WHAT IF Check report

This file was created 2012-01-25 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 pdb2e5k.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   ( 241-)  A    Zero
   2 SER   ( 242-)  A    Zero
   3 SER   ( 243-)  A    Zero
   4 GLY   ( 244-)  A    Zero
   5 SER   ( 245-)  A    Zero
   6 SER   ( 246-)  A    Zero
   7 GLY   ( 247-)  A    Zero
   8 SER   ( 248-)  A    Zero
   9 ARG   ( 249-)  A    Zero
  10 ASP   ( 250-)  A    Zero
  11 ILE   ( 251-)  A    Zero
  12 ARG   ( 252-)  A    Zero
  13 PHE   ( 253-)  A    Zero
  14 ALA   ( 254-)  A    Zero
  15 ASN   ( 255-)  A    Zero
  16 HIS   ( 256-)  A    Zero
  17 GLU   ( 257-)  A    Zero
  18 THR   ( 258-)  A    Zero
  19 LEU   ( 259-)  A    Zero
  20 GLN   ( 260-)  A    Zero
  21 VAL   ( 261-)  A    Zero
  22 ILE   ( 262-)  A    Zero
  23 TYR   ( 263-)  A    Zero
  24 PRO   ( 264-)  A    Zero
  25 TYR   ( 265-)  A    Zero
And so on for a total of 1880 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 : 0.126
Model 2 : 0.128
Model 3 : 0.128
Model 4 : 0.128
Model 5 : 0.129
Model 6 : 0.128
Model 7 : 0.127
Model 8 : 0.128
Model 9 : 0.128
Model 10 : 0.128
Model 11 : 0.127
Model 12 : 0.127
Model 13 : 0.128
Model 14 : 0.128
Model 15 : 0.129
Model 16 : 0.129
Model 17 : 0.127
Model 18 : 0.128
Model 19 : 0.127
Model 20 : 0.129

Note: Per-model averages for bond-angle check

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

Model 1 : 0.292
Model 2 : 0.292
Model 3 : 0.290
Model 4 : 0.291
Model 5 : 0.291
Model 6 : 0.291
Model 7 : 0.290
Model 8 : 0.292
Model 9 : 0.291
Model 10 : 0.291
Model 11 : 0.291
Model 12 : 0.293
Model 13 : 0.290
Model 14 : 0.291
Model 15 : 0.288
Model 16 : 0.291
Model 17 : 0.290
Model 18 : 0.290
Model 19 : 0.290
Model 20 : 0.290

Note: Per-model averages for chirality check

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

Model 1 : 0.299
Model 2 : 0.300
Model 3 : 0.299
Model 4 : 0.299
Model 5 : 0.300
Model 6 : 0.299
Model 7 : 0.299
Model 8 : 0.300
Model 9 : 0.300
Model 10 : 0.300
Model 11 : 0.299
Model 12 : 0.299
Model 13 : 0.299
Model 14 : 0.300
Model 15 : 0.299
Model 16 : 0.300
Model 17 : 0.300
Model 18 : 0.299
Model 19 : 0.299
Model 20 : 0.300

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 : -5.181

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.329
Model 2 : -5.245
Model 3 : -5.739
Model 4 : -5.295
Model 5 : -5.171
Model 6 : -5.288
Model 7 : -4.385
Model 8 : -5.118
Model 9 : -5.339
Model 10 : -5.076
Model 11 : -5.389
Model 12 : -4.638
Model 13 : -5.536
Model 14 : -5.636
Model 15 : -5.188
Model 16 : -5.465
Model 17 : -4.711
Model 18 : -5.503
Model 19 : -5.120
Model 20 : -4.458

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.

1235 PHE   ( 253-)  A 1   -2.9
 461 PHE   ( 325-)  A    -2.8
 740 THR   ( 322-)  A    -2.7
1231 ARG   ( 249-)  A 1   -2.6
1589 PHE   ( 325-)  A 1   -2.6
 458 THR   ( 322-)  A    -2.6
1683 PHE   ( 325-)  A 1   -2.6
 483 PHE   ( 253-)  A    -2.6
 751 SER   ( 333-)  A    -2.6
 764 ARG   ( 252-)  A    -2.6
  92 SER   ( 332-)  A    -2.5
1220 SER   ( 332-)  A 1   -2.5
 638 ILE   ( 314-)  A    -2.5
1785 SER   ( 333-)  A 1   -2.5
 920 ILE   ( 314-)  A 1   -2.5
1020 CYS   ( 320-)  A 1   -2.5
 451 THR   ( 315-)  A    -2.5
 826 ILE   ( 314-)  A    -2.4
1484 ILE   ( 314-)  A 1   -2.4
1234 ARG   ( 252-)  A 1   -2.4
 765 PHE   ( 253-)  A    -2.4
1014 ILE   ( 314-)  A 1   -2.4
 665 GLY   ( 247-)  A    -2.4
1390 ILE   ( 314-)  A 1   -2.4
1318 SER   ( 242-)  A 1   -2.4
And so on for a total of 200 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.

  28 GLN   ( 268-)  A  Poor phi/psi
  50 SER   ( 290-)  A  Poor phi/psi
  54 GLY   ( 294-)  A  Poor phi/psi
  84 ILE   ( 324-)  A  Poor phi/psi
 109 ASN   ( 255-)  A  Poor phi/psi
 148 GLY   ( 294-)  A  Poor phi/psi
 158 GLY   ( 304-)  A  Poor phi/psi
 238 SER   ( 290-)  A  Poor phi/psi
 242 GLY   ( 294-)  A  Poor phi/psi
 276 SER   ( 328-)  A  Poor phi/psi
 310 GLN   ( 268-)  A  Poor phi/psi
 332 SER   ( 290-)  A  Poor phi/psi
 380 GLY   ( 244-)  A  Poor phi/psi
 390 ALA   ( 254-)  A  Poor phi/psi
 430 GLY   ( 294-)  A  Poor phi/psi
 453 ALA   ( 317-)  A  Poor phi/psi
 455 GLU   ( 319-)  A  Poor phi/psi
 456 CYS   ( 320-)  A  Poor phi/psi
 457 SER   ( 321-)  A  Poor phi/psi
 458 THR   ( 322-)  A  Poor phi/psi
 483 PHE   ( 253-)  A  Poor phi/psi
 577 PHE   ( 253-)  A  Poor phi/psi
 618 GLY   ( 294-)  A  Poor phi/psi
 641 ALA   ( 317-)  A  Poor phi/psi
 653 SER   ( 329-)  A  Poor phi/psi
And so on for a total of 66 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 : -6.111

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 : -5.794
Model 2 : -6.026
Model 3 : -5.598
Model 4 : -6.344
Model 5 : -6.436
Model 6 : -6.273
Model 7 : -6.068
Model 8 : -6.115
Model 9 : -6.008
Model 10 : -6.015
Model 11 : -6.078
Model 12 : -5.769
Model 13 : -6.560
Model 14 : -6.283
Model 15 : -6.208
Model 16 : -6.081
Model 17 : -5.976
Model 18 : -5.799
Model 19 : -6.645
Model 20 : -6.145

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   ( 243-)  A      0
   6 SER   ( 246-)  A      0
  11 ILE   ( 251-)  A      0
  12 ARG   ( 252-)  A      0
  13 PHE   ( 253-)  A      0
  23 TYR   ( 263-)  A      0
  28 GLN   ( 268-)  A      0
  29 ASN   ( 269-)  A      0
  30 ASP   ( 270-)  A      0
  32 GLU   ( 272-)  A      0
  37 PRO   ( 277-)  A      0
  49 THR   ( 289-)  A      0
  50 SER   ( 290-)  A      0
  53 GLU   ( 293-)  A      0
  57 TYR   ( 297-)  A      0
  62 THR   ( 302-)  A      0
  63 THR   ( 303-)  A      0
  66 SER   ( 306-)  A      0
  73 TYR   ( 313-)  A      0
  74 ILE   ( 314-)  A      0
  78 ASP   ( 318-)  A      0
  79 GLU   ( 319-)  A      0
  80 CYS   ( 320-)  A      0
  83 TRP   ( 323-)  A      0
  84 ILE   ( 324-)  A      0
And so on for a total of 1087 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 : 0.101

Note: Per-model averages for omega angle check

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

Model 1 : 0.122
Model 2 : 0.144
Model 3 : 0.077
Model 4 : 0.096
Model 5 : 0.028
Model 6 : 0.057
Model 7 : 0.000
Model 8 : 0.000
Model 9 : 0.057
Model 10 : 0.082
Model 11 : 0.011
Model 12 : 0.000
Model 13 : 0.000
Model 14 : 0.166
Model 15 : 0.086
Model 16 : 0.000
Model 17 : 0.000
Model 18 : 0.179
Model 19 : 0.000
Model 20 : 0.124

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!

 651 GLY   ( 327-)  A   2.35   12
 278 GLY   ( 330-)  A   1.80   48
 463 GLY   ( 327-)  A   1.75   14
1038 GLY   ( 244-)  A 1  1.73   19
1229 GLY   ( 247-)  A 1  1.62   12
1027 GLY   ( 327-)  A 1  1.56   10

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.

 235 GLU   ( 287-)  A      CD  <->  245 TYR   ( 297-)  A      CE2    0.41    2.79
 137 MET   ( 283-)  A      SD  <->  138 SER   ( 284-)  A      N      0.35    2.85
 607 MET   ( 283-)  A      SD  <->  608 SER   ( 284-)  A      N      0.35    2.85
  43 MET   ( 283-)  A      SD  <->   44 SER   ( 284-)  A      N      0.35    2.85
 325 MET   ( 283-)  A      SD  <->  326 SER   ( 284-)  A      N      0.35    2.85
 419 MET   ( 283-)  A      SD  <->  420 SER   ( 284-)  A      N      0.35    2.85
1735 MET   ( 283-)  A 1    SD  <-> 1736 SER   ( 284-)  A 1    N      0.35    2.85
1077 MET   ( 283-)  A 1    SD  <-> 1078 SER   ( 284-)  A 1    N      0.35    2.85
 795 MET   ( 283-)  A      SD  <->  796 SER   ( 284-)  A      N      0.35    2.85
1265 MET   ( 283-)  A 1    SD  <-> 1266 SER   ( 284-)  A 1    N      0.35    2.85
1641 MET   ( 283-)  A 1    SD  <-> 1642 SER   ( 284-)  A 1    N      0.35    2.85
 701 MET   ( 283-)  A      SD  <->  702 SER   ( 284-)  A      N      0.34    2.86
1537 LEU   ( 273-)  A 1    CD1 <-> 1569 CYS   ( 305-)  A 1    SG     0.34    3.06
1819 LEU   ( 273-)  A 2    CD1 <-> 1851 CYS   ( 305-)  A 2    SG     0.34    3.06
1264 PHE   ( 282-)  A 1    CE2 <-> 1283 LEU   ( 301-)  A 1    CD1    0.33    2.87
1453 MET   ( 283-)  A 1    SD  <-> 1454 SER   ( 284-)  A 1    N      0.33    2.87
 513 MET   ( 283-)  A      SD  <->  514 SER   ( 284-)  A      N      0.33    2.87
 230 PHE   ( 282-)  A      CE2 <->  249 LEU   ( 301-)  A      CD1    0.33    2.87
1623 TYR   ( 265-)  A 1    CB  <-> 1633 LEU   ( 275-)  A 1    CD1    0.32    2.88
1358 PHE   ( 282-)  A 1    CE2 <-> 1377 LEU   ( 301-)  A 1    CD1    0.32    2.88
1359 MET   ( 283-)  A 1    SD  <-> 1360 SER   ( 284-)  A 1    N      0.31    2.89
1452 PHE   ( 282-)  A 1    CE2 <-> 1471 LEU   ( 301-)  A 1    CD1    0.31    2.89
1547 MET   ( 283-)  A 1    SD  <-> 1548 SER   ( 284-)  A 1    N      0.31    2.89
 418 PHE   ( 282-)  A      CE2 <->  437 LEU   ( 301-)  A      CD1    0.30    2.90
 231 MET   ( 283-)  A      SD  <->  232 SER   ( 284-)  A      N      0.30    2.90
And so on for a total of 577 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


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

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


Warning: Abnormal packing Z-score for sequential 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