WHAT IF Check report

This file was created 2012-01-04 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 pdb1m8m.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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  11 GLU   (  17-)  A
 271 VAL   (  53-)  A

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 GLU   (   7-)  A    Zero
   2 LEU   (   8-)  A    Zero
   3 VAL   (   9-)  A    Zero
   4 LEU   (  10-)  A    Zero
   5 ALA   (  11-)  A    Zero
   6 LEU   (  12-)  A    Zero
   7 TYR   (  13-)  A    Zero
   8 ASP   (  14-)  A    Zero
   9 TYR   (  15-)  A    Zero
  10 GLN   (  16-)  A    Zero
  11 GLU   (  17-)  A    Zero
  12 LYS   (  18-)  A    Zero
  13 SER   (  19-)  A    Zero
  14 PRO   (  20-)  A    Zero
  15 ARG   (  21-)  A    Zero
  16 GLU   (  22-)  A    Zero
  17 VAL   (  23-)  A    Zero
  18 THR   (  24-)  A    Zero
  19 MET   (  25-)  A    Zero
  20 LYS   (  26-)  A    Zero
  21 LYS   (  27-)  A    Zero
  22 GLY   (  28-)  A    Zero
  23 ASP   (  29-)  A    Zero
  24 ILE   (  30-)  A    Zero
  25 LEU   (  31-)  A    Zero
And so on for a total of 672 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 : 0.147
Model 2 : 0.155
Model 3 : 0.160
Model 4 : 0.157
Model 5 : 0.159
Model 6 : 0.170
Model 7 : 0.178
Model 8 : 0.173
Model 9 : 0.174
Model 10 : 0.162
Model 11 : 0.172
Model 12 : 0.163

Note: Per-model averages for bond-angle check

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

Model 1 : 0.232
Model 2 : 0.243
Model 3 : 0.245
Model 4 : 0.240
Model 5 : 0.238
Model 6 : 0.249
Model 7 : 0.252
Model 8 : 0.249
Model 9 : 0.251
Model 10 : 0.244
Model 11 : 0.251
Model 12 : 0.242

Note: Per-model averages for chirality check

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

Model 1 : 0.265
Model 2 : 0.278
Model 3 : 0.276
Model 4 : 0.264
Model 5 : 0.268
Model 6 : 0.263
Model 7 : 0.253
Model 8 : 0.244
Model 9 : 0.252
Model 10 : 0.281
Model 11 : 0.260
Model 12 : 0.279

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 : -8.532

Note: Per-model averages for Ramachandran check

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

Model 1 : -8.275
Model 2 : -7.519
Model 3 : -8.587
Model 4 : -8.284
Model 5 : -8.020
Model 6 : -9.252
Model 7 : -8.980
Model 8 : -8.312
Model 9 : -8.884
Model 10 : -8.683
Model 11 : -8.330
Model 12 : -9.255

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.

   7 TYR   (  13-)  A    -3.8
  65 TYR   (  15-)  A    -3.7
 555 TYR   (  57-)  A 1   -3.7
 591 THR   (  37-)  A 1   -3.7
 418 THR   (  32-)  A    -3.6
 298 THR   (  24-)  A    -3.6
 410 THR   (  24-)  A    -3.6
 634 THR   (  24-)  A 1   -3.5
 466 THR   (  24-)  A    -3.5
 567 TYR   (  13-)  A 1   -3.4
 177 TYR   (  15-)  A    -3.4
  63 TYR   (  13-)  A    -3.4
 550 PHE   (  52-)  A 1   -3.4
 242 THR   (  24-)  A    -3.3
 474 THR   (  32-)  A    -3.2
 586 THR   (  32-)  A 1   -3.2
 382 PHE   (  52-)  A    -3.1
 623 TYR   (  13-)  A 1   -3.1
 119 TYR   (  13-)  A    -3.0
 367 THR   (  37-)  A    -2.9
 372 TRP   (  42-)  A    -2.9
 371 TRP   (  41-)  A    -2.9
  74 THR   (  24-)  A    -2.9
 435 ARG   (  49-)  A    -2.9
 529 LEU   (  31-)  A 1   -2.9
And so on for a total of 246 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 LEU   (   8-)  A  Poor phi/psi
   6 LEU   (  12-)  A  Poor phi/psi
   7 TYR   (  13-)  A  Poor phi/psi
   8 ASP   (  14-)  A  Poor phi/psi
   9 TYR   (  15-)  A  Poor phi/psi
  12 LYS   (  18-)  A  Poor phi/psi
  13 SER   (  19-)  A  Poor phi/psi
  14 PRO   (  20-)  A  Poor phi/psi
  21 LYS   (  27-)  A  Poor phi/psi
  24 ILE   (  30-)  A  Poor phi/psi
  29 ASN   (  35-)  A  Poor phi/psi
  30 SER   (  36-)  A  Poor phi/psi
  35 TRP   (  41-)  A  Poor phi/psi
  42 ASP   (  48-)  A  Poor phi/psi
  43 ARG   (  49-)  A  Poor phi/psi
  49 ALA   (  55-)  A  Poor phi/psi
  52 VAL   (  58-)  A  Poor phi/psi
  58 LEU   (   8-)  A  Poor phi/psi
  61 ALA   (  11-)  A  Poor phi/psi
  63 TYR   (  13-)  A  Poor phi/psi
  64 ASP   (  14-)  A  Poor phi/psi
  65 TYR   (  15-)  A  Poor phi/psi
  69 SER   (  19-)  A  Poor phi/psi
  71 ARG   (  21-)  A  Poor phi/psi
  74 THR   (  24-)  A  Poor phi/psi
And so on for a total of 274 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 : -7.719

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 : -7.470
Model 2 : -7.310
Model 3 : -7.724
Model 4 : -7.806
Model 5 : -7.960
Model 6 : -8.114
Model 7 : -8.013
Model 8 : -7.414
Model 9 : -7.528
Model 10 : -7.249
Model 11 : -7.769
Model 12 : -8.270

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 VAL   (   9-)  A      0
   5 ALA   (  11-)  A      0
   6 LEU   (  12-)  A      0
   7 TYR   (  13-)  A      0
   8 ASP   (  14-)  A      0
   9 TYR   (  15-)  A      0
  10 GLN   (  16-)  A      0
  11 GLU   (  17-)  A      0
  12 LYS   (  18-)  A      0
  13 SER   (  19-)  A      0
  14 PRO   (  20-)  A      0
  15 ARG   (  21-)  A      0
  16 GLU   (  22-)  A      0
  17 VAL   (  23-)  A      0
  21 LYS   (  27-)  A      0
  23 ASP   (  29-)  A      0
  24 ILE   (  30-)  A      0
  28 LEU   (  34-)  A      0
  29 ASN   (  35-)  A      0
  30 SER   (  36-)  A      0
  31 THR   (  37-)  A      0
  34 ASP   (  40-)  A      0
  35 TRP   (  41-)  A      0
  36 TRP   (  42-)  A      0
  37 LYS   (  43-)  A      0
And so on for a total of 610 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 : -3.323

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 : 0.155

Note: Per-model averages for omega angle check

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

Model 1 : 0.166
Model 2 : 0.132
Model 3 : 0.140
Model 4 : 0.104
Model 5 : 0.195
Model 6 : 0.125
Model 7 : 0.190
Model 8 : 0.217
Model 9 : 0.133
Model 10 : 0.289
Model 11 : 0.221
Model 12 : 0.234

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].

 126 PRO   (  20-)  A  -115.9 envelop C-gamma (-108 degrees)
 384 PRO   (  54-)  A    48.3 half-chair C-delta/C-gamma (54 degrees)
 518 PRO   (  20-)  A 1 -121.3 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.

 515 GLU   (  17-)  A 1    N   <->  522 THR   (  24-)  A 1    CG2    0.29    2.81
 651 TRP   (  41-)  A 1    CG  <->  652 TRP   (  42-)  A 1    N      0.28    2.72
  35 TRP   (  41-)  A      NE1 <->   36 TRP   (  42-)  A      CZ2    0.26    2.84
 241 VAL   (  23-)  A      CG1 <->  267 ARG   (  49-)  A      NE     0.26    2.84
 598 VAL   (  44-)  A 1    CG2 <->  607 VAL   (  53-)  A 1    CG2    0.24    2.96
 452 LEU   (  10-)  A      CD2 <->  501 LYS   (  59-)  A      CD     0.24    2.96
 374 VAL   (  44-)  A      CG1 <->  383 VAL   (  53-)  A      CG2    0.24    2.96
 565 ALA   (  11-)  A 1    CB  <->  579 MET   (  25-)  A 1    SD     0.23    3.17
 650 ASP   (  40-)  A 1    O   <->  652 TRP   (  42-)  A 1    N      0.23    2.47
  58 LEU   (   8-)  A      CD1 <->  109 LYS   (  59-)  A      NZ     0.23    2.87
 409 VAL   (  23-)  A      CG2 <->  411 MET   (  25-)  A      SD     0.22    3.18
 341 ALA   (  11-)  A      O   <->  343 TYR   (  13-)  A      N      0.22    2.48
 117 ALA   (  11-)  A      CB  <->  131 MET   (  25-)  A      SD     0.21    3.19
 355 MET   (  25-)  A      SD  <->  376 VAL   (  46-)  A      CG2    0.21    3.19
 456 ASP   (  14-)  A      CG  <->  495 VAL   (  53-)  A      CG1    0.21    2.99
 370 ASP   (  40-)  A      O   <->  372 TRP   (  42-)  A      N      0.21    2.49
 229 ALA   (  11-)  A      CB  <->  231 TYR   (  13-)  A      CE1    0.21    2.99
 452 LEU   (  10-)  A      CD2 <->  501 LYS   (  59-)  A      CE     0.21    2.99
 451 VAL   (   9-)  A      CG2 <->  473 LEU   (  31-)  A      CD1    0.21    2.99
  28 LEU   (  34-)  A      CD2 <->   29 ASN   (  35-)  A      CG     0.21    2.99
 409 VAL   (  23-)  A      CG2 <->  410 THR   (  24-)  A      N      0.21    2.79
 286 LEU   (  12-)  A      CD1 <->  331 TYR   (  57-)  A      CZ     0.20    3.00
 285 ALA   (  11-)  A      CB  <->  329 ALA   (  55-)  A      CB     0.20    3.00
 258 ASP   (  40-)  A      CG  <->  276 VAL   (  58-)  A      CG1    0.20    3.00
 595 TRP   (  41-)  A 1    CH2 <->  606 PHE   (  52-)  A 1    CD2    0.20    3.00
And so on for a total of 380 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


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

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

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

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