WHAT IF Check report

This file was created 2012-01-31 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 pdb2uz5.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

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.219
Model 2 : 0.212
Model 3 : 0.208
Model 4 : 0.213
Model 5 : 0.215
Model 6 : 0.212
Model 7 : 0.212
Model 8 : 0.216
Model 9 : 0.215
Model 10 : 0.219

Note: Per-model averages for bond-angle check

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

Model 1 : 0.357
Model 2 : 0.346
Model 3 : 0.344
Model 4 : 0.340
Model 5 : 0.352
Model 6 : 0.339
Model 7 : 0.357
Model 8 : 0.350
Model 9 : 0.351
Model 10 : 0.347

Note: Per-model averages for chirality check

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

Model 1 : 0.375
Model 2 : 0.375
Model 3 : 0.383
Model 4 : 0.375
Model 5 : 0.372
Model 6 : 0.373
Model 7 : 0.379
Model 8 : 0.368
Model 9 : 0.375
Model 10 : 0.378

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 : -3.408

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.398
Model 2 : -3.403
Model 3 : -3.452
Model 4 : -3.357
Model 5 : -3.034
Model 6 : -3.058
Model 7 : -3.488
Model 8 : -3.732
Model 9 : -3.366
Model 10 : -3.790

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.

 372 THR   (  98-)  A    -2.8
 509 THR   (  98-)  A    -2.7
  98 THR   (  98-)  A    -2.7
1057 THR   (  98-)  A    -2.6
 646 THR   (  98-)  A    -2.5
 632 PRO   (  84-)  A    -2.5
  84 PRO   (  84-)  A    -2.5
1286 VAL   (  53-)  A 1   -2.4
 920 THR   (  98-)  A    -2.4
 318 LYS   (  44-)  A    -2.4
 235 THR   (  98-)  A    -2.4
 726 ASN   (  41-)  A    -2.4
 875 VAL   (  53-)  A    -2.4
1225 HIS   ( 129-)  A    -2.4
 495 PRO   (  84-)  A    -2.4
1088 HIS   ( 129-)  A    -2.4
 129 HIS   ( 129-)  A    -2.3
 247 GLY   ( 110-)  A    -2.3
 535 LEU   ( 124-)  A    -2.3
 403 HIS   ( 129-)  A    -2.3
 932 GLY   ( 110-)  A    -2.3
  53 VAL   (  53-)  A    -2.3
  44 LYS   (  44-)  A    -2.3
 814 HIS   ( 129-)  A    -2.3
 951 HIS   ( 129-)  A    -2.3
And so on for a total of 99 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.

  41 ASN   (  41-)  A  Poor phi/psi
  44 LYS   (  44-)  A  Poor phi/psi
  47 LYS   (  47-)  A  Poor phi/psi
  66 ASP   (  66-)  A  Poor phi/psi
 108 ALA   ( 108-)  A  Poor phi/psi
 113 SER   ( 113-)  A  Poor phi/psi
 119 GLY   ( 119-)  A  Poor phi/psi
 134 LYS   ( 134-)  A  Poor phi/psi
 135 LYS   ( 135-)  A  Poor phi/psi
 178 ASN   (  41-)  A  Poor phi/psi
 181 LYS   (  44-)  A  Poor phi/psi
 184 LYS   (  47-)  A  Poor phi/psi
 203 ASP   (  66-)  A  Poor phi/psi
 245 ALA   ( 108-)  A  Poor phi/psi
 247 GLY   ( 110-)  A  Poor phi/psi
 271 LYS   ( 134-)  A  Poor phi/psi
 273 SER   ( 136-)  A  Poor phi/psi
 315 ASN   (  41-)  A  Poor phi/psi
 318 LYS   (  44-)  A  Poor phi/psi
 321 LYS   (  47-)  A  Poor phi/psi
 340 ASP   (  66-)  A  Poor phi/psi
 359 GLY   (  85-)  A  Poor phi/psi
 382 ALA   ( 108-)  A  Poor phi/psi
 387 SER   ( 113-)  A  Poor phi/psi
 409 LYS   ( 135-)  A  Poor phi/psi
And so on for a total of 79 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 : -4.202

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 : -3.195
Model 2 : -5.397
Model 3 : -3.775
Model 4 : -4.249
Model 5 : -4.373
Model 6 : -4.465
Model 7 : -3.517
Model 8 : -4.050
Model 9 : -4.271
Model 10 : -4.726

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!

  23 PRO   (  23-)  A      0
  30 SER   (  30-)  A      0
  33 GLN   (  33-)  A      0
  38 ASN   (  38-)  A      0
  39 SER   (  39-)  A      0
  41 ASN   (  41-)  A      0
  43 VAL   (  43-)  A      0
  53 VAL   (  53-)  A      0
  59 LEU   (  59-)  A      0
  65 PHE   (  65-)  A      0
  66 ASP   (  66-)  A      0
  81 GLN   (  81-)  A      0
  82 VAL   (  82-)  A      0
  83 ILE   (  83-)  A      0
  95 ALA   (  95-)  A      0
  97 SER   (  97-)  A      0
 108 ALA   ( 108-)  A      0
 109 TYR   ( 109-)  A      0
 111 PRO   ( 111-)  A      0
 112 ARG   ( 112-)  A      0
 114 VAL   ( 114-)  A      0
 117 PRO   ( 117-)  A      0
 121 ASN   ( 121-)  A      0
 133 VAL   ( 133-)  A      0
 134 LYS   ( 134-)  A      0
And so on for a total of 494 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 : 1.061

Note: Per-model averages for omega angle check

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

Model 1 : 1.072
Model 2 : 1.073
Model 3 : 1.105
Model 4 : 1.044
Model 5 : 1.112
Model 6 : 1.066
Model 7 : 1.116
Model 8 : 1.086
Model 9 : 1.081
Model 10 : 1.073

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].

  45 PRO   (  45-)  A    30.8 envelop C-delta (36 degrees)
  84 PRO   (  84-)  A   100.7 envelop C-beta (108 degrees)
 111 PRO   ( 111-)  A  -113.5 envelop C-gamma (-108 degrees)
 182 PRO   (  45-)  A    25.4 half-chair N/C-delta (18 degrees)
 221 PRO   (  84-)  A  -127.9 half-chair C-delta/C-gamma (-126 degrees)
 248 PRO   ( 111-)  A  -115.4 envelop C-gamma (-108 degrees)
 319 PRO   (  45-)  A    25.5 half-chair N/C-delta (18 degrees)
 358 PRO   (  84-)  A  -127.9 half-chair C-delta/C-gamma (-126 degrees)
 385 PRO   ( 111-)  A  -112.0 envelop C-gamma (-108 degrees)
 456 PRO   (  45-)  A    51.5 half-chair C-delta/C-gamma (54 degrees)
 495 PRO   (  84-)  A  -131.6 half-chair C-delta/C-gamma (-126 degrees)
 515 PRO   ( 104-)  A  -112.4 envelop C-gamma (-108 degrees)
 593 PRO   (  45-)  A    28.2 envelop C-delta (36 degrees)
 632 PRO   (  84-)  A   104.9 envelop C-beta (108 degrees)
 642 PRO   (  94-)  A    49.5 half-chair C-delta/C-gamma (54 degrees)
 730 PRO   (  45-)  A    47.8 half-chair C-delta/C-gamma (54 degrees)
 789 PRO   ( 104-)  A  -112.3 envelop C-gamma (-108 degrees)
 867 PRO   (  45-)  A    26.7 half-chair N/C-delta (18 degrees)
 926 PRO   ( 104-)  A  -124.9 half-chair C-delta/C-gamma (-126 degrees)
 933 PRO   ( 111-)  A  -114.0 envelop C-gamma (-108 degrees)
 942 PRO   ( 120-)  A  -115.8 envelop C-gamma (-108 degrees)
1004 PRO   (  45-)  A    46.5 half-chair C-delta/C-gamma (54 degrees)
1063 PRO   ( 104-)  A  -119.5 half-chair C-delta/C-gamma (-126 degrees)
1070 PRO   ( 111-)  A  -115.3 envelop C-gamma (-108 degrees)
1079 PRO   ( 120-)  A  -113.8 envelop C-gamma (-108 degrees)
1141 PRO   (  45-)  A    28.0 envelop C-delta (36 degrees)
1200 PRO   ( 104-)  A  -121.1 half-chair C-delta/C-gamma (-126 degrees)
1278 PRO   (  45-)  A 1   30.5 envelop C-delta (36 degrees)
1327 PRO   (  94-)  A 1   44.2 envelop C-delta (36 degrees)
1337 PRO   ( 104-)  A 1 -120.9 half-chair C-delta/C-gamma (-126 degrees)
1344 PRO   ( 111-)  A 1 -114.9 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.

 457 GLY   (  46-)  A      O   <->  459 SER   (  48-)  A      N      0.27    2.43
 183 GLY   (  46-)  A      O   <->  185 SER   (  48-)  A      N      0.27    2.43
 594 GLY   (  46-)  A      O   <->  596 SER   (  48-)  A      N      0.26    2.44
 320 GLY   (  46-)  A      O   <->  322 SER   (  48-)  A      N      0.25    2.45
1005 GLY   (  46-)  A      O   <-> 1007 SER   (  48-)  A      N      0.25    2.45
 731 GLY   (  46-)  A      O   <->  733 SER   (  48-)  A      N      0.24    2.46
  46 GLY   (  46-)  A      O   <->   48 SER   (  48-)  A      N      0.24    2.46
1279 GLY   (  46-)  A 1    O   <-> 1281 SER   (  48-)  A 1    N      0.24    2.46
 868 GLY   (  46-)  A      O   <->  870 SER   (  48-)  A      N      0.24    2.46
 597 ASP   (  49-)  A      O   <->  626 GLN   (  78-)  A      NE2    0.22    2.48
 538 LYS   ( 127-)  A      NZ  <->  540 HIS   ( 129-)  A      ND1    0.22    2.78
 871 ASP   (  49-)  A      CG  <->  872 THR   (  50-)  A      N      0.22    2.78
1142 GLY   (  46-)  A      O   <-> 1144 SER   (  48-)  A      N      0.22    2.48
 339 PHE   (  65-)  A      CD1 <->  340 ASP   (  66-)  A      N      0.22    2.78
1343 GLY   ( 110-)  A 1    N   <-> 1344 PRO   ( 111-)  A 1    CD     0.21    2.79
  46 GLY   (  46-)  A      O   <->   49 ASP   (  49-)  A      N      0.21    2.49
1142 GLY   (  46-)  A      O   <-> 1145 ASP   (  49-)  A      N      0.21    2.49
 887 PHE   (  65-)  A      CD1 <->  888 ASP   (  66-)  A      N      0.20    2.80
1298 PHE   (  65-)  A 1    CD1 <-> 1299 ASP   (  66-)  A 1    N      0.19    2.81
 476 PHE   (  65-)  A      CD1 <->  477 ASP   (  66-)  A      N      0.19    2.81
1161 PHE   (  65-)  A      CD1 <-> 1162 ASP   (  66-)  A      N      0.19    2.81
 750 PHE   (  65-)  A      CD1 <->  751 ASP   (  66-)  A      N      0.19    2.81
  65 PHE   (  65-)  A      CD1 <->   66 ASP   (  66-)  A      N      0.19    2.81
 731 GLY   (  46-)  A      O   <->  734 ASP   (  49-)  A      N      0.19    2.51
 868 GLY   (  46-)  A      O   <->  871 ASP   (  49-)  A      N      0.19    2.51
And so on for a total of 211 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