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 pdb2htf.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

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.207
Model 2 : 0.296
Model 3 : 0.293
Model 4 : 0.288
Model 5 : 0.295
Model 6 : 0.309
Model 7 : 0.322
Model 8 : 0.294
Model 9 : 0.297
Model 10 : 0.309
Model 11 : 0.327

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 889 HIS   (  68-)  A      CG   ND1  CE1 109.63    4.0

Note: Per-model averages for bond-angle check

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

Model 1 : 0.368
Model 2 : 0.480
Model 3 : 0.476
Model 4 : 0.477
Model 5 : 0.476
Model 6 : 0.519
Model 7 : 0.485
Model 8 : 0.492
Model 9 : 0.493
Model 10 : 0.494
Model 11 : 0.501

Note: Per-model averages for chirality check

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

Model 1 : 0.311
Model 2 : 0.509
Model 3 : 0.475
Model 4 : 0.542
Model 5 : 0.484
Model 6 : 0.513
Model 7 : 0.464
Model 8 : 0.490
Model 9 : 0.537
Model 10 : 0.502
Model 11 : 0.556

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 : -3.839

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.146
Model 2 : -3.438
Model 3 : -3.777
Model 4 : -3.735
Model 5 : -4.158
Model 6 : -3.992
Model 7 : -3.947
Model 8 : -3.573
Model 9 : -4.439
Model 10 : -3.531
Model 11 : -3.496

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.

1099 HIS   (  68-)  A 1   -3.2
 889 HIS   (  68-)  A    -3.1
 154 HIS   (  68-)  A    -3.1
 888 THR   (  67-)  A    -3.1
1098 THR   (  67-)  A 1   -3.0
 574 HIS   (  68-)  A    -3.0
 531 THR   (  25-)  A    -2.9
 921 LEU   ( 100-)  A    -2.9
1026 LEU   ( 100-)  A 1   -2.8
 711 LEU   ( 100-)  A    -2.8
1131 LEU   ( 100-)  A 1   -2.8
 949 PRO   (  23-)  A 1   -2.8
 501 LEU   ( 100-)  A    -2.8
 291 LEU   ( 100-)  A    -2.8
 319 PRO   (  23-)  A    -2.7
1054 PRO   (  23-)  A 1   -2.7
 573 THR   (  67-)  A    -2.7
 816 LEU   ( 100-)  A    -2.6
 396 LEU   ( 100-)  A    -2.6
 742 ARG   (  26-)  A    -2.6
 606 LEU   ( 100-)  A    -2.5
 598 PRO   (  92-)  A    -2.5
 186 LEU   ( 100-)  A    -2.5
 427 ARG   (  26-)  A    -2.5
  81 LEU   ( 100-)  A    -2.5
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.

   7 ARG   (  26-)  A  Poor phi/psi
  42 ALA   (  61-)  A  Poor phi/psi
  74 GLY   (  93-)  A  Poor phi/psi
 114 PRO   (  28-)  A  Poor phi/psi
 154 HIS   (  68-)  A  Poor phi/psi
 209 LEU   ( 123-)  A  Poor phi/psi
 214 PRO   (  23-)  A  Poor phi/psi
 216 THR   (  25-)  A  Poor phi/psi
 217 ARG   (  26-)  A  Poor phi/psi
 220 GLY   (  29-)  A  Poor phi/psi
 228 PRO   (  37-)  A  Poor phi/psi
 246 GLY   (  55-)  A  Poor phi/psi
 251 ASP   (  60-)  A  Poor phi/psi
 253 CYS   (  62-)  A  Poor phi/psi
 314 LEU   ( 123-)  A  Poor phi/psi
 322 ARG   (  26-)  A  Poor phi/psi
 324 PRO   (  28-)  A  Poor phi/psi
 358 CYS   (  62-)  A  Poor phi/psi
 369 GLU   (  73-)  A  Poor phi/psi
 395 LEU   (  99-)  A  omega poor
 396 LEU   ( 100-)  A  Poor phi/psi
 418 ARG   ( 122-)  A  omega poor
 419 LEU   ( 123-)  A  Poor phi/psi
 424 PRO   (  23-)  A  Poor phi/psi
 427 ARG   (  26-)  A  Poor phi/psi
And so on for a total of 72 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 : -4.758

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 : -3.547
Model 2 : -5.311
Model 3 : -4.984
Model 4 : -4.809
Model 5 : -5.506
Model 6 : -4.633
Model 7 : -5.268
Model 8 : -4.074
Model 9 : -4.646
Model 10 : -4.521
Model 11 : -5.039

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 167 SER   (  81-)  A    0.34
 128 SER   (  42-)  A    0.36
 824 SER   ( 108-)  A    0.36
 509 SER   ( 108-)  A    0.36
 299 SER   ( 108-)  A    0.37

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 PRO   (  23-)  A      0
   5 SER   (  24-)  A      0
   6 THR   (  25-)  A      0
   7 ARG   (  26-)  A      0
   8 PHE   (  27-)  A      0
   9 PRO   (  28-)  A      0
  19 ARG   (  38-)  A      0
  35 LYS   (  54-)  A      0
  41 ASP   (  60-)  A      0
  42 ALA   (  61-)  A      0
  43 CYS   (  62-)  A      0
  46 GLU   (  65-)  A      0
  53 GLU   (  72-)  A      0
  54 GLU   (  73-)  A      0
  70 ALA   (  89-)  A      0
  71 ALA   (  90-)  A      0
  73 PRO   (  92-)  A      0
  81 LEU   ( 100-)  A      0
  92 ALA   ( 111-)  A      0
  94 GLN   ( 113-)  A      0
  96 VAL   ( 115-)  A      0
 103 ARG   ( 122-)  A      0
 104 LEU   ( 123-)  A      0
 105 GLU   ( 124-)  A      0
 106 GLY   (  20-)  A      0
And so on for a total of 461 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 0.502
Model 2 : 3.903
Model 3 : 4.607
Model 4 : 5.255
Model 5 : 5.251
Model 6 : 5.469
Model 7 : 5.379
Model 8 : 5.347
Model 9 : 4.984
Model 10 : 4.929
Model 11 : 5.381

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].

   4 PRO   (  23-)  A   -65.3 envelop C-beta (-72 degrees)
 109 PRO   (  23-)  A  -117.1 half-chair C-delta/C-gamma (-126 degrees)
 114 PRO   (  28-)  A    44.9 envelop C-delta (36 degrees)
 219 PRO   (  28-)  A   -63.9 envelop C-beta (-72 degrees)
 319 PRO   (  23-)  A   107.9 envelop C-beta (108 degrees)
 324 PRO   (  28-)  A   -63.5 envelop C-beta (-72 degrees)
 429 PRO   (  28-)  A    43.7 envelop C-delta (36 degrees)
 598 PRO   (  92-)  A   101.2 envelop C-beta (108 degrees)
 634 PRO   (  23-)  A  -115.0 envelop C-gamma (-108 degrees)
 707 PRO   (  96-)  A    42.8 envelop C-delta (36 degrees)
 738 PRO   (  22-)  A  -114.2 envelop C-gamma (-108 degrees)
 739 PRO   (  23-)  A  -113.8 envelop C-gamma (-108 degrees)
 807 PRO   (  91-)  A  -117.5 half-chair C-delta/C-gamma (-126 degrees)
 913 PRO   (  92-)  A  -118.7 half-chair C-delta/C-gamma (-126 degrees)
 918 PRO   (  97-)  A  -116.9 envelop C-gamma (-108 degrees)
 949 PRO   (  23-)  A 1  113.5 envelop C-beta (108 degrees)
1053 PRO   (  22-)  A 1  104.3 envelop C-beta (108 degrees)
1054 PRO   (  23-)  A 1  112.8 envelop C-beta (108 degrees)
1059 PRO   (  28-)  A 1   35.9 envelop C-delta (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.

 860 MET   (  39-)  A      SD  <->  864 ARG   (  43-)  A      NH1    0.37    2.93
 755 MET   (  39-)  A      SD  <->  759 ARG   (  43-)  A      NH2    0.28    3.02
 860 MET   (  39-)  A      SD  <->  864 ARG   (  43-)  A      NH2    0.26    3.04
 650 MET   (  39-)  A      SD  <->  654 ARG   (  43-)  A      NH1    0.25    3.05
 951 THR   (  25-)  A 1    CB  <->  983 ARG   (  57-)  A 1    CB     0.22    2.98
 208 ARG   ( 122-)  A      O   <->  210 GLU   ( 124-)  A      N      0.20    2.50
 157 MET   (  71-)  A      SD  <->  165 ALA   (  79-)  A      CB     0.19    3.21
 238 LEU   (  47-)  A      O   <->  242 ALA   (  51-)  A      N      0.17    2.53
   4 PRO   (  23-)  A      O   <->    6 THR   (  25-)  A      N      0.16    2.54
   2 THR   (  21-)  A      N   <->    3 PRO   (  22-)  A      CD     0.16    2.84
 426 THR   (  25-)  A      CB  <->  458 ARG   (  57-)  A      CB     0.15    3.05
 261 VAL   (  70-)  A      CG1 <->  293 ILE   ( 102-)  A      CA     0.15    3.05
   3 PRO   (  22-)  A      N   <->    4 PRO   (  23-)  A      CD     0.15    2.85
 395 LEU   (  99-)  A      C   <->  396 LEU   ( 100-)  A      CG     0.15    2.95
 920 LEU   (  99-)  A      C   <->  921 LEU   ( 100-)  A      CG     0.15    2.95
  17 GLU   (  36-)  A      N   <->   18 PRO   (  37-)  A      CD     0.15    2.85
 733 ARG   ( 122-)  A      O   <->  735 GLU   ( 124-)  A      N      0.15    2.55
 118 ILE   (  32-)  A      O   <->  145 LEU   (  59-)  A      N      0.14    2.56
   5 SER   (  24-)  A      CB  <->   33 ARG   (  52-)  A      NE     0.14    2.96
 997 MET   (  71-)  A 1    SD  <-> 1005 ALA   (  79-)  A 1    CB     0.14    3.26
 776 ASP   (  60-)  A      CG  <->  777 ALA   (  61-)  A      N      0.14    2.86
1027 ASP   ( 101-)  A 1    O   <-> 1029 SER   ( 103-)  A 1    N      0.14    2.56
 367 MET   (  71-)  A      SD  <->  375 ALA   (  79-)  A      CB     0.13    3.27
1102 MET   (  71-)  A 1    SD  <-> 1105 THR   (  74-)  A 1    CG2    0.12    3.28
 961 VAL   (  35-)  A 1    CG2 <->  965 MET   (  39-)  A 1    SD     0.12    3.28
And so on for a total of 149 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

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

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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

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