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 pdb1ix5.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   (   4-)  A    Zero
   2 VAL   (   5-)  A    Zero
   3 ASP   (   6-)  A    Zero
   4 LYS   (   7-)  A    Zero
   5 GLY   (   8-)  A    Zero
   6 VAL   (   9-)  A    Zero
   7 LYS   (  10-)  A    Zero
   8 ILE   (  11-)  A    Zero
   9 LYS   (  12-)  A    Zero
  10 VAL   (  13-)  A    Zero
  11 ASP   (  14-)  A    Zero
  12 TYR   (  15-)  A    Zero
  13 ILE   (  16-)  A    Zero
  14 GLY   (  17-)  A    Zero
  15 LYS   (  18-)  A    Zero
  16 LEU   (  19-)  A    Zero
  17 GLU   (  20-)  A    Zero
  18 SER   (  21-)  A    Zero
  19 GLY   (  22-)  A    Zero
  20 ASP   (  23-)  A    Zero
  21 VAL   (  24-)  A    Zero
  22 PHE   (  25-)  A    Zero
  23 ASP   (  26-)  A    Zero
  24 THR   (  27-)  A    Zero
  25 SER   (  28-)  A    Zero
And so on for a total of 1510 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 : 0.374
Model 2 : 0.373
Model 3 : 0.374
Model 4 : 0.372
Model 5 : 0.374
Model 6 : 0.374
Model 7 : 0.372
Model 8 : 0.375
Model 9 : 0.374
Model 10 : 0.373

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.701
Model 2 : 0.701
Model 3 : 0.701
Model 4 : 0.700
Model 5 : 0.701
Model 6 : 0.702
Model 7 : 0.701
Model 8 : 0.701
Model 9 : 0.701
Model 10 : 0.701

Note: Per-model averages for chirality check

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

Model 1 : 0.705
Model 2 : 0.706
Model 3 : 0.706
Model 4 : 0.704
Model 5 : 0.704
Model 6 : 0.703
Model 7 : 0.705
Model 8 : 0.704
Model 9 : 0.707
Model 10 : 0.705

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 : -6.745

Note: Per-model averages for Ramachandran check

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

Model 1 : -6.727
Model 2 : -7.090
Model 3 : -6.985
Model 4 : -6.074
Model 5 : -7.297
Model 6 : -6.735
Model 7 : -6.394
Model 8 : -6.943
Model 9 : -6.145
Model 10 : -7.064

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.

1490 PHE   ( 134-)  A 1   -3.6
 433 PHE   ( 134-)  A    -3.5
 857 PHE   ( 105-)  A    -3.1
 946 ARG   (  43-)  A    -3.1
1097 ARG   (  43-)  A    -3.1
 102 PHE   ( 105-)  A    -2.9
1310 PHE   ( 105-)  A    -2.9
1477 THR   ( 121-)  A 1   -2.9
 269 THR   ( 121-)  A    -2.8
 447 LYS   ( 148-)  A    -2.8
1159 PHE   ( 105-)  A    -2.8
 131 PHE   ( 134-)  A    -2.8
 385 ASN   (  86-)  A    -2.7
 337 ILE   (  38-)  A    -2.7
 186 ILE   (  38-)  A    -2.7
1394 ILE   (  38-)  A 1   -2.7
 838 ASN   (  86-)  A    -2.7
 525 THR   (  75-)  A    -2.7
1339 PHE   ( 134-)  A    -2.7
  91 LYS   (  94-)  A    -2.7
1024 THR   ( 121-)  A    -2.7
 283 ASN   ( 135-)  A    -2.7
 695 LYS   (  94-)  A    -2.7
 242 LYS   (  94-)  A    -2.6
 947 GLU   (  44-)  A    -2.6
And so on for a total of 263 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.

   5 GLY   (   8-)  A  Poor phi/psi
  37 ALA   (  40-)  A  Poor phi/psi
  38 PRO   (  41-)  A  Poor phi/psi
  51 GLU   (  54-)  A  Poor phi/psi
  53 GLN   (  56-)  A  Poor phi/psi
  57 GLY   (  60-)  A  Poor phi/psi
  80 ALA   (  83-)  A  Poor phi/psi
  82 GLY   (  85-)  A  Poor phi/psi
  83 ASN   (  86-)  A  Poor phi/psi
  97 PHE   ( 100-)  A  Poor phi/psi
 103 GLU   ( 106-)  A  Poor phi/psi
 106 GLU   ( 109-)  A  Poor phi/psi
 107 GLY   ( 110-)  A  Poor phi/psi
 113 GLU   ( 116-)  A  Poor phi/psi
 124 ASP   ( 127-)  A  Poor phi/psi
 126 GLU   ( 129-)  A  Poor phi/psi
 132 ASN   ( 135-)  A  Poor phi/psi
 133 HIS   ( 136-)  A  Poor phi/psi
 137 GLY   ( 140-)  A  Poor phi/psi
 143 THR   ( 146-)  A  Poor phi/psi
 145 LYS   ( 148-)  A  Poor phi/psi
 150 VAL   ( 153-)  A  Poor phi/psi
 155 LYS   (   7-)  A  Poor phi/psi
 156 GLY   (   8-)  A  Poor phi/psi
 162 ASP   (  14-)  A  Poor phi/psi
And so on for a total of 235 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 : -7.480

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 : -7.464
Model 2 : -7.114
Model 3 : -7.734
Model 4 : -7.588
Model 5 : -7.508
Model 6 : -7.807
Model 7 : -7.264
Model 8 : -7.307
Model 9 : -7.739
Model 10 : -7.279

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 LYS   (   7-)  A      0
   9 LYS   (  12-)  A      0
  16 LEU   (  19-)  A      0
  18 SER   (  21-)  A      0
  23 ASP   (  26-)  A      0
  35 ILE   (  38-)  A      0
  37 ALA   (  40-)  A      0
  38 PRO   (  41-)  A      0
  40 ARG   (  43-)  A      0
  51 GLU   (  54-)  A      0
  53 GLN   (  56-)  A      0
  64 ASP   (  67-)  A      0
  67 VAL   (  70-)  A      0
  72 THR   (  75-)  A      0
  80 ALA   (  83-)  A      0
  81 TYR   (  84-)  A      0
  83 ASN   (  86-)  A      0
  84 ARG   (  87-)  A      0
  97 PHE   ( 100-)  A      0
  99 GLU   ( 102-)  A      0
 100 ALA   ( 103-)  A      0
 102 PHE   ( 105-)  A      0
 103 GLU   ( 106-)  A      0
 106 GLU   ( 109-)  A      0
 108 MET   ( 111-)  A      0
And so on for a total of 698 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 : 0.167

Note: Per-model averages for omega angle check

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

Model 1 : 0.196
Model 2 : 0.080
Model 3 : 0.000
Model 4 : 0.000
Model 5 : 0.140
Model 6 : 0.117
Model 7 : 0.080
Model 8 : 0.043
Model 9 : 0.126
Model 10 : 0.107

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!

1258 GLY   (  53-)  A   2.38   21
  50 GLY   (  53-)  A   2.01   40
 956 GLY   (  53-)  A   1.95   38
1409 GLY   (  53-)  A 1  1.88   23
 201 GLY   (  53-)  A   1.62   28

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.

1492 HIS   ( 136-)  A 1    ND1 <-> 1494 LEU   ( 138-)  A 1    N      0.65    2.35
 888 HIS   ( 136-)  A      ND1 <->  890 LEU   ( 138-)  A      N      0.62    2.38
 737 HIS   ( 136-)  A      ND1 <->  739 LEU   ( 138-)  A      N      0.62    2.38
 435 HIS   ( 136-)  A      ND1 <->  437 LEU   ( 138-)  A      N      0.60    2.40
1190 HIS   ( 136-)  A      ND1 <-> 1191 GLU   ( 137-)  A      N      0.59    2.31
 586 HIS   ( 136-)  A      ND1 <->  588 LEU   ( 138-)  A      N      0.58    2.42
1039 HIS   ( 136-)  A      ND1 <-> 1041 LEU   ( 138-)  A      N      0.58    2.42
 888 HIS   ( 136-)  A      ND1 <->  889 GLU   ( 137-)  A      N      0.57    2.33
 130 ASP   ( 133-)  A      CG  <->  132 ASN   ( 135-)  A      ND2    0.57    2.53
 133 HIS   ( 136-)  A      ND1 <->  135 LEU   ( 138-)  A      N      0.56    2.44
1424 MET   (  68-)  A 1    SD  <-> 1429 GLU   (  73-)  A 1    N      0.56    2.74
 878 THR   ( 126-)  A      CG2 <->  880 ASN   ( 128-)  A      ND2    0.56    2.54
 734 ASP   ( 133-)  A      CG  <->  736 ASN   ( 135-)  A      ND2    0.56    2.54
 583 ASP   ( 133-)  A      CG  <->  585 ASN   ( 135-)  A      ND2    0.56    2.54
 303 MET   (   4-)  A      N   <->  367 MET   (  68-)  A      C      0.55    2.55
1492 HIS   ( 136-)  A 1    ND1 <-> 1493 GLU   ( 137-)  A 1    N      0.55    2.35
1341 HIS   ( 136-)  A      ND1 <-> 1343 LEU   ( 138-)  A      N      0.54    2.46
 586 HIS   ( 136-)  A      ND1 <->  587 GLU   ( 137-)  A      N      0.54    2.36
1036 ASP   ( 133-)  A      CG  <-> 1038 ASN   ( 135-)  A      ND2    0.54    2.56
 284 HIS   ( 136-)  A      CG  <->  285 GLU   ( 137-)  A      N      0.53    2.47
1187 ASP   ( 133-)  A      CG  <-> 1189 ASN   ( 135-)  A      ND2    0.53    2.57
 685 TYR   (  84-)  A      CE2 <->  737 HIS   ( 136-)  A      NE2    0.53    2.57
1453 ARG   (  97-)  A 1    NH2 <-> 1486 VAL   ( 130-)  A 1    CG2    0.53    2.57
1406 PHE   (  50-)  A 1    CB  <-> 1412 GLN   (  56-)  A 1    NE2    0.53    2.57
1190 HIS   ( 136-)  A      ND1 <-> 1192 LEU   ( 138-)  A      N      0.52    2.48
And so on for a total of 1625 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

Warning: Low packing Z-score for some residues


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