WHAT IF Check report

This file was created 2011-12-22 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 pdb1eik.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   (   1-)  A    Zero
   2 LYS   (   2-)  A    Zero
   3 ARG   (   3-)  A    Zero
   4 GLU   (   4-)  A    Zero
   5 ILE   (   5-)  A    Zero
   6 LEU   (   6-)  A    Zero
   7 LYS   (   7-)  A    Zero
   8 HIS   (   8-)  A    Zero
   9 GLN   (   9-)  A    Zero
  10 LEU   (  10-)  A    Zero
  11 VAL   (  11-)  A    Zero
  12 PRO   (  12-)  A    Zero
  13 GLU   (  13-)  A    Zero
  14 HIS   (  14-)  A    Zero
  15 VAL   (  15-)  A    Zero
  16 ILE   (  16-)  A    Zero
  17 LEU   (  17-)  A    Zero
  18 ASN   (  18-)  A    Zero
  19 GLU   (  19-)  A    Zero
  20 SER   (  20-)  A    Zero
  21 GLU   (  21-)  A    Zero
  22 ALA   (  22-)  A    Zero
  23 LYS   (  23-)  A    Zero
  24 ARG   (  24-)  A    Zero
  25 VAL   (  25-)  A    Zero
And so on for a total of 770 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 : 0.233
Model 2 : 0.234
Model 3 : 0.235
Model 4 : 0.223
Model 5 : 0.233
Model 6 : 0.227
Model 7 : 0.235
Model 8 : 0.247
Model 9 : 0.235
Model 10 : 0.228

Note: Per-model averages for bond-angle check

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

Model 1 : 0.466
Model 2 : 0.464
Model 3 : 0.476
Model 4 : 0.448
Model 5 : 0.463
Model 6 : 0.458
Model 7 : 0.468
Model 8 : 0.465
Model 9 : 0.473
Model 10 : 0.451

Note: Per-model averages for chirality check

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

Model 1 : 0.569
Model 2 : 0.481
Model 3 : 0.568
Model 4 : 0.444
Model 5 : 0.468
Model 6 : 0.451
Model 7 : 0.493
Model 8 : 0.496
Model 9 : 0.531
Model 10 : 0.453

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 : -3.216

Note: Per-model averages for Ramachandran check

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

Model 1 : -2.919
Model 2 : -3.018
Model 3 : -2.955
Model 4 : -3.703
Model 5 : -3.050
Model 6 : -2.976
Model 7 : -3.152
Model 8 : -2.775
Model 9 : -3.558
Model 10 : -4.054

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.

 296 THR   (  65-)  A    -3.6
 373 THR   (  65-)  A    -3.5
 758 THR   (  65-)  A 1   -3.5
 527 THR   (  65-)  A    -3.5
  65 THR   (  65-)  A    -3.5
 142 THR   (  65-)  A    -3.5
 219 THR   (  65-)  A    -3.5
 681 THR   (  65-)  A    -3.5
 450 THR   (  65-)  A    -3.3
 604 THR   (  65-)  A    -3.3
  85 HIS   (   8-)  A    -3.0
   5 ILE   (   5-)  A    -2.9
 742 ILE   (  49-)  A 1   -2.8
 280 ILE   (  49-)  A    -2.8
 588 ILE   (  49-)  A    -2.8
 357 ILE   (  49-)  A    -2.8
 665 ILE   (  49-)  A    -2.8
 511 ILE   (  49-)  A    -2.8
 313 ILE   (   5-)  A    -2.8
 545 LEU   (   6-)  A    -2.7
 392 LYS   (   7-)  A    -2.7
 236 ILE   (   5-)  A    -2.7
 241 LEU   (  10-)  A    -2.6
   6 LEU   (   6-)  A    -2.6
 238 LYS   (   7-)  A    -2.6
And so on for a total of 98 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 LYS   (   2-)  A  Poor phi/psi
   7 LYS   (   7-)  A  Poor phi/psi
  30 ASP   (  30-)  A  Poor phi/psi
  50 GLY   (  50-)  A  Poor phi/psi
  54 GLY   (  54-)  A  Poor phi/psi
  65 THR   (  65-)  A  Poor phi/psi
  81 GLU   (   4-)  A  Poor phi/psi
  84 LYS   (   7-)  A  Poor phi/psi
  85 HIS   (   8-)  A  Poor phi/psi
 107 ASP   (  30-)  A  Poor phi/psi
 127 GLY   (  50-)  A  Poor phi/psi
 131 GLY   (  54-)  A  Poor phi/psi
 142 THR   (  65-)  A  Poor phi/psi
 158 GLU   (   4-)  A  Poor phi/psi
 159 ILE   (   5-)  A  Poor phi/psi
 160 LEU   (   6-)  A  Poor phi/psi
 161 LYS   (   7-)  A  Poor phi/psi
 166 PRO   (  12-)  A  Poor phi/psi
 184 ASP   (  30-)  A  Poor phi/psi
 204 GLY   (  50-)  A  Poor phi/psi
 208 GLY   (  54-)  A  Poor phi/psi
 219 THR   (  65-)  A  Poor phi/psi
 234 ARG   (   3-)  A  Poor phi/psi
 238 LYS   (   7-)  A  Poor phi/psi
 241 LEU   (  10-)  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 : -7.899

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 : -8.104
Model 2 : -7.974
Model 3 : -7.973
Model 4 : -7.974
Model 5 : -7.547
Model 6 : -7.621
Model 7 : -7.707
Model 8 : -7.816
Model 9 : -7.943
Model 10 : -8.327

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.

  97 SER   (  20-)  A    0.33
 477 VAL   (  15-)  A    0.36

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 ARG   (   3-)  A      0
   4 GLU   (   4-)  A      0
   5 ILE   (   5-)  A      0
   6 LEU   (   6-)  A      0
   7 LYS   (   7-)  A      0
   8 HIS   (   8-)  A      0
   9 GLN   (   9-)  A      0
  10 LEU   (  10-)  A      0
  29 LEU   (  29-)  A      0
  30 ASP   (  30-)  A      0
  31 ALA   (  31-)  A      0
  43 ASP   (  43-)  A      0
  48 ALA   (  48-)  A      0
  49 ILE   (  49-)  A      0
  53 ARG   (  53-)  A      0
  64 PRO   (  64-)  A      0
  65 THR   (  65-)  A      0
  66 ALA   (  66-)  A      0
  76 GLN   (  76-)  A      0
  77 ASP   (  77-)  A      0
  78 MET   (   1-)  A      0
  79 LYS   (   2-)  A      0
  82 ILE   (   5-)  A      0
  83 LEU   (   6-)  A      0
  84 LYS   (   7-)  A      0
And so on for a total of 313 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 : 1.492

Note: Per-model averages for omega angle check

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

Model 1 : 1.444
Model 2 : 1.261
Model 3 : 2.098
Model 4 : 1.175
Model 5 : 1.394
Model 6 : 1.099
Model 7 : 1.454
Model 8 : 1.456
Model 9 : 1.887
Model 10 : 1.309

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].

  44 PRO   (  44-)  A  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 110 PRO   (  33-)  A  -119.1 half-chair C-delta/C-gamma (-126 degrees)
 121 PRO   (  44-)  A  -124.4 half-chair C-delta/C-gamma (-126 degrees)
 166 PRO   (  12-)  A   115.7 envelop C-beta (108 degrees)
 187 PRO   (  33-)  A  -113.3 envelop C-gamma (-108 degrees)
 198 PRO   (  44-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 264 PRO   (  33-)  A  -114.2 envelop C-gamma (-108 degrees)
 268 PRO   (  37-)  A   -65.4 envelop C-beta (-72 degrees)
 275 PRO   (  44-)  A  -119.2 half-chair C-delta/C-gamma (-126 degrees)
 341 PRO   (  33-)  A  -116.1 envelop C-gamma (-108 degrees)
 352 PRO   (  44-)  A  -120.2 half-chair C-delta/C-gamma (-126 degrees)
 418 PRO   (  33-)  A  -114.8 envelop C-gamma (-108 degrees)
 429 PRO   (  44-)  A  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 495 PRO   (  33-)  A  -116.0 envelop C-gamma (-108 degrees)
 506 PRO   (  44-)  A  -120.3 half-chair C-delta/C-gamma (-126 degrees)
 572 PRO   (  33-)  A  -115.2 envelop C-gamma (-108 degrees)
 583 PRO   (  44-)  A  -120.0 half-chair C-delta/C-gamma (-126 degrees)
 603 PRO   (  64-)  A    49.1 half-chair C-delta/C-gamma (54 degrees)
 649 PRO   (  33-)  A  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 653 PRO   (  37-)  A    47.9 half-chair C-delta/C-gamma (54 degrees)
 660 PRO   (  44-)  A  -125.8 half-chair C-delta/C-gamma (-126 degrees)
 726 PRO   (  33-)  A 1 -116.1 envelop C-gamma (-108 degrees)
 737 PRO   (  44-)  A 1 -120.1 half-chair C-delta/C-gamma (-126 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.

 560 GLU   (  21-)  A      CG  <->  563 ARG   (  24-)  A      NH2    0.33    2.77
 252 GLU   (  21-)  A      CG  <->  255 ARG   (  24-)  A      NH2    0.30    2.80
 180 LEU   (  26-)  A      CD2 <->  190 LEU   (  36-)  A      CD1    0.30    2.90
  27 LYS   (  27-)  A      CE  <->   32 HIS   (  32-)  A      CG     0.30    2.90
 565 LEU   (  26-)  A      CD2 <->  575 LEU   (  36-)  A      CD1    0.30    2.90
 732 ILE   (  39-)  A 1    CG1 <->  766 ARG   (  73-)  A 1    NE     0.29    2.81
 655 ILE   (  39-)  A      CG2 <->  659 ASP   (  43-)  A      CG     0.29    2.91
 719 LEU   (  26-)  A 1    CD2 <->  725 HIS   (  32-)  A 1    C      0.29    2.91
 116 ILE   (  39-)  A      CG2 <->  120 ASP   (  43-)  A      CG     0.29    2.91
 334 LEU   (  26-)  A      CD2 <->  344 LEU   (  36-)  A      CD2    0.28    2.92
 488 LEU   (  26-)  A      CD2 <->  494 HIS   (  32-)  A      C      0.28    2.92
 732 ILE   (  39-)  A 1    CG2 <->  736 ASP   (  43-)  A 1    CB     0.28    2.92
 556 LEU   (  17-)  A      CD1 <->  597 LYS   (  58-)  A      CB     0.28    2.92
 411 LEU   (  26-)  A      CD2 <->  421 LEU   (  36-)  A      CD2    0.28    2.92
 333 VAL   (  25-)  A      CG1 <->  380 TYR   (  72-)  A      CZ     0.28    2.92
 118 THR   (  41-)  A      CG2 <->  152 VAL   (  75-)  A      CG1    0.28    2.92
 633 LEU   (  17-)  A      CB  <->  638 ALA   (  22-)  A      CB     0.28    2.92
 347 ILE   (  39-)  A      CG2 <->  351 ASP   (  43-)  A      CB     0.28    2.92
 657 THR   (  41-)  A      CG2 <->  691 VAL   (  75-)  A      CG1    0.28    2.92
  94 LEU   (  17-)  A      CD1 <->  135 LYS   (  58-)  A      CB     0.28    2.92
 270 ILE   (  39-)  A      CG2 <->  274 ASP   (  43-)  A      CB     0.28    2.92
 426 THR   (  41-)  A      CG2 <->  460 VAL   (  75-)  A      CG1    0.28    2.92
 248 LEU   (  17-)  A      CD1 <->  289 LYS   (  58-)  A      CB     0.27    2.93
 486 ARG   (  24-)  A      O   <->  490 GLU   (  28-)  A      N      0.27    2.43
 325 LEU   (  17-)  A      CD1 <->  380 TYR   (  72-)  A      CE2    0.27    2.93
And so on for a total of 465 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