WHAT IF Check report

This file was created 2012-06-08 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 pdb2lln.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 MET   (   1-)  A    Zero
1256 ILE   ( 122-)  A 1   Zero
1280 GLY   (  20-)  A 1   Zero
1554 LEU   (  42-)  A 1   Zero
2285 ARG   (  17-)  A 1   Zero

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.144
Model 2 : 0.144
Model 3 : 0.143
Model 4 : 0.143
Model 5 : 0.144
Model 6 : 0.144
Model 7 : 0.143
Model 8 : 0.143
Model 9 : 0.145
Model 10 : 0.144
Model 11 : 0.144
Model 12 : 0.143
Model 13 : 0.143
Model 14 : 0.144
Model 15 : 0.144
Model 16 : 0.144
Model 17 : 0.144
Model 18 : 0.144
Model 19 : 0.143
Model 20 : 0.145

Note: Per-model averages for bond-angle check

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

Model 1 : 0.316
Model 2 : 0.317
Model 3 : 0.317
Model 4 : 0.316
Model 5 : 0.318
Model 6 : 0.317
Model 7 : 0.317
Model 8 : 0.316
Model 9 : 0.315
Model 10 : 0.315
Model 11 : 0.316
Model 12 : 0.316
Model 13 : 0.318
Model 14 : 0.315
Model 15 : 0.315
Model 16 : 0.317
Model 17 : 0.317
Model 18 : 0.316
Model 19 : 0.317
Model 20 : 0.315

Note: Per-model averages for chirality check

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

Model 1 : 0.349
Model 2 : 0.349
Model 3 : 0.349
Model 4 : 0.350
Model 5 : 0.351
Model 6 : 0.349
Model 7 : 0.349
Model 8 : 0.348
Model 9 : 0.350
Model 10 : 0.348
Model 11 : 0.348
Model 12 : 0.349
Model 13 : 0.350
Model 14 : 0.350
Model 15 : 0.349
Model 16 : 0.349
Model 17 : 0.349
Model 18 : 0.348
Model 19 : 0.350
Model 20 : 0.349

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 : -5.258

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.814
Model 2 : -5.186
Model 3 : -5.226
Model 4 : -5.058
Model 5 : -5.138
Model 6 : -5.404
Model 7 : -5.013
Model 8 : -4.976
Model 9 : -5.475
Model 10 : -5.098
Model 11 : -5.345
Model 12 : -5.388
Model 13 : -5.404
Model 14 : -5.381
Model 15 : -5.237
Model 16 : -5.019
Model 17 : -5.469
Model 18 : -5.412
Model 19 : -5.241
Model 20 : -4.872

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.

 362 TYR   ( 110-)  A    -3.7
1874 TYR   ( 110-)  A 1   -3.7
1370 TYR   ( 110-)  A 1   -3.4
 771 THR   (  15-)  A    -3.3
1496 TYR   ( 110-)  A 1   -3.3
1779 THR   (  15-)  A 1   -3.3
1778 THR   (  14-)  A 1   -3.3
1527 THR   (  15-)  A 1   -3.2
 115 HIS   ( 115-)  A    -3.2
1653 THR   (  15-)  A 1   -3.2
1401 THR   (  15-)  A 1   -3.2
1023 THR   (  15-)  A    -3.2
1149 THR   (  15-)  A 1   -3.2
 645 THR   (  15-)  A    -3.1
1526 THR   (  14-)  A 1   -3.1
2257 HIS   ( 115-)  A 1   -3.1
2283 THR   (  15-)  A 1   -3.1
 110 TYR   ( 110-)  A    -3.1
 518 THR   (  14-)  A    -3.0
 979 PHE   (  97-)  A    -3.0
2365 PHE   (  97-)  A 1   -2.9
 770 THR   (  14-)  A    -2.9
1087 THR   (  79-)  A    -2.9
1735 PHE   (  97-)  A 1   -2.9
  97 PHE   (  97-)  A    -2.9
And so on for a total of 443 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.

   5 ALA   (   5-)  A  Poor phi/psi
   8 LEU   (   8-)  A  Poor phi/psi
  28 ALA   (  28-)  A  Poor phi/psi
  72 HIS   (  72-)  A  Poor phi/psi
  80 ASN   (  80-)  A  Poor phi/psi
 107 CYS   ( 107-)  A  Poor phi/psi
 110 TYR   ( 110-)  A  Poor phi/psi
 114 GLY   ( 114-)  A  Poor phi/psi
 115 HIS   ( 115-)  A  Poor phi/psi
 120 GLY   ( 120-)  A  Poor phi/psi
 133 LYS   (   7-)  A  Poor phi/psi
 154 ALA   (  28-)  A  Poor phi/psi
 178 PRO   (  52-)  A  Poor phi/psi
 230 ARG   ( 104-)  A  Poor phi/psi
 231 ILE   ( 105-)  A  Poor phi/psi
 236 TYR   ( 110-)  A  Poor phi/psi
 237 CYS   ( 111-)  A  Poor phi/psi
 239 LEU   ( 113-)  A  Poor phi/psi
 242 GLN   ( 116-)  A  Poor phi/psi
 243 ASN   ( 117-)  A  Poor phi/psi
 259 LYS   (   7-)  A  Poor phi/psi
 260 LEU   (   8-)  A  Poor phi/psi
 280 ALA   (  28-)  A  Poor phi/psi
 357 ILE   ( 105-)  A  Poor phi/psi
 361 GLN   ( 109-)  A  Poor phi/psi
And so on for a total of 165 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 : -6.970

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 : -6.472
Model 2 : -7.121
Model 3 : -6.556
Model 4 : -7.248
Model 5 : -7.277
Model 6 : -6.991
Model 7 : -6.925
Model 8 : -7.118
Model 9 : -6.928
Model 10 : -6.830
Model 11 : -7.160
Model 12 : -6.960
Model 13 : -7.383
Model 14 : -6.745
Model 15 : -7.085
Model 16 : -6.773
Model 17 : -7.171
Model 18 : -6.808
Model 19 : -7.098
Model 20 : -6.742

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

1605 VAL   (  93-)  A 1   0.36

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!

   4 PRO   (   4-)  A      0
   5 ALA   (   5-)  A      0
   7 LYS   (   7-)  A      0
   8 LEU   (   8-)  A      0
  14 THR   (  14-)  A      0
  15 THR   (  15-)  A      0
  16 VAL   (  16-)  A      0
  18 GLN   (  18-)  A      0
  19 GLU   (  19-)  A      0
  23 ALA   (  23-)  A      0
  29 VAL   (  29-)  A      0
  34 PRO   (  34-)  A      0
  35 ASN   (  35-)  A      0
  46 PHE   (  46-)  A      0
  48 TYR   (  48-)  A      0
  52 PRO   (  52-)  A      0
  53 ILE   (  53-)  A      0
  57 GLN   (  57-)  A      0
  68 PRO   (  68-)  A      0
  69 ASP   (  69-)  A      0
  72 HIS   (  72-)  A      0
  77 GLU   (  77-)  A      0
  80 ASN   (  80-)  A      0
  84 GLU   (  84-)  A      0
  87 PRO   (  87-)  A      0
And so on for a total of 1399 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 : 0.228

Note: Per-model averages for omega angle check

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

Model 1 : 0.100
Model 2 : 0.178
Model 3 : 0.172
Model 4 : 0.067
Model 5 : 0.000
Model 6 : 0.106
Model 7 : 0.106
Model 8 : 0.000
Model 9 : 0.123
Model 10 : 0.000
Model 11 : 0.170
Model 12 : 0.000
Model 13 : 0.024
Model 14 : 0.000
Model 15 : 0.120
Model 16 : 0.104
Model 17 : 0.068
Model 18 : 0.000
Model 19 : 0.000
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!

 618 GLY   ( 114-)  A   2.16   80
 994 GLY   ( 112-)  A   2.12   15
2467 GLY   (  73-)  A 2  1.81   23
 451 GLY   (  73-)  A   1.74   22
1963 GLY   (  73-)  A 1  1.68   53
1081 GLY   (  73-)  A   1.66   41
2089 GLY   (  73-)  A 1  1.64   52
 983 GLY   ( 101-)  A   1.61   33
2495 GLY   ( 101-)  A 2  1.56   28
 731 GLY   ( 101-)  A   1.56   28
 577 GLY   (  73-)  A   1.54   43

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.

2376 ASN   ( 108-)  A 1    O   <-> 2378 TYR   ( 110-)  A 1    N      0.24    2.46
 296 PHE   (  44-)  A      CZ  <->  301 GLN   (  49-)  A      CD     0.19    3.01
1838 PHE   (  74-)  A 1    C   <-> 1873 GLN   ( 109-)  A 1    NE2    0.18    2.92
1049 VAL   (  41-)  A      CG2 <-> 1073 ILE   (  65-)  A      CG1    0.17    3.03
1616 ARG   ( 104-)  A 1    O   <-> 1617 ILE   ( 105-)  A 1    CG2    0.16    2.54
1082 PHE   (  74-)  A      C   <-> 1117 GLN   ( 109-)  A      NE2    0.16    2.94
 734 ARG   ( 104-)  A      O   <->  735 ILE   ( 105-)  A      CG2    0.16    2.54
2279 VAL   (  11-)  A 1    CG1 <-> 2284 VAL   (  16-)  A 1    CG2    0.16    3.04
 127 MET   (   1-)  A      C   <->  128 VAL   (   2-)  A      CG2    0.16    2.94
 230 ARG   ( 104-)  A      O   <->  231 ILE   ( 105-)  A      CG2    0.16    2.54
1556 PHE   (  44-)  A 1    CE2 <-> 1558 PHE   (  46-)  A 1    C      0.15    3.05
 326 PHE   (  74-)  A      C   <->  361 GLN   ( 109-)  A      NE2    0.15    2.95
1364 ARG   ( 104-)  A 1    O   <-> 1365 ILE   ( 105-)  A 1    CG2    0.15    2.55
1709 ILE   (  71-)  A 1    CG2 <-> 1710 HIS   (  72-)  A 1    N      0.15    2.85
1490 ARG   ( 104-)  A 1    O   <-> 1491 ILE   ( 105-)  A 1    CG2    0.15    2.55
1919 VAL   (  29-)  A 1    CG2 <-> 1929 VAL   (  39-)  A 1    CG1    0.15    3.05
2143 MET   (   1-)  A 1    C   <-> 2144 VAL   (   2-)  A 1    CG1    0.15    2.95
1742 ARG   ( 104-)  A 1    O   <-> 1743 ILE   ( 105-)  A 1    CG2    0.14    2.56
 937 VAL   (  55-)  A      CG1 <->  945 PHE   (  63-)  A      CZ     0.14    3.06
1929 VAL   (  39-)  A 1    CG2 <-> 1953 PHE   (  63-)  A 1    CD2    0.14    3.06
2215 GLY   (  73-)  A 1    C   <-> 2251 GLN   ( 109-)  A 1    NE2    0.14    2.96
1301 VAL   (  41-)  A 1    CG2 <-> 1325 ILE   (  65-)  A 1    CG1    0.14    3.06
 535 GLN   (  31-)  A      NE2 <->  537 GLY   (  33-)  A      O      0.13    2.57
 535 GLN   (  31-)  A      NE2 <->  541 TYR   (  37-)  A      CE2    0.13    2.97
1175 VAL   (  41-)  A 1    CG2 <-> 1199 ILE   (  65-)  A 1    CG1    0.13    3.07
And so on for a total of 344 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