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 pdb2js2.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

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

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   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 MET   (   3-)  A    Zero
   4 ALA   (   4-)  A    Zero
   5 GLU   (   5-)  A    Zero
   6 GLU   (   6-)  A    Zero
   7 VAL   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 VAL   (   9-)  A    Zero
  10 VAL   (  10-)  A    Zero
  11 ALA   (  11-)  A    Zero
  12 LYS   (  12-)  A    Zero
  13 PHE   (  13-)  A    Zero
  14 ASP   (  14-)  A    Zero
  15 TYR   (  15-)  A    Zero
  16 VAL   (  16-)  A    Zero
  17 ALA   (  17-)  A    Zero
  18 GLN   (  18-)  A    Zero
  19 GLN   (  19-)  A    Zero
  20 GLU   (  20-)  A    Zero
  21 GLN   (  21-)  A    Zero
  22 GLU   (  22-)  A    Zero
  23 LEU   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 ILE   (  25-)  A    Zero
And so on for a total of 1260 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 : 0.265
Model 2 : 0.247
Model 3 : 0.259
Model 4 : 0.261
Model 5 : 0.240
Model 6 : 0.254
Model 7 : 0.244
Model 8 : 0.256
Model 9 : 0.262
Model 10 : 0.263
Model 11 : 0.284
Model 12 : 0.262
Model 13 : 0.262
Model 14 : 0.251
Model 15 : 0.255
Model 16 : 0.266
Model 17 : 0.257
Model 18 : 0.251
Model 19 : 0.273
Model 20 : 0.262

Note: Per-model averages for bond-angle check

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

Model 1 : 0.396
Model 2 : 0.397
Model 3 : 0.387
Model 4 : 0.381
Model 5 : 0.367
Model 6 : 0.367
Model 7 : 0.387
Model 8 : 0.383
Model 9 : 0.374
Model 10 : 0.384
Model 11 : 0.396
Model 12 : 0.411
Model 13 : 0.406
Model 14 : 0.388
Model 15 : 0.365
Model 16 : 0.398
Model 17 : 0.409
Model 18 : 0.367
Model 19 : 0.400
Model 20 : 0.379

Note: Per-model averages for chirality check

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

Model 1 : 0.411
Model 2 : 0.410
Model 3 : 0.398
Model 4 : 0.413
Model 5 : 0.421
Model 6 : 0.417
Model 7 : 0.423
Model 8 : 0.428
Model 9 : 0.425
Model 10 : 0.442
Model 11 : 0.437
Model 12 : 0.455
Model 13 : 0.436
Model 14 : 0.425
Model 15 : 0.417
Model 16 : 0.402
Model 17 : 0.440
Model 18 : 0.383
Model 19 : 0.413
Model 20 : 0.418

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -2.479
Model 2 : -1.833
Model 3 : -2.552
Model 4 : -2.260
Model 5 : -2.766
Model 6 : -2.915
Model 7 : -2.853
Model 8 : -1.897
Model 9 : -2.050
Model 10 : -2.925
Model 11 : -2.440
Model 12 : -3.312
Model 13 : -2.988
Model 14 : -2.684
Model 15 : -2.941
Model 16 : -2.838
Model 17 : -2.581
Model 18 : -1.592
Model 19 : -3.741
Model 20 : -2.725

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.

 879 ARG   (  60-)  A 1   -2.7
1235 LYS   (  38-)  A 2   -2.5
 970 ILE   (  25-)  A 1   -2.4
 277 ILE   (  25-)  A    -2.4
1033 ILE   (  25-)  A 1   -2.4
 529 ILE   (  25-)  A    -2.4
 278 LYS   (  26-)  A    -2.4
 592 ILE   (  25-)  A 1   -2.4
  88 ILE   (  25-)  A    -2.4
 403 ILE   (  25-)  A    -2.4
1160 LYS   (  26-)  A 1   -2.4
 781 ILE   (  25-)  A 1   -2.4
 844 ILE   (  25-)  A 1   -2.3
1173 SER   (  39-)  A 1   -2.3
1070 ASN   (  62-)  A 1   -2.3
 214 ILE   (  25-)  A    -2.3
 151 ILE   (  25-)  A    -2.3
 466 ILE   (  25-)  A    -2.3
 984 SER   (  39-)  A 1   -2.3
 907 ILE   (  25-)  A 1   -2.2
1159 ILE   (  25-)  A 1   -2.2
 656 LYS   (  26-)  A 1   -2.2
 718 ILE   (  25-)  A 1   -2.2
 418 TRP   (  40-)  A    -2.2
 340 ILE   (  25-)  A    -2.2
  25 ILE   (  25-)  A    -2.2
1096 ILE   (  25-)  A 1   -2.2
  78 TYR   (  15-)  A    -2.2
 669 SER   (  39-)  A 1   -2.2
 655 ILE   (  25-)  A 1   -2.1
1222 ILE   (  25-)  A 2   -2.1
 695 SER   (   2-)  A 1   -2.1
 960 TYR   (  15-)  A 1   -2.1
1086 TYR   (  15-)  A 1   -2.1
 502 LYS   (  61-)  A    -2.1
 317 SER   (   2-)  A    -2.1
 257 GLU   (   5-)  A    -2.1
  89 LYS   (  26-)  A    -2.0
 666 ASP   (  36-)  A 1   -2.0
   6 GLU   (   6-)  A    -2.0
   7 VAL   (   7-)  A    -2.0
 229 TRP   (  40-)  A    -2.0
 708 TYR   (  15-)  A 1   -2.0
 291 SER   (  39-)  A    -2.0
 771 TYR   (  15-)  A 1   -2.0

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.

  28 ASN   (  28-)  A  Poor phi/psi
  91 ASN   (  28-)  A  Poor phi/psi
 102 SER   (  39-)  A  Poor phi/psi
 111 ASN   (  48-)  A  Poor phi/psi
 154 ASN   (  28-)  A  Poor phi/psi
 164 LYS   (  38-)  A  Poor phi/psi
 174 ASN   (  48-)  A  Poor phi/psi
 188 ASN   (  62-)  A  Poor phi/psi
 217 ASN   (  28-)  A  Poor phi/psi
 237 ASN   (  48-)  A  Poor phi/psi
 249 ARG   (  60-)  A  Poor phi/psi
 280 ASN   (  28-)  A  Poor phi/psi
 291 SER   (  39-)  A  Poor phi/psi
 300 ASN   (  48-)  A  Poor phi/psi
 312 ARG   (  60-)  A  Poor phi/psi
 343 ASN   (  28-)  A  Poor phi/psi
 353 LYS   (  38-)  A  Poor phi/psi
 355 TRP   (  40-)  A  Poor phi/psi
 363 ASN   (  48-)  A  Poor phi/psi
 375 ARG   (  60-)  A  Poor phi/psi
 381 MET   (   3-)  A  Poor phi/psi
 406 ASN   (  28-)  A  Poor phi/psi
 417 SER   (  39-)  A  Poor phi/psi
 418 TRP   (  40-)  A  Poor phi/psi
 426 ASN   (  48-)  A  Poor phi/psi
And so on for a total of 79 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 : -3.744

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 : -3.580
Model 2 : -3.169
Model 3 : -4.235
Model 4 : -2.881
Model 5 : -2.955
Model 6 : -4.228
Model 7 : -3.109
Model 8 : -3.672
Model 9 : -3.593
Model 10 : -3.626
Model 11 : -4.270
Model 12 : -4.207
Model 13 : -2.992
Model 14 : -4.111
Model 15 : -4.324
Model 16 : -4.764
Model 17 : -4.696
Model 18 : -2.851
Model 19 : -4.097
Model 20 : -3.517

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!

   7 VAL   (   7-)  A      0
  13 PHE   (  13-)  A      0
  18 GLN   (  18-)  A      0
  19 GLN   (  19-)  A      0
  20 GLU   (  20-)  A      0
  21 GLN   (  21-)  A      0
  27 LYS   (  27-)  A      0
  28 ASN   (  28-)  A      0
  35 ASP   (  35-)  A      0
  36 ASP   (  36-)  A      0
  37 SER   (  37-)  A      0
  40 TRP   (  40-)  A      0
  47 MET   (  47-)  A      0
  50 THR   (  50-)  A      0
  52 PHE   (  52-)  A      0
  57 TYR   (  57-)  A      0
  59 GLU   (  59-)  A      0
  62 ASN   (  62-)  A      0
  63 SER   (  63-)  A      0
  64 GLY   (   1-)  A      0
  65 SER   (   2-)  A      0
  76 PHE   (  13-)  A      0
  82 GLN   (  19-)  A      0
  83 GLU   (  20-)  A      0
  84 GLN   (  21-)  A      0
And so on for a total of 713 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 : 3.538

Note: Per-model averages for omega angle check

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

Model 1 : 3.898
Model 2 : 3.857
Model 3 : 3.459
Model 4 : 3.516
Model 5 : 3.603
Model 6 : 3.866
Model 7 : 3.255
Model 8 : 3.554
Model 9 : 3.649
Model 10 : 3.637
Model 11 : 3.709
Model 12 : 3.730
Model 13 : 3.491
Model 14 : 3.712
Model 15 : 3.177
Model 16 : 3.368
Model 17 : 3.645
Model 18 : 3.294
Model 19 : 3.115
Model 20 : 3.393

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].

 999 PRO   (  54-)  A 1 -112.7 envelop C-gamma (-108 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.

1242 ASN   (  45-)  A 2    CG  <-> 1243 SER   (  46-)  A 2    N      0.16    2.84
1116 ASN   (  45-)  A 1    CG  <-> 1117 SER   (  46-)  A 1    N      0.15    2.85
1053 ASN   (  45-)  A 1    CG  <-> 1054 SER   (  46-)  A 1    N      0.15    2.85
1020 LYS   (  12-)  A 1    NZ  <-> 1067 GLU   (  59-)  A 1    CD     0.15    2.95
 965 GLU   (  20-)  A 1    OE1 <->  994 LYS   (  49-)  A 1    NZ     0.15    2.55
 666 ASP   (  36-)  A 1    OD1 <->  671 TRP   (  41-)  A 1    NE1    0.11    2.59
 549 ASN   (  45-)  A      CG  <->  550 SER   (  46-)  A      N      0.10    2.90
1179 ASN   (  45-)  A 1    CG  <-> 1180 SER   (  46-)  A 1    N      0.10    2.90
 956 ALA   (  11-)  A 1    N   <->  974 GLU   (  29-)  A 1    O      0.10    2.60
 414 ASP   (  36-)  A      OD2 <->  438 ARG   (  60-)  A      NH2    0.10    2.60
 209 GLU   (  20-)  A      OE1 <->  238 LYS   (  49-)  A      NZ     0.10    2.60
 830 ALA   (  11-)  A 1    N   <->  848 GLU   (  29-)  A 1    O      0.10    2.60
 234 ASN   (  45-)  A      CG  <->  235 SER   (  46-)  A      N      0.10    2.90
 540 ASP   (  36-)  A      OD1 <->  545 TRP   (  41-)  A      NE1    0.09    2.61
 218 GLU   (  29-)  A      OE2 <->  219 ARG   (  30-)  A      NH1    0.09    2.61
 389 ALA   (  11-)  A      N   <->  407 GLU   (  29-)  A      O      0.09    2.61
 264 LYS   (  12-)  A      NZ  <->  311 GLU   (  59-)  A      OE2    0.09    2.61
 360 ASN   (  45-)  A      CG  <->  361 SER   (  46-)  A      N      0.09    2.91
 636 GLU   (   6-)  A 1    OE1 <->  674 ARG   (  44-)  A 1    NH2    0.09    2.61
1211 ASP   (  14-)  A 2    OD1 <-> 1223 LYS   (  26-)  A 2    NZ     0.09    2.61
 162 ASP   (  36-)  A      OD2 <->  186 ARG   (  60-)  A      NH2    0.09    2.61
 516 LYS   (  12-)  A      NZ  <->  563 GLU   (  59-)  A      OE2    0.09    2.61
 339 ASP   (  24-)  A      OD2 <->  364 LYS   (  49-)  A      NZ     0.09    2.61
1145 ALA   (  11-)  A 1    N   <-> 1163 GLU   (  29-)  A 1    O      0.09    2.61
1106 ASP   (  35-)  A 1    OD1 <-> 1113 ARG   (  42-)  A 1    NH2    0.08    2.62
And so on for a total of 108 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

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: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure