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 pdb1iyf.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 ILE   (   2-)  A    Zero
   3 VAL   (   3-)  A    Zero
   4 PHE   (   4-)  A    Zero
   5 VAL   (   5-)  A    Zero
   6 ARG   (   6-)  A    Zero
   7 PHE   (   7-)  A    Zero
   8 ASN   (   8-)  A    Zero
   9 SER   (   9-)  A    Zero
  10 SER   (  10-)  A    Zero
  11 HIS   (  11-)  A    Zero
  12 GLY   (  12-)  A    Zero
  13 PHE   (  13-)  A    Zero
  14 PRO   (  14-)  A    Zero
  15 VAL   (  15-)  A    Zero
  16 GLU   (  16-)  A    Zero
  17 VAL   (  17-)  A    Zero
  18 ASP   (  18-)  A    Zero
  19 SER   (  19-)  A    Zero
  20 ASP   (  20-)  A    Zero
  21 THR   (  21-)  A    Zero
  22 SER   (  22-)  A    Zero
  23 ILE   (  23-)  A    Zero
  24 PHE   (  24-)  A    Zero
  25 GLN   (  25-)  A    Zero
And so on for a total of 760 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 : 0.304
Model 2 : 0.301
Model 3 : 0.307
Model 4 : 0.294
Model 5 : 0.298
Model 6 : 0.299
Model 7 : 0.300
Model 8 : 0.305
Model 9 : 0.298
Model 10 : 0.304

Note: Per-model averages for bond-angle check

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

Model 1 : 0.562
Model 2 : 0.573
Model 3 : 0.564
Model 4 : 0.549
Model 5 : 0.575
Model 6 : 0.559
Model 7 : 0.575
Model 8 : 0.566
Model 9 : 0.560
Model 10 : 0.562

Note: Per-model averages for chirality check

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

Model 1 : 0.631
Model 2 : 0.662
Model 3 : 0.627
Model 4 : 0.645
Model 5 : 0.651
Model 6 : 0.648
Model 7 : 0.644
Model 8 : 0.673
Model 9 : 0.648
Model 10 : 0.639

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 : -5.264

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.027
Model 2 : -5.220
Model 3 : -5.688
Model 4 : -5.509
Model 5 : -5.834
Model 6 : -4.758
Model 7 : -5.610
Model 8 : -5.081
Model 9 : -4.792
Model 10 : -5.121

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.

 477 THR   (  21-)  A    -3.0
 629 THR   (  21-)  A    -2.8
  50 LEU   (  50-)  A    -2.8
 354 LEU   (  50-)  A    -2.8
 582 LEU   (  50-)  A    -2.8
 473 VAL   (  17-)  A    -2.7
  97 THR   (  21-)  A    -2.7
 625 VAL   (  17-)  A    -2.7
 705 THR   (  21-)  A 1   -2.7
 401 THR   (  21-)  A    -2.6
 249 THR   (  21-)  A    -2.6
 430 LEU   (  50-)  A    -2.6
 173 THR   (  21-)  A    -2.6
 325 THR   (  21-)  A    -2.6
 553 THR   (  21-)  A    -2.6
 506 LEU   (  50-)  A    -2.6
  21 THR   (  21-)  A    -2.6
 340 VAL   (  36-)  A    -2.5
 658 LEU   (  50-)  A    -2.5
 720 VAL   (  36-)  A 1   -2.5
 264 VAL   (  36-)  A    -2.5
 416 VAL   (  36-)  A    -2.5
 188 VAL   (  36-)  A    -2.5
 112 VAL   (  36-)  A    -2.5
 568 VAL   (  36-)  A    -2.5
And so on for a total of 119 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.

   8 ASN   (   8-)  A  Poor phi/psi
  10 SER   (  10-)  A  Poor phi/psi
  17 VAL   (  17-)  A  Poor phi/psi
  22 SER   (  22-)  A  Poor phi/psi
  37 PRO   (  37-)  A  Poor phi/psi
  41 LEU   (  41-)  A  Poor phi/psi
  46 ALA   (  46-)  A  Poor phi/psi
  50 LEU   (  50-)  A  Poor phi/psi
  56 VAL   (  56-)  A  Poor phi/psi
  59 CYS   (  59-)  A  Poor phi/psi
  84 ASN   (   8-)  A  Poor phi/psi
  86 SER   (  10-)  A  Poor phi/psi
  93 VAL   (  17-)  A  Poor phi/psi
  97 THR   (  21-)  A  Poor phi/psi
  98 SER   (  22-)  A  Poor phi/psi
 113 PRO   (  37-)  A  Poor phi/psi
 116 GLN   (  40-)  A  Poor phi/psi
 117 LEU   (  41-)  A  Poor phi/psi
 122 ALA   (  46-)  A  Poor phi/psi
 126 LEU   (  50-)  A  Poor phi/psi
 132 VAL   (  56-)  A  Poor phi/psi
 135 CYS   (  59-)  A  Poor phi/psi
 160 ASN   (   8-)  A  Poor phi/psi
 162 SER   (  10-)  A  Poor phi/psi
 169 VAL   (  17-)  A  Poor phi/psi
And so on for a total of 106 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 : -8.028

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 : -7.823
Model 2 : -8.346
Model 3 : -7.909
Model 4 : -8.150
Model 5 : -7.855
Model 6 : -8.265
Model 7 : -7.844
Model 8 : -8.017
Model 9 : -7.880
Model 10 : -8.194

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 PHE   (   7-)  A      0
   8 ASN   (   8-)  A      0
   9 SER   (   9-)  A      0
  11 HIS   (  11-)  A      0
  16 GLU   (  16-)  A      0
  17 VAL   (  17-)  A      0
  19 SER   (  19-)  A      0
  21 THR   (  21-)  A      0
  22 SER   (  22-)  A      0
  23 ILE   (  23-)  A      0
  34 GLN   (  34-)  A      0
  38 ALA   (  38-)  A      0
  40 GLN   (  40-)  A      0
  41 LEU   (  41-)  A      0
  45 PHE   (  45-)  A      0
  46 ALA   (  46-)  A      0
  49 GLU   (  49-)  A      0
  50 LEU   (  50-)  A      0
  51 ARG   (  51-)  A      0
  52 ASN   (  52-)  A      0
  56 VAL   (  56-)  A      0
  57 GLN   (  57-)  A      0
  59 CYS   (  59-)  A      0
  60 ASP   (  60-)  A      0
  64 GLN   (  64-)  A      0
And so on for a total of 420 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 : 1.845

Note: Per-model averages for omega angle check

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

Model 1 : 1.828
Model 2 : 1.912
Model 3 : 1.816
Model 4 : 1.840
Model 5 : 1.834
Model 6 : 1.870
Model 7 : 1.838
Model 8 : 1.931
Model 9 : 1.861
Model 10 : 1.867

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  37 PRO   (  37-)  A    0.45 HIGH
 341 PRO   (  37-)  A    0.46 HIGH

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.

 639 ALA   (  31-)  A      CB  <->  645 PRO   (  37-)  A      O      0.57    2.23
 563 ALA   (  31-)  A      CB  <->  569 PRO   (  37-)  A      O      0.53    2.27
 692 ASN   (   8-)  A 1    O   <->  694 SER   (  10-)  A 1    N      0.52    2.18
 107 ALA   (  31-)  A      CB  <->  113 PRO   (  37-)  A      O      0.51    2.29
 411 ALA   (  31-)  A      CB  <->  417 PRO   (  37-)  A      O      0.51    2.29
 183 ALA   (  31-)  A      CB  <->  189 PRO   (  37-)  A      O      0.50    2.30
 259 ALA   (  31-)  A      CB  <->  265 PRO   (  37-)  A      O      0.49    2.31
 487 ALA   (  31-)  A      CB  <->  493 PRO   (  37-)  A      O      0.48    2.32
 435 THR   (  55-)  A      C   <->  439 CYS   (  59-)  A      CB     0.47    2.73
 715 ALA   (  31-)  A 1    CB  <->  721 PRO   (  37-)  A 1    O      0.46    2.34
 207 THR   (  55-)  A      C   <->  211 CYS   (  59-)  A      CB     0.46    2.74
  31 ALA   (  31-)  A      CB  <->   37 PRO   (  37-)  A      O      0.45    2.35
 463 PHE   (   7-)  A      O   <->  465 SER   (   9-)  A      N      0.43    2.27
 739 THR   (  55-)  A 1    C   <->  743 CYS   (  59-)  A 1    CB     0.43    2.77
 359 THR   (  55-)  A      C   <->  363 CYS   (  59-)  A      CB     0.43    2.77
 283 THR   (  55-)  A      C   <->  287 CYS   (  59-)  A      CB     0.42    2.78
 587 THR   (  55-)  A      C   <->  591 CYS   (  59-)  A      CB     0.42    2.78
 335 ALA   (  31-)  A      CB  <->  341 PRO   (  37-)  A      O      0.42    2.38
 131 THR   (  55-)  A      C   <->  135 CYS   (  59-)  A      CB     0.41    2.79
 311 PHE   (   7-)  A      O   <->  313 SER   (   9-)  A      N      0.41    2.29
  55 THR   (  55-)  A      C   <->   59 CYS   (  59-)  A      CB     0.41    2.79
 663 THR   (  55-)  A      C   <->  667 CYS   (  59-)  A      CB     0.40    2.80
 477 THR   (  21-)  A      CA  <->  512 VAL   (  56-)  A      CG1    0.39    2.81
 511 THR   (  55-)  A      C   <->  515 CYS   (  59-)  A      CB     0.39    2.81
 349 PHE   (  45-)  A      O   <->  352 LYS   (  48-)  A      N      0.39    2.31
And so on for a total of 1088 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: Structural average packing environment a bit worrysome

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