (  21-)  3  -   C2   N3    1.36    4.2
  30 OGUA  (  30-)  3  -   C2   N3    1.36    4.3
  33 OURA  (  33-)  3  -   C1'  N1    1.51    4.3
  46 OADE  (  46-)  3  -   C5'  C4'   1.58    5.4
  51 OGUA  (  51-)  3  -   C2   N3    1.36    4.4
  62 OGUA  (  63-)  3  -   C2   N3    1.36    4.0
  71 OGUA  (  75-)  3  -   C2   N3    1.36    4.4
  75 OURA  (  79-)  3  -   C1'  N1    1.51    4.6
  91 OGUA  (  96-)  3  -   C2   N3    1.36    4.0
 101 OGUA  ( 106-)  3  -   C2   N3    1.36    4.2
 128 OGUA  (  15-)  4  -   C2   N3    1.36    4.2
 137 OGUA  (  24-)  4  -   C2   N3    1.36    4.3
 139 OURA  (  26-)  4  -   C1'  N1    1.51    4.8
 156 OADE  (  43-)  4  -   C6   N6    1.37    4.0
 161 OADE  (  48-)  4  -   C6   N6    1.37    4.2
 162 OGUA  (  49-)  4  -   C2   N3    1.36    4.3
 173 OURA  (  60-)  4  -   C5'  C4'   1.56    4.2
 176 OGUA  (  63-)  4  -   C2   N3    1.36    4.3
 181 OGUA  (  68-)  4  -   C2   N3    1.36    4.2
 183 OADE  (  70-)  4  -   C6   N6    1.37    4.0
 201 OADE  (  88-)  4  -   C6   N6    1.37    4.0
 215 OGUA  ( 103-)  4  -   C2   N3    1.36    4.3
 234 OGUA  ( 123-)  4  -   C2   N3    1.36    4.2
 285 OGUA  (  17-)  5  -   C2   N3    1.36    4.2
And so on for a total of 368 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 OGUA  (   1-)  3  -   N9   C8   N7  113.37    4.5
   1 OGUA  (   1-)  3  -   C5   C6   O6  124.51   -6.8
   1 OGUA  (   1-)  3  -   O6   C6   N1  125.02    8.5
   2 OGUA  (   2-)  3  -   O4'  C1'  N9  114.00    5.8
   2 OGUA  (   2-)  3  -   C5   C6   O6  125.60   -5.0
   2 OGUA  (   2-)  3  -   O6   C6   N1  123.72    6.4
   3 OURA  (   3-)  3  -   O4'  C1'  N1  113.38    5.2
   4 OURA  (   4-)  3  -   O4'  C1'  N1  114.01    5.8
   5 OGUA  (   5-)  3  -   O4'  C1'  N9  113.53    5.3
   5 OGUA  (   5-)  3  -   C5   C6   O6  126.10   -4.2
   5 OGUA  (   5-)  3  -   O6   C6   N1  123.46    5.9
   6 OCYT  (   6-)  3  -   O4'  C1'  N1  114.26    6.1
   6 OCYT  (   6-)  3  -   C5   C4   N3  120.07   -4.6
   6 OCYT  (   6-)  3  -   N4   C4   N3  121.21    4.6
   7 OGUA  (   7-)  3  -   O4'  C1'  N9  112.46    4.3
   7 OGUA  (   7-)  3  -   N9   C8   N7  113.45    4.7
   7 OGUA  (   7-)  3  -   C5   C6   O6  126.03   -4.3
   7 OGUA  (   7-)  3  -   O6   C6   N1  123.48    6.0
   8 OGUA  (   8-)  3  -   O4'  C1'  N9  112.48    4.3
   8 OGUA  (   8-)  3  -   N9   C8   N7  113.70    5.2
   8 OGUA  (   8-)  3  -   C5   C6   O6  124.83   -6.3
   8 OGUA  (   8-)  3  -   O6   C6   N1  124.76    8.1
   9 OCYT  (   9-)  3  -   O4'  C1'  N1  113.85    5.6
   9 OCYT  (   9-)  3  -   N4   C4   N3  120.91    4.2
  10 OCYT  (  10-)  3  -   O4'  C1'  N1  113.69    5.5
And so on for a total of 10156 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: 2.023
RMS-deviation in bond angles: 1.913

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.

1586 OURA  (1347-)  5  -   0.14
1649 OGUA  (1421-)  5  -   0.13
 277 OCYT  (   8-)  5  -   0.11
1723 OCYT  (1496-)  5  -   0.11
 601 OGUA  ( 337-)  5  -   0.11
1585 OGUA  (1346-)  5  -   0.11
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.

2676 OGUA  (2621-)  5  -   C8  <-> 2677 OCYT  (2622-)  5  -   C5     0.11    3.09  INTRA BL
1677 OADE  (1449-)  5  -   C2  <-> 2412 OADE  (2356-)  5  -   C4     0.09    3.11  INTRA BL
1076 OCYT  ( 818-)  5  -   C2  <-> 1177 OADE  ( 920-)  5  -   C8     0.08    3.12  INTRA BL
1480 OADE  (1240-)  5  -   C2  <-> 1488 OCYT  (1248-)  5  -   N3     0.08    3.02  INTRA BL
1232 OGUA  ( 975-)  5  -   C5  <-> 1233 OCYT  ( 976-)  5  -   N3     0.08    3.02  INTRA BL
2543 OURA  (2487-)  5  -   C6  <-> 2544 OADE  (2488-)  5  -   C8     0.07    3.13  INTRA BL
 918 OADE  ( 656-)  5  -   N1  <-> 1667 OURA  (1439-)  5  -   N3     0.06    2.94  INTRA BL
 758 OCYT  ( 496-)  5  -   N4  <->  876 OCYT  ( 614-)  5  -   C6     0.06    3.04  INTRA BL
  77 OURA  (  81-)  3  -   N3  <->   89 OADE  (  94-)  3  -   N1     0.06    2.94  INTRA BL
3118 OURA  (3068-)  5  -   N3  <-> 3123 OADE  (3073-)  5  -   N1     0.06    2.94  INTRA BL
1241 OADE  ( 990-)  5  -   C2  <-> 1308 OADE  (1061-)  5  -   C2     0.06    3.14  INTRA BL
2776 OURA  (2722-)  5  -   N3  <-> 2787 OADE  (2734-)  5  -   N1     0.05    2.95  INTRA BL
3197 OURA  (3148-)  5  -   C5  <-> 3198 OGUA  (3149-)  5  -   C5     0.05    3.15  INTRA BL
1236 OGUA  ( 979-)  5  -   C8  <-> 1237 OURA  ( 986-)  5  -   N3     0.05    3.05  INTRA BL
2216 OADE  (2158-)  5  -   C2  <-> 2218 OGUA  (2160-)  5  -   C5     0.05    3.15  INTRA BL
1371 OURA  (1125-)  5  -   N3  <-> 1379 OADE  (1133-)  5  -   N1     0.05    2.95  INTRA BL
1616 OGUA  (1387-)  5  -   C6  <-> 1617 OURA  (1388-)  5  -   C4     0.05    3.15  INTRA BL
2517 OADE  (2461-)  5  -   N1  <-> 2539 OGUA  (2483-)  5  -   N2     0.05    2.95  INTRA BL
 936 OGUA  ( 674-)  5  -   N7  <->  937 OCYT  ( 675-)  5  -   C4     0.05    3.05  INTRA BL
1167 OGUA  ( 910-)  5  -   N7  <-> 1168 OCYT  ( 911-)  5  -   C5     0.05    3.05  INTRA BL
3162 OADE  (3113-)  5  -   C2  <-> 3171 OADE  (3122-)  5  -   C8     0.05    3.15  INTRA BL
2526 OCYT  (2470-)  5  -   C5  <-> 2531 OGUA  (2475-)  5  -   C5     0.04    3.16  INTRA BL
1889 OCYT  (1670-)  5  -   C6  <-> 1993 OURA  (1777-)  5  -   C6     0.04    3.16  INTRA BL
1760 OURA  (1533-)  5  -   N3  <-> 1814 OADE  (1587-)  5  -   N7     0.04    2.96  INTRA BL
1873 OURA  (1651-)  5  -   C5  <-> 1874 OGUA  (1652-)  5  -   C4     0.04    3.16  INTRA BL
And so on for a total of 60 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.

  16 OURA  (  16-)  3  -   N3
  26 OCYT  (  26-)  3  -   N4
  31 OURA  (  31-)  3  -   N3
  41 OGUA  (  41-)  3  -   N1
  41 OGUA  (  41-)  3  -   N2
  43 OURA  (  43-)  3  -   N3
  51 OGUA  (  51-)  3  -   N2
  56 OGUA  (  56-)  3  -   N1
  67 OGUA  (  69-)  3  -   N2
  79 OGUA  (  84-)  3  -   N2
  80 OGUA  (  85-)  3  -   N1
  91 OGUA  (  96-)  3  -   N2
 129 OGUA  (  16-)  4  -   N2
 137 OGUA  (  24-)  4  -   N2
 150 OADE  (  37-)  4  -   N6
 155 OGUA  (  42-)  4  -   N2
 164 OGUA  (  51-)  4  -   N1
 168 OURA  (  55-)  4  -   N3
 177 OURA  (  64-)  4  -   N3
 184 OGUA  (  71-)  4  -   N2
 261 OGUA  ( 150-)  4  -   N1
 263 OGUA  ( 152-)  4  -   N1
 277 OCYT  (   8-)  5  -   N4
 289 OGUA  (  21-)  5  -   N1
 310 OCYT  (  42-)  5  -   N4
And so on for a total of 309 lines.

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.

Final summary