WHAT IF Check report

This file was created 2012-01-19 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 pdb2d9f.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

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

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 GLY   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 GLY   (   4-)  A    Zero
   5 SER   (   5-)  A    Zero
   6 SER   (   6-)  A    Zero
   7 GLY   (   7-)  A    Zero
   8 GLU   (   8-)  A    Zero
   9 GLU   (   9-)  A    Zero
  10 TRP   (  10-)  A    Zero
  11 LEU   (  11-)  A    Zero
  12 ASP   (  12-)  A    Zero
  13 ILE   (  13-)  A    Zero
  14 LEU   (  14-)  A    Zero
  15 GLY   (  15-)  A    Zero
  16 ASN   (  16-)  A    Zero
  17 GLY   (  17-)  A    Zero
  18 LEU   (  18-)  A    Zero
  19 LEU   (  19-)  A    Zero
  20 ARG   (  20-)  A    Zero
  21 LYS   (  21-)  A    Zero
  22 LYS   (  22-)  A    Zero
  23 THR   (  23-)  A    Zero
  24 LEU   (  24-)  A    Zero
  25 VAL   (  25-)  A    Zero
And so on for a total of 2700 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 : 0.127
Model 2 : 0.127
Model 3 : 0.127
Model 4 : 0.125
Model 5 : 0.126
Model 6 : 0.126
Model 7 : 0.126
Model 8 : 0.126
Model 9 : 0.126
Model 10 : 0.125
Model 11 : 0.126
Model 12 : 0.126
Model 13 : 0.127
Model 14 : 0.127
Model 15 : 0.125
Model 16 : 0.126
Model 17 : 0.125
Model 18 : 0.126
Model 19 : 0.126
Model 20 : 0.126

Note: Per-model averages for bond-angle check

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

Model 1 : 0.275
Model 2 : 0.276
Model 3 : 0.275
Model 4 : 0.276
Model 5 : 0.275
Model 6 : 0.275
Model 7 : 0.275
Model 8 : 0.273
Model 9 : 0.276
Model 10 : 0.276
Model 11 : 0.276
Model 12 : 0.277
Model 13 : 0.276
Model 14 : 0.275
Model 15 : 0.276
Model 16 : 0.275
Model 17 : 0.276
Model 18 : 0.276
Model 19 : 0.276
Model 20 : 0.275

Note: Per-model averages for chirality check

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

Model 1 : 0.304
Model 2 : 0.303
Model 3 : 0.302
Model 4 : 0.303
Model 5 : 0.303
Model 6 : 0.303
Model 7 : 0.302
Model 8 : 0.304
Model 9 : 0.303
Model 10 : 0.303
Model 11 : 0.303
Model 12 : 0.303
Model 13 : 0.304
Model 14 : 0.302
Model 15 : 0.303
Model 16 : 0.303
Model 17 : 0.302
Model 18 : 0.302
Model 19 : 0.302
Model 20 : 0.301

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 : -5.281

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.155
Model 2 : -5.629
Model 3 : -5.631
Model 4 : -5.504
Model 5 : -4.933
Model 6 : -5.095
Model 7 : -5.151
Model 8 : -5.453
Model 9 : -5.121
Model 10 : -5.166
Model 11 : -5.144
Model 12 : -4.938
Model 13 : -5.314
Model 14 : -5.720
Model 15 : -5.402
Model 16 : -5.159
Model 17 : -5.150
Model 18 : -5.056
Model 19 : -5.638
Model 20 : -5.271

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.

1186 ILE   ( 106-)  A    -2.6
 511 ILE   ( 106-)  A    -2.6
 241 ILE   ( 106-)  A    -2.6
1861 ILE   ( 106-)  A 1   -2.6
1591 ILE   ( 106-)  A 1   -2.5
 106 ILE   ( 106-)  A    -2.5
1726 ILE   ( 106-)  A 1   -2.5
1012 CYS   (  67-)  A    -2.5
 646 ILE   ( 106-)  A    -2.5
 781 ILE   ( 106-)  A    -2.5
2497 CYS   (  67-)  A 1   -2.5
2365 ILE   (  70-)  A 1   -2.5
 805 SER   ( 130-)  A    -2.5
  67 CYS   (  67-)  A    -2.5
2131 ILE   ( 106-)  A 1   -2.5
2500 ILE   (  70-)  A 1   -2.5
 742 CYS   (  67-)  A    -2.5
1124 LEU   (  44-)  A    -2.5
 202 CYS   (  67-)  A    -2.5
 916 ILE   ( 106-)  A    -2.5
2568 SER   (   3-)  A 2   -2.5
1015 ILE   (  70-)  A    -2.4
 989 LEU   (  44-)  A    -2.4
1957 CYS   (  67-)  A 1   -2.4
 607 CYS   (  67-)  A    -2.4
And so on for a total of 201 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.

  51 GLY   (  51-)  A  Poor phi/psi
  96 TYR   (  96-)  A  Poor phi/psi
 103 SER   ( 103-)  A  PRO omega poor
 129 MET   ( 129-)  A  Poor phi/psi
 186 GLY   (  51-)  A  Poor phi/psi
 238 SER   ( 103-)  A  PRO omega poor
 304 PRO   (  34-)  A  Poor phi/psi
 321 GLY   (  51-)  A  Poor phi/psi
 337 CYS   (  67-)  A  Poor phi/psi
 373 SER   ( 103-)  A  PRO omega poor
 413 GLU   (   8-)  A  Poor phi/psi
 456 GLY   (  51-)  A  Poor phi/psi
 508 SER   ( 103-)  A  PRO omega poor
 549 GLU   (   9-)  A  Poor phi/psi
 591 GLY   (  51-)  A  Poor phi/psi
 636 TYR   (  96-)  A  Poor phi/psi
 643 SER   ( 103-)  A  PRO omega poor
 726 GLY   (  51-)  A  Poor phi/psi
 742 CYS   (  67-)  A  Poor phi/psi
 771 TYR   (  96-)  A  Poor phi/psi
 778 SER   ( 103-)  A  PRO omega poor
 805 SER   ( 130-)  A  Poor phi/psi
 906 TYR   (  96-)  A  Poor phi/psi
 913 SER   ( 103-)  A  PRO omega poor
 947 SER   (   2-)  A  Poor phi/psi
And so on for a total of 82 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 : -6.097

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 : -5.968
Model 2 : -6.263
Model 3 : -5.499
Model 4 : -6.181
Model 5 : -6.425
Model 6 : -5.981
Model 7 : -5.292
Model 8 : -6.440
Model 9 : -6.158
Model 10 : -5.990
Model 11 : -6.053
Model 12 : -6.207
Model 13 : -5.725
Model 14 : -5.978
Model 15 : -6.209
Model 16 : -6.301
Model 17 : -6.228
Model 18 : -6.327
Model 19 : -6.185
Model 20 : -6.526

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 SER   (   3-)  A      0
   5 SER   (   5-)  A      0
   6 SER   (   6-)  A      0
   9 GLU   (   9-)  A      0
  10 TRP   (  10-)  A      0
  13 ILE   (  13-)  A      0
  16 ASN   (  16-)  A      0
  19 LEU   (  19-)  A      0
  31 SER   (  31-)  A      0
  33 ARG   (  33-)  A      0
  36 LYS   (  36-)  A      0
  48 LEU   (  48-)  A      0
  50 ASN   (  50-)  A      0
  53 ARG   (  53-)  A      0
  59 GLU   (  59-)  A      0
  64 LEU   (  64-)  A      0
  66 ASP   (  66-)  A      0
  67 CYS   (  67-)  A      0
  68 ASP   (  68-)  A      0
  69 VAL   (  69-)  A      0
  70 ILE   (  70-)  A      0
  79 LEU   (  79-)  A      0
  82 VAL   (  82-)  A      0
  95 CYS   (  95-)  A      0
  96 TYR   (  96-)  A      0
And so on for a total of 1245 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 : 0.000

Note: Per-model averages for omega angle check

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

Model 1 : 0.196
Model 2 : 0.000
Model 3 : 0.176
Model 4 : 0.058
Model 5 : 0.099
Model 6 : 0.000
Model 7 : 0.093
Model 8 : 0.000
Model 9 : 0.093
Model 10 : 0.000
Model 11 : 0.098
Model 12 : 0.000
Model 13 : 0.064
Model 14 : 0.109
Model 15 : 0.162
Model 16 : 0.096
Model 17 : 0.143
Model 18 : 0.077
Model 19 : 0.113
Model 20 : 0.000

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2434 GLY   (   4-)  A 1  1.99   13
2021 GLY   ( 131-)  A 1  1.81   11
1751 GLY   ( 131-)  A 1  1.77   15
1616 GLY   ( 131-)  A 1  1.58   16
 705 GLY   (  30-)  A   1.52   17

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.

 510 TYR   ( 105-)  A      CD1 <->  511 ILE   ( 106-)  A      N      0.36    2.64
1390 VAL   (  40-)  A 1    CG2 <-> 1412 PHE   (  62-)  A 1    CE1    0.36    2.84
1930 VAL   (  40-)  A 1    CG2 <-> 1952 PHE   (  62-)  A 1    CE1    0.36    2.84
 854 LEU   (  44-)  A      CD2 <->  855 GLN   (  45-)  A      N      0.35    2.65
 719 LEU   (  44-)  A      CD2 <->  720 GLN   (  45-)  A      N      0.35    2.65
1799 LEU   (  44-)  A 1    CD2 <-> 1800 GLN   (  45-)  A 1    N      0.35    2.65
1938 LEU   (  48-)  A 1    CD2 <-> 1944 VAL   (  54-)  A 1    CG2    0.35    2.85
 993 LEU   (  48-)  A      CD2 <->  999 VAL   (  54-)  A      CG2    0.34    2.86
1124 LEU   (  44-)  A      CD2 <-> 1125 GLN   (  45-)  A      N      0.34    2.66
2328 ARG   (  33-)  A 1    NH1 <-> 2374 LEU   (  79-)  A 1    C      0.33    2.77
2478 LEU   (  48-)  A 1    CD2 <-> 2484 VAL   (  54-)  A 1    CG2    0.32    2.88
1520 VAL   (  35-)  A 1    CG1 <-> 1523 GLN   (  38-)  A 1    CD     0.31    2.89
 989 LEU   (  44-)  A      CD2 <->  990 GLN   (  45-)  A      N      0.31    2.69
1903 ILE   (  13-)  A 1    CG1 <-> 1969 LEU   (  79-)  A 1    CD1    0.30    2.90
1664 LEU   (  44-)  A 1    CD2 <-> 1665 GLN   (  45-)  A 1    N      0.30    2.70
2204 LEU   (  44-)  A 1    CD2 <-> 2205 GLN   (  45-)  A 1    N      0.30    2.70
1529 LEU   (  44-)  A 1    CD2 <-> 1530 GLN   (  45-)  A 1    N      0.30    2.70
 627 MET   (  87-)  A      SD  <->  654 LEU   ( 114-)  A      C      0.30    3.10
1533 LEU   (  48-)  A 1    CD2 <-> 1539 VAL   (  54-)  A 1    CG2    0.29    2.91
 580 VAL   (  40-)  A      CG2 <->  602 PHE   (  62-)  A      CE1    0.29    2.91
 445 VAL   (  40-)  A      CG2 <->  467 PHE   (  62-)  A      CE1    0.29    2.91
  40 VAL   (  40-)  A      CG2 <->   62 PHE   (  62-)  A      CE1    0.29    2.91
1094 LEU   (  14-)  A      CD1 <-> 1174 TYR   (  94-)  A      CZ     0.29    2.91
1677 GLU   (  57-)  A 1    OE1 <-> 1679 GLU   (  59-)  A 1    N      0.29    2.41
1185 TYR   ( 105-)  A      CD1 <-> 1186 ILE   ( 106-)  A      N      0.29    2.71
And so on for a total of 713 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential 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: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

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