WHAT IF Check report

This file was created 2011-12-28 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 pdb1hxv.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

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

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 LYS   (  29-)  A    Zero
   2 LEU   (  30-)  A    Zero
   3 ALA   (  31-)  A    Zero
   4 ASN   (  32-)  A    Zero
   5 GLY   (  33-)  A    Zero
   6 ASP   (  34-)  A    Zero
   7 ILE   (  35-)  A    Zero
   8 ALA   (  36-)  A    Zero
   9 ILE   (  37-)  A    Zero
  10 ILE   (  38-)  A    Zero
  11 ASP   (  39-)  A    Zero
  12 PHE   (  40-)  A    Zero
  13 THR   (  41-)  A    Zero
  14 GLY   (  42-)  A    Zero
  15 ILE   (  43-)  A    Zero
  16 VAL   (  44-)  A    Zero
  17 ASP   (  45-)  A    Zero
  18 ASN   (  46-)  A    Zero
  19 LYS   (  47-)  A    Zero
  20 LYS   (  48-)  A    Zero
  21 LEU   (  49-)  A    Zero
  22 ALA   (  50-)  A    Zero
  23 SER   (  51-)  A    Zero
  24 ALA   (  52-)  A    Zero
  25 SER   (  53-)  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 : 0.235
Model 2 : 0.235
Model 3 : 0.231
Model 4 : 0.236
Model 5 : 0.237
Model 6 : 0.223
Model 7 : 0.239
Model 8 : 0.234
Model 9 : 0.241
Model 10 : 0.234
Model 11 : 0.235
Model 12 : 0.246

Note: Per-model averages for bond-angle check

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

Model 1 : 0.426
Model 2 : 0.426
Model 3 : 0.422
Model 4 : 0.435
Model 5 : 0.429
Model 6 : 0.426
Model 7 : 0.428
Model 8 : 0.430
Model 9 : 0.423
Model 10 : 0.424
Model 11 : 0.430
Model 12 : 0.429

Note: Per-model averages for chirality check

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

Model 1 : 0.522
Model 2 : 0.529
Model 3 : 0.522
Model 4 : 0.524
Model 5 : 0.516
Model 6 : 0.534
Model 7 : 0.514
Model 8 : 0.526
Model 9 : 0.532
Model 10 : 0.513
Model 11 : 0.531
Model 12 : 0.510

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 : -5.943

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.949
Model 2 : -6.140
Model 3 : -6.100
Model 4 : -5.866
Model 5 : -5.973
Model 6 : -5.823
Model 7 : -5.907
Model 8 : -5.860
Model 9 : -5.778
Model 10 : -5.731
Model 11 : -5.863
Model 12 : -6.322

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.

 774 ILE   (  37-)  A 1   -2.7
 519 ILE   (  37-)  A    -2.7
 349 ILE   (  37-)  A    -2.7
 944 ILE   (  37-)  A 1   -2.7
 859 ILE   (  37-)  A 1   -2.7
 821 THR   (  84-)  A 1   -2.6
  94 ILE   (  37-)  A    -2.6
   9 ILE   (  37-)  A    -2.6
 604 ILE   (  37-)  A    -2.6
 264 ILE   (  37-)  A    -2.6
 190 LYS   (  48-)  A    -2.6
 991 THR   (  84-)  A 1   -2.6
 501 THR   ( 104-)  A    -2.6
 481 THR   (  84-)  A    -2.6
 955 LYS   (  48-)  A 1   -2.6
 931 LEU   ( 109-)  A 1   -2.5
 735 LYS   (  83-)  A    -2.5
 689 ILE   (  37-)  A    -2.5
 785 LYS   (  48-)  A 1   -2.5
 479 LYS   (  82-)  A    -2.5
 179 ILE   (  37-)  A    -2.5
1008 LYS   ( 101-)  A 1   -2.5
 841 THR   ( 104-)  A 1   -2.5
 583 LYS   ( 101-)  A    -2.5
1011 THR   ( 104-)  A 1   -2.5
And so on for a total of 205 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.

   4 ASN   (  32-)  A  Poor phi/psi
  18 ASN   (  46-)  A  Poor phi/psi
  27 GLN   (  55-)  A  Poor phi/psi
  34 GLY   (  62-)  A  Poor phi/psi
  36 ASN   (  64-)  A  Poor phi/psi
  42 PHE   (  70-)  A  Poor phi/psi
  50 LYS   (  78-)  A  Poor phi/psi
  52 ASN   (  80-)  A  Poor phi/psi
  81 LEU   ( 109-)  A  Poor phi/psi
  89 ASN   (  32-)  A  Poor phi/psi
 102 ASP   (  45-)  A  Poor phi/psi
 103 ASN   (  46-)  A  Poor phi/psi
 108 SER   (  51-)  A  Poor phi/psi
 112 GLN   (  55-)  A  Poor phi/psi
 119 GLY   (  62-)  A  Poor phi/psi
 121 ASN   (  64-)  A  Poor phi/psi
 127 PHE   (  70-)  A  Poor phi/psi
 135 LYS   (  78-)  A  Poor phi/psi
 137 ASN   (  80-)  A  Poor phi/psi
 166 LEU   ( 109-)  A  Poor phi/psi
 174 ASN   (  32-)  A  Poor phi/psi
 188 ASN   (  46-)  A  Poor phi/psi
 193 SER   (  51-)  A  Poor phi/psi
 197 GLN   (  55-)  A  Poor phi/psi
 204 GLY   (  62-)  A  Poor phi/psi
And so on for a total of 117 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 : -7.758

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 : -7.939
Model 2 : -7.987
Model 3 : -7.929
Model 4 : -8.212
Model 5 : -7.755
Model 6 : -7.539
Model 7 : -7.533
Model 8 : -7.854
Model 9 : -7.364
Model 10 : -7.524
Model 11 : -7.917
Model 12 : -7.549

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!

   4 ASN   (  32-)  A      0
  16 VAL   (  44-)  A      0
  17 ASP   (  45-)  A      0
  18 ASN   (  46-)  A      0
  22 ALA   (  50-)  A      0
  24 ALA   (  52-)  A      0
  25 SER   (  53-)  A      0
  27 GLN   (  55-)  A      0
  28 ASN   (  56-)  A      0
  33 ILE   (  61-)  A      0
  35 SER   (  63-)  A      0
  36 ASN   (  64-)  A      0
  37 SER   (  65-)  A      0
  39 ILE   (  67-)  A      0
  42 PHE   (  70-)  A      0
  48 ALA   (  76-)  A      0
  51 VAL   (  79-)  A      0
  52 ASN   (  80-)  A      0
  55 LYS   (  83-)  A      0
  56 THR   (  84-)  A      0
  58 ALA   (  86-)  A      0
  65 TYR   (  93-)  A      0
  66 HIS   (  94-)  A      0
  70 LEU   (  98-)  A      0
  71 GLN   (  99-)  A      0
And so on for a total of 533 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 : -2.022

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 : 1.500

Note: Per-model averages for omega angle check

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

Model 1 : 1.511
Model 2 : 1.486
Model 3 : 1.491
Model 4 : 1.483
Model 5 : 1.470
Model 6 : 1.424
Model 7 : 1.515
Model 8 : 1.510
Model 9 : 1.505
Model 10 : 1.474
Model 11 : 1.502
Model 12 : 1.437

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].

 329 PRO   ( 102-)  A    48.1 half-chair C-delta/C-gamma (54 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.

 902 ASN   (  80-)  A 1    N   <->  931 LEU   ( 109-)  A 1    O      0.35    2.35
 307 ASN   (  80-)  A      N   <->  336 LEU   ( 109-)  A      O      0.35    2.35
 732 ASN   (  80-)  A      N   <->  761 LEU   ( 109-)  A      O      0.35    2.35
 562 ASN   (  80-)  A      N   <->  591 LEU   ( 109-)  A      O      0.34    2.36
 537 GLN   (  55-)  A      O   <->  539 TYR   (  57-)  A      N      0.34    2.36
 688 ALA   (  36-)  A      N   <->  711 LEU   (  59-)  A      O      0.33    2.37
  27 GLN   (  55-)  A      O   <->   29 TYR   (  57-)  A      N      0.33    2.37
 792 GLN   (  55-)  A 1    O   <->  794 TYR   (  57-)  A 1    N      0.32    2.38
 622 GLN   (  55-)  A      O   <->  624 TYR   (  57-)  A      N      0.32    2.38
 817 ASN   (  80-)  A 1    N   <->  846 LEU   ( 109-)  A 1    O      0.32    2.38
 112 GLN   (  55-)  A      O   <->  114 TYR   (  57-)  A      N      0.32    2.38
 137 ASN   (  80-)  A      N   <->  166 LEU   ( 109-)  A      O      0.32    2.38
 858 ALA   (  36-)  A 1    N   <->  881 LEU   (  59-)  A 1    O      0.32    2.38
 348 ALA   (  36-)  A      N   <->  371 LEU   (  59-)  A      O      0.32    2.38
 282 GLN   (  55-)  A      O   <->  284 TYR   (  57-)  A      N      0.31    2.39
 707 GLN   (  55-)  A      O   <->  709 TYR   (  57-)  A      N      0.31    2.39
 647 ASN   (  80-)  A      N   <->  676 LEU   ( 109-)  A      O      0.31    2.39
 392 ASN   (  80-)  A      N   <->  421 LEU   ( 109-)  A      O      0.31    2.39
 197 GLN   (  55-)  A      O   <->  199 TYR   (  57-)  A      N      0.30    2.40
 877 GLN   (  55-)  A 1    O   <->  879 TYR   (  57-)  A 1    N      0.30    2.40
  52 ASN   (  80-)  A      N   <->   81 LEU   ( 109-)  A      O      0.30    2.40
 477 ASN   (  80-)  A      N   <->  506 LEU   ( 109-)  A      O      0.30    2.40
 987 ASN   (  80-)  A 1    N   <-> 1016 LEU   ( 109-)  A 1    O      0.30    2.40
 522 PHE   (  40-)  A      N   <->  536 ALA   (  54-)  A      O      0.30    2.40
 222 ASN   (  80-)  A      N   <->  251 LEU   ( 109-)  A      O      0.30    2.40
And so on for a total of 670 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Warning: Abnormal packing environment for some 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: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

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