WHAT IF Check report

This file was created 2011-12-28 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 pdb1f40.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1081 GPI   ( 108-)  A  1

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 : 0.832
Model 2 : 0.832
Model 3 : 0.832
Model 4 : 0.834
Model 5 : 0.834
Model 6 : 0.834
Model 7 : 0.831
Model 8 : 0.834
Model 9 : 0.833
Model 10 : 0.833

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

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.

  14 THR   (  14-)  A      CA   CB   CG2 118.17    4.5
  14 THR   (  14-)  A      CA   CB   OG1 103.06   -4.4
  20 GLN   (  20-)  A      NE2  CD   OE1 118.26   -4.3
  25 HIS   (  25-)  A      CA   CB   CG  109.39   -4.4
  25 HIS   (  25-)  A      CB   CG   ND1 129.29    5.1
  25 HIS   (  25-)  A      CG   ND1  CE1 110.46    4.9
  32 ASP   (  32-)  A      CA   CB   CG  116.71    4.1
  36 PHE   (  36-)  A      CA   CB   CG  119.40    5.6
  42 ARG   (  42-)  A      CG   CD   NE  120.46    5.9
  43 ASN   (  43-)  A      CB   CG   ND2 123.56    4.8
  43 ASN   (  43-)  A      ND2  CG   OD1 116.26   -6.3
  52 LYS   (  52-)  A      CB   CG   CD   96.08   -6.6
  59 TRP   (  59-)  A      CG   CD2  CE2 102.04   -4.3
  70 GLN   (  70-)  A      NE2  CD   OE1 118.37   -4.2
  73 LYS   (  73-)  A      CB   CG   CD  100.52   -4.7
  79 ASP   (  79-)  A      CA   CB   CG  118.81    6.2
  87 HIS   (  87-)  A      CB   CG   ND1 129.55    5.3
  87 HIS   (  87-)  A      CB   CG   CD2 123.43   -4.4
 100 ASP   ( 100-)  A      N    CA   C    98.87   -4.4
 101 VAL   ( 101-)  A      CG1  CB   CG2 101.31   -4.3
 121 THR   (  14-)  A      CA   CB   CG2 118.17    4.5
 121 THR   (  14-)  A      CA   CB   OG1 103.05   -4.4
 127 GLN   (  20-)  A      NE2  CD   OE1 118.27   -4.3
 132 HIS   (  25-)  A      CA   CB   CG  109.38   -4.4
 132 HIS   (  25-)  A      CB   CG   ND1 129.28    5.1
And so on for a total of 202 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.473
Model 2 : 1.476
Model 3 : 1.474
Model 4 : 1.475
Model 5 : 1.476
Model 6 : 1.475
Model 7 : 1.476
Model 8 : 1.474
Model 9 : 1.475
Model 10 : 1.475

Note: Per-model averages for chirality check

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

Model 1 : 1.252
Model 2 : 1.254
Model 3 : 1.252
Model 4 : 1.255
Model 5 : 1.252
Model 6 : 1.253
Model 7 : 1.254
Model 8 : 1.254
Model 9 : 1.252
Model 10 : 1.253

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : 0.252
Model 2 : 0.268
Model 3 : 0.258
Model 4 : 0.246
Model 5 : 0.261
Model 6 : 0.255
Model 7 : 0.257
Model 8 : 0.273
Model 9 : 0.235
Model 10 : 0.229

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.

 870 THR   (  14-)  A    -2.2
 549 THR   (  14-)  A    -2.2
 335 THR   (  14-)  A    -2.2
 763 THR   (  14-)  A    -2.2
 228 THR   (  14-)  A    -2.2
  14 THR   (  14-)  A    -2.2
 442 THR   (  14-)  A    -2.2
 656 THR   (  14-)  A    -2.2
 121 THR   (  14-)  A    -2.2
 977 THR   (  14-)  A 1   -2.2
  30 LEU   (  30-)  A    -2.2
 886 LEU   (  30-)  A    -2.2
 351 LEU   (  30-)  A    -2.2
 993 LEU   (  30-)  A 1   -2.2
 672 LEU   (  30-)  A    -2.2
 137 LEU   (  30-)  A    -2.2
 244 LEU   (  30-)  A    -2.2
 565 LEU   (  30-)  A    -2.2
 458 LEU   (  30-)  A    -2.2
 779 LEU   (  30-)  A    -2.2
 219 GLU   (   5-)  A    -2.1
 326 GLU   (   5-)  A    -2.1
 112 GLU   (   5-)  A    -2.1
 647 GLU   (   5-)  A    -2.1
 968 GLU   (   5-)  A 1   -2.1
 540 GLU   (   5-)  A    -2.1
   5 GLU   (   5-)  A    -2.1
 861 GLU   (   5-)  A    -2.1
 754 GLU   (   5-)  A    -2.1
 433 GLU   (   5-)  A    -2.1
 716 LEU   (  74-)  A    -2.0
 609 LEU   (  74-)  A    -2.0
 288 LEU   (  74-)  A    -2.0
 823 LEU   (  74-)  A    -2.0
 395 LEU   (  74-)  A    -2.0
 930 LEU   (  74-)  A    -2.0
 502 LEU   (  74-)  A    -2.0
 181 LEU   (  74-)  A    -2.0
1037 LEU   (  74-)  A 1   -2.0
  74 LEU   (  74-)  A    -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.

  13 ARG   (  13-)  A  Poor phi/psi
  43 ASN   (  43-)  A  Poor phi/psi
  53 GLN   (  53-)  A  Poor phi/psi
  81 ALA   (  81-)  A  Poor phi/psi
  89 GLY   (  89-)  A  Poor phi/psi
  94 HIS   (  94-)  A  Poor phi/psi
 120 ARG   (  13-)  A  Poor phi/psi
 150 ASN   (  43-)  A  Poor phi/psi
 160 GLN   (  53-)  A  Poor phi/psi
 188 ALA   (  81-)  A  Poor phi/psi
 196 GLY   (  89-)  A  Poor phi/psi
 201 HIS   (  94-)  A  Poor phi/psi
 227 ARG   (  13-)  A  Poor phi/psi
 257 ASN   (  43-)  A  Poor phi/psi
 267 GLN   (  53-)  A  Poor phi/psi
 295 ALA   (  81-)  A  Poor phi/psi
 303 GLY   (  89-)  A  Poor phi/psi
 308 HIS   (  94-)  A  Poor phi/psi
 334 ARG   (  13-)  A  Poor phi/psi
 364 ASN   (  43-)  A  Poor phi/psi
 374 GLN   (  53-)  A  Poor phi/psi
 402 ALA   (  81-)  A  Poor phi/psi
 410 GLY   (  89-)  A  Poor phi/psi
 415 HIS   (  94-)  A  Poor phi/psi
 441 ARG   (  13-)  A  Poor phi/psi
And so on for a total of 60 lines.

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 : -1.149
Model 2 : -1.143
Model 3 : -1.152
Model 4 : -1.140
Model 5 : -1.132
Model 6 : -1.211
Model 7 : -1.127
Model 8 : -1.107
Model 9 : -1.128
Model 10 : -1.146

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!

  11 ASP   (  11-)  A      0
  13 ARG   (  13-)  A      0
  14 THR   (  14-)  A      0
  18 ARG   (  18-)  A      0
  35 LYS   (  35-)  A      0
  36 PHE   (  36-)  A      0
  37 ASP   (  37-)  A      0
  42 ARG   (  42-)  A      0
  50 LEU   (  50-)  A      0
  52 LYS   (  52-)  A      0
  54 GLU   (  54-)  A      0
  68 VAL   (  68-)  A      0
  80 TYR   (  80-)  A      0
  81 ALA   (  81-)  A      0
  82 TYR   (  82-)  A      0
  84 ALA   (  84-)  A      0
  85 THR   (  85-)  A      0
  87 HIS   (  87-)  A      0
  88 PRO   (  88-)  A      0
  90 ILE   (  90-)  A      0
  93 PRO   (  93-)  A      0
  94 HIS   (  94-)  A      0
 106 LEU   ( 106-)  A      0
 107 GLU   ( 107-)  A      0
 108 GLY   (   1-)  A      0
And so on for a total of 456 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 5.506
Model 2 : 5.497
Model 3 : 5.503
Model 4 : 5.501
Model 5 : 5.508
Model 6 : 5.510
Model 7 : 5.513
Model 8 : 5.510
Model 9 : 5.515
Model 10 : 5.504

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].

  78 PRO   (  78-)  A  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 185 PRO   (  78-)  A  -126.0 half-chair C-delta/C-gamma (-126 degrees)
 292 PRO   (  78-)  A  -126.1 half-chair C-delta/C-gamma (-126 degrees)
 399 PRO   (  78-)  A  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 506 PRO   (  78-)  A  -126.3 half-chair C-delta/C-gamma (-126 degrees)
 613 PRO   (  78-)  A  -126.1 half-chair C-delta/C-gamma (-126 degrees)
 720 PRO   (  78-)  A  -126.1 half-chair C-delta/C-gamma (-126 degrees)
 827 PRO   (  78-)  A  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 934 PRO   (  78-)  A  -126.1 half-chair C-delta/C-gamma (-126 degrees)
1041 PRO   (  78-)  A 1 -126.1 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.

  87 HIS   (  87-)  A      NE2 <-> 1081 GPI   ( 108-)  A      C10    0.15    2.95
  87 HIS   (  87-)  A      CE1 <-> 1081 GPI   ( 108-)  A      C11    0.12    3.08
 433 GLU   (   5-)  A      O   <->  501 LYS   (  73-)  A      N      0.01    2.69
 219 GLU   (   5-)  A      O   <->  287 LYS   (  73-)  A      N      0.01    2.69
 754 GLU   (   5-)  A      O   <->  822 LYS   (  73-)  A      N      0.01    2.69
   5 GLU   (   5-)  A      O   <->   73 LYS   (  73-)  A      N      0.01    2.69
 861 GLU   (   5-)  A      O   <->  929 LYS   (  73-)  A      N      0.01    2.69
 647 GLU   (   5-)  A      O   <->  715 LYS   (  73-)  A      N      0.01    2.69
 326 GLU   (   5-)  A      O   <->  394 LYS   (  73-)  A      N      0.01    2.69
 540 GLU   (   5-)  A      O   <->  608 LYS   (  73-)  A      N      0.01    2.69
 112 GLU   (   5-)  A      O   <->  180 LYS   (  73-)  A      N      0.01    2.69
 968 GLU   (   5-)  A 1    O   <-> 1036 LYS   (  73-)  A 1    N      0.01    2.69

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


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