WHAT IF Check report

This file was created 2012-01-30 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 pdb2kgj.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 THR   (   1-)  A    Zero
   2 GLN   (   2-)  A    Zero
   3 PRO   (   3-)  A    Zero
   4 GLN   (   4-)  A    Zero
   5 ARG   (   5-)  A    Zero
   6 THR   (   6-)  A    Zero
   7 ARG   (   7-)  A    Zero
   8 TYR   (   8-)  A    Zero
   9 SER   (   9-)  A    Zero
  10 ILE   (  10-)  A    Zero
  11 ILE   (  11-)  A    Zero
  12 GLN   (  12-)  A    Zero
  13 THR   (  13-)  A    Zero
  14 LYS   (  14-)  A    Zero
  15 THR   (  15-)  A    Zero
  16 GLU   (  16-)  A    Zero
  17 ASP   (  17-)  A    Zero
  18 GLU   (  18-)  A    Zero
  19 ALA   (  19-)  A    Zero
  20 LYS   (  20-)  A    Zero
  21 ALA   (  21-)  A    Zero
  22 VAL   (  22-)  A    Zero
  23 LEU   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 GLU   (  25-)  A    Zero
And so on for a total of 1020 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 : 0.302
Model 2 : 0.296
Model 3 : 0.318
Model 4 : 0.321
Model 5 : 0.297
Model 6 : 0.310
Model 7 : 0.312
Model 8 : 0.319
Model 9 : 0.303
Model 10 : 0.311

Note: Per-model averages for bond-angle check

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

Model 1 : 0.554
Model 2 : 0.564
Model 3 : 0.566
Model 4 : 0.560
Model 5 : 0.555
Model 6 : 0.575
Model 7 : 0.545
Model 8 : 0.575
Model 9 : 0.556
Model 10 : 0.556

Note: Per-model averages for chirality check

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

Model 1 : 0.497
Model 2 : 0.496
Model 3 : 0.504
Model 4 : 0.504
Model 5 : 0.479
Model 6 : 0.498
Model 7 : 0.499
Model 8 : 0.531
Model 9 : 0.467
Model 10 : 0.486

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -1.960
Model 2 : -2.371
Model 3 : -2.415
Model 4 : -2.276
Model 5 : -2.258
Model 6 : -2.444
Model 7 : -1.888
Model 8 : -2.449
Model 9 : -1.757
Model 10 : -2.566

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.

 609 HIS   (  99-)  A    -3.0
 831 THR   (  15-)  A    -2.8
 921 PRO   (   3-)  A 1   -2.8
 933 THR   (  15-)  A 1   -2.8
 309 PRO   (   3-)  A    -2.7
 627 THR   (  15-)  A    -2.6
  43 ILE   (  43-)  A    -2.5
 814 HIS   ( 100-)  A    -2.5
 247 ILE   (  43-)  A    -2.5
 349 ILE   (  43-)  A    -2.5
 423 THR   (  15-)  A    -2.4
 826 ILE   (  10-)  A    -2.4
 113 ILE   (  11-)  A    -2.4
 757 ILE   (  43-)  A    -2.4
  99 HIS   (  99-)  A    -2.4
 520 ILE   (  10-)  A    -2.4
 655 ILE   (  43-)  A    -2.4
 112 ILE   (  10-)  A    -2.4
 521 ILE   (  11-)  A    -2.3
 961 ILE   (  43-)  A 1   -2.3
 725 ILE   (  11-)  A    -2.3
  10 ILE   (  10-)  A    -2.3
 316 ILE   (  10-)  A    -2.3
 929 ILE   (  11-)  A 1   -2.3
 859 ILE   (  43-)  A    -2.3
And so on for a total of 67 lines.

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.

  42 ASP   (  42-)  A  omega poor
  58 ALA   (  58-)  A  Poor phi/psi
  76 SER   (  76-)  A  Poor phi/psi
  96 ALA   (  96-)  A  Poor phi/psi
  99 HIS   (  99-)  A  Poor phi/psi
 144 ASP   (  42-)  A  omega poor
 160 ALA   (  58-)  A  Poor phi/psi
 178 SER   (  76-)  A  Poor phi/psi
 197 ALA   (  95-)  A  Poor phi/psi
 198 ALA   (  96-)  A  Poor phi/psi
 202 HIS   ( 100-)  A  Poor phi/psi
 243 LYS   (  39-)  A  omega poor
 246 ASP   (  42-)  A  omega poor
 262 ALA   (  58-)  A  Poor phi/psi
 280 SER   (  76-)  A  Poor phi/psi
 299 ALA   (  95-)  A  Poor phi/psi
 300 ALA   (  96-)  A  Poor phi/psi
 302 HIS   (  98-)  A  Poor phi/psi
 348 ASP   (  42-)  A  omega poor
 364 ALA   (  58-)  A  Poor phi/psi
 382 SER   (  76-)  A  Poor phi/psi
 401 ALA   (  95-)  A  Poor phi/psi
 403 HIS   (  97-)  A  Poor phi/psi
 406 HIS   ( 100-)  A  Poor phi/psi
 450 ASP   (  42-)  A  omega poor
And so on for a total of 56 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.859

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 : -4.003
Model 2 : -2.715
Model 3 : -3.713
Model 4 : -4.651
Model 5 : -3.598
Model 6 : -4.667
Model 7 : -3.042
Model 8 : -3.951
Model 9 : -4.439
Model 10 : -3.815

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!

  31 ASP   (  31-)  A      0
  32 PHE   (  32-)  A      0
  39 LYS   (  39-)  A      0
  41 ALA   (  41-)  A      0
  44 ILE   (  44-)  A      0
  45 SER   (  45-)  A      0
  48 ASN   (  48-)  A      0
  52 MET   (  52-)  A      0
  54 TRP   (  54-)  A      0
  57 ASP   (  57-)  A      0
  58 ALA   (  58-)  A      0
  67 ALA   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 LYS   (  70-)  A      0
  72 LYS   (  72-)  A      0
  75 LEU   (  75-)  A      0
  76 SER   (  76-)  A      0
  83 VAL   (  83-)  A      0
  85 PHE   (  85-)  A      0
  92 ASP   (  92-)  A      0
  95 ALA   (  95-)  A      0
  96 ALA   (  96-)  A      0
  97 HIS   (  97-)  A      0
  98 HIS   (  98-)  A      0
  99 HIS   (  99-)  A      0
And so on for a total of 421 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 5.389
Model 2 : 5.501
Model 3 : 5.959
Model 4 : 5.878
Model 5 : 5.360
Model 6 : 5.265
Model 7 : 5.163
Model 8 : 5.914
Model 9 : 5.726
Model 10 : 5.815

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 594 GLY   (  84-)  A   1.74   17

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 105 PRO   (   3-)  A   -54.2 half-chair C-beta/C-alpha (-54 degrees)
 309 PRO   (   3-)  A   -21.2 half-chair C-alpha/N (-18 degrees)
 513 PRO   (   3-)  A    29.2 envelop C-delta (36 degrees)
 717 PRO   (   3-)  A   -43.6 envelop C-alpha (-36 degrees)
 819 PRO   (   3-)  A   -48.0 half-chair C-beta/C-alpha (-54 degrees)
 921 PRO   (   3-)  A 1  -43.9 envelop C-alpha (-36 degrees)

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.

 756 ASP   (  42-)  A      O   <->  759 SER   (  45-)  A      N      0.14    2.56
 858 ASP   (  42-)  A      O   <->  861 SER   (  45-)  A      N      0.13    2.57
 825 SER   (   9-)  A      O   <->  905 ARG   (  89-)  A      N      0.12    2.58
 888 LYS   (  72-)  A      NZ  <->  908 ASP   (  92-)  A      OD1    0.12    2.58
 784 LYS   (  70-)  A      NZ  <-> 1028 HIS   ( 102-)  A      O''    0.11    2.59
 217 THR   (  13-)  A      N   <->  289 PHE   (  85-)  A      O      0.11    2.59
 913 HIS   (  97-)  A      ND1 <->  918 HIS   ( 102-)  A      O      0.11    2.59
 506 HIS   (  98-)  A      N   <->  510 HIS   ( 102-)  A      C      0.10    3.00
 348 ASP   (  42-)  A      O   <->  351 SER   (  45-)  A      N      0.10    2.60
 709 HIS   (  97-)  A      O   <->  711 HIS   (  99-)  A      N      0.10    2.60
 348 ASP   (  42-)  A      O   <->  350 ILE   (  44-)  A      N      0.10    2.60
 246 ASP   (  42-)  A      O   <->  248 ILE   (  44-)  A      N      0.10    2.60
 724 ILE   (  10-)  A      CG1 <->  766 MET   (  52-)  A      SD     0.09    3.31
 514 GLN   (   4-)  A      O   <->  567 ASP   (  57-)  A      N      0.09    2.61
  18 GLU   (  18-)  A      OE2 <->   39 LYS   (  39-)  A      NZ     0.09    2.61
  42 ASP   (  42-)  A      O   <->   44 ILE   (  44-)  A      N      0.09    2.61
 246 ASP   (  42-)  A      O   <->  249 SER   (  45-)  A      N      0.09    2.61
   9 SER   (   9-)  A      O   <->   89 ARG   (  89-)  A      N      0.08    2.62
 412 GLN   (   4-)  A      O   <->  465 ASP   (  57-)  A      N      0.08    2.62
 161 THR   (  59-)  A      N   <->  162 ILE   (  60-)  A      N      0.08    2.52        B3
 144 ASP   (  42-)  A      O   <->  147 SER   (  45-)  A      N      0.08    2.62
 771 ASP   (  57-)  A      OD1 <->  779 LYS   (  65-)  A      NZ     0.08    2.62
 760 ALA   (  46-)  A      O   <->  763 GLY   (  49-)  A      N      0.08    2.62
 451 ILE   (  43-)  A      CA  <->  454 ALA   (  46-)  A      CB     0.08    3.12
  42 ASP   (  42-)  A      O   <->   45 SER   (  45-)  A      N      0.07    2.63
And so on for a total of 129 lines.

Packing, accessibility and threading

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










Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Per-model averages for NQA










Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure