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 pdb2kyx.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 GLY   (  -2-)  A    Zero
   2 SER   (  -1-)  A    Zero
   3 THR   (   3-)  A    Zero
   4 THR   (   4-)  A    Zero
   5 LYS   (   5-)  A    Zero
   6 ARG   (   6-)  A    Zero
   7 VAL   (   7-)  A    Zero
   8 LEU   (   8-)  A    Zero
   9 TYR   (   9-)  A    Zero
  10 VAL   (  10-)  A    Zero
  11 GLY   (  11-)  A    Zero
  12 GLY   (  12-)  A    Zero
  13 LEU   (  13-)  A    Zero
  14 ALA   (  14-)  A    Zero
  15 GLU   (  15-)  A    Zero
  16 GLU   (  16-)  A    Zero
  17 VAL   (  17-)  A    Zero
  18 ASP   (  18-)  A    Zero
  19 ASP   (  19-)  A    Zero
  20 LYS   (  20-)  A    Zero
  21 VAL   (  21-)  A    Zero
  22 LEU   (  22-)  A    Zero
  23 HIS   (  23-)  A    Zero
  24 ALA   (  24-)  A    Zero
  25 ALA   (  25-)  A    Zero
And so on for a total of 830 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 : 0.240
Model 2 : 0.247
Model 3 : 0.242
Model 4 : 0.250
Model 5 : 0.242
Model 6 : 0.245
Model 7 : 0.239
Model 8 : 0.244
Model 9 : 0.238
Model 10 : 0.237

Note: Per-model averages for bond-angle check

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

Model 1 : 0.425
Model 2 : 0.423
Model 3 : 0.428
Model 4 : 0.439
Model 5 : 0.436
Model 6 : 0.431
Model 7 : 0.427
Model 8 : 0.434
Model 9 : 0.420
Model 10 : 0.428

Note: Per-model averages for chirality check

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

Model 1 : 0.388
Model 2 : 0.376
Model 3 : 0.371
Model 4 : 0.385
Model 5 : 0.394
Model 6 : 0.386
Model 7 : 0.397
Model 8 : 0.372
Model 9 : 0.378
Model 10 : 0.376

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.467

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.235
Model 2 : -3.193
Model 3 : -3.571
Model 4 : -3.670
Model 5 : -3.684
Model 6 : -3.028
Model 7 : -3.354
Model 8 : -3.833
Model 9 : -3.532
Model 10 : -3.575

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.

 502 THR   (   4-)  A    -3.7
 253 THR   (   4-)  A    -3.5
 501 THR   (   3-)  A    -3.5
 170 THR   (   4-)  A    -3.4
 667 THR   (   3-)  A    -3.1
 373 TYR   (  41-)  A    -3.0
   4 THR   (   4-)  A    -2.9
 454 LEU   (  39-)  A    -2.8
 654 PHE   (  73-)  A    -2.8
 750 THR   (   3-)  A 1   -2.7
 788 TYR   (  41-)  A 1   -2.7
 235 GLU   (  69-)  A    -2.7
 752 LYS   (   5-)  A 1   -2.6
 171 LYS   (   5-)  A    -2.6
 542 GLU   (  44-)  A    -2.6
 625 GLU   (  44-)  A    -2.5
 628 ARG   (  47-)  A    -2.5
 318 GLU   (  69-)  A    -2.5
 254 LYS   (   5-)  A    -2.5
 419 THR   (   4-)  A    -2.5
 335 THR   (   3-)  A    -2.5
  73 PHE   (  73-)  A    -2.4
 816 GLU   (  69-)  A 1   -2.4
 213 ARG   (  47-)  A    -2.4
 293 GLU   (  44-)  A    -2.4
And so on for a total of 97 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.

   2 SER   (  -1-)  A  Poor phi/psi
  12 GLY   (  12-)  A  Poor phi/psi
  69 GLU   (  69-)  A  Poor phi/psi
  73 PHE   (  73-)  A  Poor phi/psi
  89 ARG   (   6-)  A  Poor phi/psi
 127 GLU   (  44-)  A  Poor phi/psi
 152 GLU   (  69-)  A  Poor phi/psi
 153 SER   (  70-)  A  Poor phi/psi
 165 ALA   (  82-)  A  Poor phi/psi
 171 LYS   (   5-)  A  Poor phi/psi
 172 ARG   (   6-)  A  Poor phi/psi
 210 GLU   (  44-)  A  Poor phi/psi
 214 GLY   (  48-)  A  Poor phi/psi
 235 GLU   (  69-)  A  Poor phi/psi
 239 PHE   (  73-)  A  Poor phi/psi
 248 ALA   (  82-)  A  Poor phi/psi
 251 SER   (  -1-)  A  Poor phi/psi
 252 THR   (   3-)  A  Poor phi/psi
 253 THR   (   4-)  A  Poor phi/psi
 261 GLY   (  12-)  A  Poor phi/psi
 318 GLU   (  69-)  A  Poor phi/psi
 322 PHE   (  73-)  A  Poor phi/psi
 335 THR   (   3-)  A  Poor phi/psi
 376 GLU   (  44-)  A  Poor phi/psi
 401 GLU   (  69-)  A  Poor phi/psi
And so on for a total of 60 lines.

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 : -6.891

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 : -6.851
Model 2 : -7.094
Model 3 : -7.065
Model 4 : -6.729
Model 5 : -6.788
Model 6 : -6.963
Model 7 : -6.650
Model 8 : -6.987
Model 9 : -6.998
Model 10 : -6.790

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 THR   (   3-)  A      0
   4 THR   (   4-)  A      0
   5 LYS   (   5-)  A      0
   6 ARG   (   6-)  A      0
  18 ASP   (  18-)  A      0
  29 PHE   (  29-)  A      0
  34 ASP   (  34-)  A      0
  43 THR   (  43-)  A      0
  47 ARG   (  47-)  A      0
  49 PHE   (  49-)  A      0
  68 ASN   (  68-)  A      0
  69 GLU   (  69-)  A      0
  72 LEU   (  72-)  A      0
  73 PHE   (  73-)  A      0
  82 ALA   (  82-)  A      0
  83 LYS   (  83-)  A      0
  84 GLY   (  -2-)  A      0
  85 SER   (  -1-)  A      0
  87 THR   (   4-)  A      0
  88 LYS   (   5-)  A      0
  89 ARG   (   6-)  A      0
 112 PHE   (  29-)  A      0
 117 ASP   (  34-)  A      0
 126 THR   (  43-)  A      0
 130 ARG   (  47-)  A      0
And so on for a total of 343 lines.

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 : 0.795

Note: Per-model averages for omega angle check

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

Model 1 : 0.767
Model 2 : 0.815
Model 3 : 0.758
Model 4 : 0.681
Model 5 : 0.861
Model 6 : 0.779
Model 7 : 0.740
Model 8 : 0.770
Model 9 : 0.779
Model 10 : 0.728

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!

 380 GLY   (  48-)  A   1.51   43

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.

 131 GLY   (  48-)  A      O   <->  132 PHE   (  49-)  A      CD1    0.33    2.37
 629 GLY   (  48-)  A      O   <->  630 PHE   (  49-)  A      CD1    0.30    2.40
 646 ASP   (  65-)  A      C   <->  649 ASN   (  68-)  A      ND2    0.28    2.82
 380 GLY   (  48-)  A      O   <->  381 PHE   (  49-)  A      CD1    0.27    2.43
  27 ILE   (  27-)  A      N   <->   28 PRO   (  28-)  A      CD     0.25    2.75
 524 PHE   (  26-)  A      CZ  <->  565 MET   (  67-)  A      SD     0.25    3.15
 214 GLY   (  48-)  A      O   <->  215 PHE   (  49-)  A      CD1    0.25    2.45
  67 MET   (  67-)  A      SD  <->   77 ILE   (  77-)  A      CD1    0.24    3.16
 278 PHE   (  29-)  A      CE2 <->  316 MET   (  67-)  A      SD     0.24    3.16
 712 GLY   (  48-)  A      O   <->  713 PHE   (  49-)  A      CD1    0.24    2.46
 442 ILE   (  27-)  A      N   <->  443 PRO   (  28-)  A      CD     0.24    2.76
 691 ILE   (  27-)  A      N   <->  692 PRO   (  28-)  A      CD     0.24    2.76
 110 ILE   (  27-)  A      N   <->  111 PRO   (  28-)  A      CD     0.24    2.76
 359 ILE   (  27-)  A      N   <->  360 PRO   (  28-)  A      CD     0.24    2.76
 608 ILE   (  27-)  A      N   <->  609 PRO   (  28-)  A      CD     0.24    2.76
 774 ILE   (  27-)  A 1    N   <->  775 PRO   (  28-)  A 1    CD     0.24    2.76
 685 VAL   (  21-)  A      CG1 <->  686 LEU   (  22-)  A      N      0.24    2.76
 278 PHE   (  29-)  A      CZ  <->  316 MET   (  67-)  A      SD     0.24    3.16
 525 ILE   (  27-)  A      N   <->  526 PRO   (  28-)  A      CD     0.23    2.77
 276 ILE   (  27-)  A      N   <->  277 PRO   (  28-)  A      CD     0.23    2.77
 463 GLY   (  48-)  A      O   <->  464 PHE   (  49-)  A      CD1    0.23    2.47
 104 VAL   (  21-)  A      CG1 <->  105 LEU   (  22-)  A      N      0.23    2.77
 297 GLY   (  48-)  A      O   <->  298 PHE   (  49-)  A      CD1    0.23    2.47
 193 ILE   (  27-)  A      N   <->  194 PRO   (  28-)  A      CD     0.23    2.77
 546 GLY   (  48-)  A      O   <->  547 PHE   (  49-)  A      CD1    0.22    2.48
And so on for a total of 327 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