WHAT IF Check report

This file was created 2012-01-25 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 pdb2jn5.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

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 MET   (   1-)  A    Zero
   2 ASP   (   2-)  A    Zero
   3 VAL   (   3-)  A    Zero
   4 PHE   (   4-)  A    Zero
   5 MET   (   5-)  A    Zero
   6 LYS   (   6-)  A    Zero
   7 GLY   (   7-)  A    Zero
   8 LEU   (   8-)  A    Zero
   9 SER   (   9-)  A    Zero
  10 LYS   (  10-)  A    Zero
  11 ALA   (  11-)  A    Zero
  12 LYS   (  12-)  A    Zero
  13 MET   (   1-)  A    Zero
  14 ASP   (   2-)  A    Zero
  15 VAL   (   3-)  A    Zero
  16 PHE   (   4-)  A    Zero
  17 MET   (   5-)  A    Zero
  18 LYS   (   6-)  A    Zero
  19 GLY   (   7-)  A    Zero
  20 LEU   (   8-)  A    Zero
  21 SER   (   9-)  A    Zero
  22 LYS   (  10-)  A    Zero
  23 ALA   (  11-)  A    Zero
  24 LYS   (  12-)  A    Zero
  25 MET   (   1-)  A    Zero
And so on for a total of 120 lines.

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.213
Model 2 : 0.210
Model 3 : 0.212
Model 4 : 0.210
Model 5 : 0.213
Model 6 : 0.218
Model 7 : 0.200
Model 8 : 0.209
Model 9 : 0.211
Model 10 : 0.216

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.220
Model 2 : 0.208
Model 3 : 0.215
Model 4 : 0.208
Model 5 : 0.205
Model 6 : 0.222
Model 7 : 0.202
Model 8 : 0.216
Model 9 : 0.227
Model 10 : 0.229

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 0.220
Model 2 : 0.218
Model 3 : 0.250
Model 4 : 0.225
Model 5 : 0.228
Model 6 : 0.219
Model 7 : 0.221
Model 8 : 0.219
Model 9 : 0.210
Model 10 : 0.227

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -5.882

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -7.306
Model 2 : -5.409
Model 3 : -5.379
Model 4 : -5.099
Model 5 : -6.714
Model 6 : -6.326
Model 7 : -5.370
Model 8 : -6.262
Model 9 : -5.067
Model 10 : -5.889

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

  94 LYS   (  10-)  A    -2.5
  46 LYS   (  10-)  A    -2.5
  27 VAL   (   3-)  A    -2.5
  39 VAL   (   3-)  A    -2.5
  75 VAL   (   3-)  A    -2.5
   3 VAL   (   3-)  A    -2.5
  51 VAL   (   3-)  A    -2.5
  15 VAL   (   3-)  A    -2.4
 111 VAL   (   3-)  A 1   -2.4
  99 VAL   (   3-)  A    -2.4
  87 VAL   (   3-)  A    -2.4
  91 GLY   (   7-)  A    -2.2
  55 GLY   (   7-)  A    -2.2
  67 GLY   (   7-)  A    -2.2
  19 GLY   (   7-)  A    -2.2
 103 GLY   (   7-)  A    -2.2
  31 GLY   (   7-)  A    -2.2
  63 VAL   (   3-)  A    -2.1
  43 GLY   (   7-)  A    -2.1
 115 GLY   (   7-)  A 1   -2.1
  79 GLY   (   7-)  A    -2.1
  70 LYS   (  10-)  A    -2.1
   7 GLY   (   7-)  A    -2.1
  58 LYS   (  10-)  A    -2.1
 106 LYS   (  10-)  A    -2.1
 118 LYS   (  10-)  A 1   -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   3 VAL   (   3-)  A  Poor phi/psi
  15 VAL   (   3-)  A  Poor phi/psi
  20 LEU   (   8-)  A  Poor phi/psi
  27 VAL   (   3-)  A  Poor phi/psi
  39 VAL   (   3-)  A  Poor phi/psi
  51 VAL   (   3-)  A  Poor phi/psi
  63 VAL   (   3-)  A  Poor phi/psi
  75 VAL   (   3-)  A  Poor phi/psi
  87 VAL   (   3-)  A  Poor phi/psi
  93 SER   (   9-)  A  Poor phi/psi
  99 VAL   (   3-)  A  Poor phi/psi
 110 ASP   (   2-)  A 1 Poor phi/psi
 111 VAL   (   3-)  A 1 Poor phi/psi
 chi-1/chi-2 correlation Z-score : -6.221

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -6.221

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -4.415
Model 2 : -6.759
Model 3 : -6.013
Model 4 : -7.230
Model 5 : -6.049
Model 6 : -5.914
Model 7 : -7.323
Model 8 : -6.607
Model 9 : -5.735
Model 10 : -6.169

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 VAL   (   3-)  A      0
   4 PHE   (   4-)  A      0
   5 MET   (   5-)  A      0
   6 LYS   (   6-)  A      0
   8 LEU   (   8-)  A      0
   9 SER   (   9-)  A      0
  10 LYS   (  10-)  A      0
  11 ALA   (  11-)  A      0
  12 LYS   (  12-)  A      0
  13 MET   (   1-)  A      0
  14 ASP   (   2-)  A      0
  15 VAL   (   3-)  A      0
  17 MET   (   5-)  A      0
  18 LYS   (   6-)  A      0
  20 LEU   (   8-)  A      0
  21 SER   (   9-)  A      0
  22 LYS   (  10-)  A      0
  23 ALA   (  11-)  A      0
  24 LYS   (  12-)  A      0
  25 MET   (   1-)  A      0
  26 ASP   (   2-)  A      0
  27 VAL   (   3-)  A      0
  28 PHE   (   4-)  A      0
  29 MET   (   5-)  A      0
  30 LYS   (   6-)  A      0
And so on for a total of 106 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -3.178

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.257

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 0.339
Model 2 : 0.181
Model 3 : 0.296
Model 4 : 0.225
Model 5 : 0.256
Model 6 : 0.222
Model 7 : 0.202
Model 8 : 0.222
Model 9 : 0.413
Model 10 : 0.248

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

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).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

   2 ASP   (   2-)  A      N   <->   12 LYS   (  12-)  A      NZ     0.07    2.78
   6 LYS   (   6-)  A      C   <->   10 LYS   (  10-)  A      NZ     0.06    3.04
 109 MET   (   1-)  A 1    O   <->  120 LYS   (  12-)  A 1    NZ     0.05    2.65
 104 LEU   (   8-)  A      CG  <->  105 SER   (   9-)  A      N      0.04    2.96
  68 LEU   (   8-)  A      CG  <->   69 SER   (   9-)  A      N      0.04    2.96
  56 LEU   (   8-)  A      CG  <->   57 SER   (   9-)  A      N      0.03    2.97
  80 LEU   (   8-)  A      CG  <->   81 SER   (   9-)  A      N      0.03    2.97
  61 MET   (   1-)  A      C   <->   62 ASP   (   2-)  A      CG     0.02    3.08
  26 ASP   (   2-)  A      CG  <->   36 LYS   (  12-)  A      NZ     0.01    3.09
  62 ASP   (   2-)  A      N   <->   72 LYS   (  12-)  A      NZ     0.01    2.84

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.476

Note: Per-model averages for inside/outside residue distributi ...heck










Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

Note: Per-model averages for NQA










Water, ion, and hydrogenbond related checks

Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure