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 pdb2jmo.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.

1102 ARG   (  62-)  A 1   Zero
1122 HIS   (   2-)  A 1   Zero
1528 TYR   (   8-)  A 2   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 : 0.138
Model 2 : 0.136
Model 3 : 0.138
Model 4 : 0.137
Model 5 : 0.136
Model 6 : 0.138
Model 7 : 0.137
Model 8 : 0.140
Model 9 : 0.137
Model 10 : 0.139
Model 11 : 0.137
Model 12 : 0.138
Model 13 : 0.139
Model 14 : 0.136
Model 15 : 0.137
Model 16 : 0.138
Model 17 : 0.141
Model 18 : 0.141
Model 19 : 0.137
Model 20 : 0.139

Note: Per-model averages for bond-angle check

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

Model 1 : 0.419
Model 2 : 0.419
Model 3 : 0.419
Model 4 : 0.420
Model 5 : 0.419
Model 6 : 0.422
Model 7 : 0.417
Model 8 : 0.418
Model 9 : 0.420
Model 10 : 0.419
Model 11 : 0.420
Model 12 : 0.419
Model 13 : 0.417
Model 14 : 0.420
Model 15 : 0.420
Model 16 : 0.420
Model 17 : 0.419
Model 18 : 0.418
Model 19 : 0.419
Model 20 : 0.419

Note: Per-model averages for chirality check

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

Model 1 : 0.292
Model 2 : 0.293
Model 3 : 0.290
Model 4 : 0.296
Model 5 : 0.294
Model 6 : 0.289
Model 7 : 0.293
Model 8 : 0.290
Model 9 : 0.296
Model 10 : 0.294
Model 11 : 0.290
Model 12 : 0.297
Model 13 : 0.292
Model 14 : 0.293
Model 15 : 0.292
Model 16 : 0.290
Model 17 : 0.293
Model 18 : 0.298
Model 19 : 0.292
Model 20 : 0.292

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 : -5.115

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.747
Model 2 : -5.095
Model 3 : -5.790
Model 4 : -5.198
Model 5 : -5.410
Model 6 : -4.209
Model 7 : -4.349
Model 8 : -5.315
Model 9 : -4.994
Model 10 : -5.254
Model 11 : -4.605
Model 12 : -5.012
Model 13 : -6.113
Model 14 : -5.164
Model 15 : -4.974
Model 16 : -4.871
Model 17 : -4.874
Model 18 : -4.853
Model 19 : -5.881
Model 20 : -4.600

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.

 562 HIS   (   2-)  A    -3.1
 654 TYR   (  14-)  A    -3.0
1451 TYR   (  11-)  A 1   -2.9
1368 TYR   (   8-)  A 1   -2.9
 648 TYR   (   8-)  A    -2.8
 365 LYS   (  45-)  A    -2.8
 248 TYR   (   8-)  A    -2.8
 808 TYR   (   8-)  A 1   -2.7
 285 LYS   (  45-)  A    -2.7
 980 VAL   (  20-)  A 1   -2.7
 900 VAL   (  20-)  A 1   -2.7
1211 TYR   (  11-)  A 1   -2.7
1374 TYR   (  14-)  A 1   -2.6
1510 GLU   (  70-)  A 1   -2.6
1565 LYS   (  45-)  A 2   -2.6
 987 LEU   (  27-)  A 1   -2.6
 882 HIS   (   2-)  A 1   -2.6
 125 LYS   (  45-)  A    -2.6
  45 LYS   (  45-)  A    -2.6
1217 GLU   (  17-)  A 1   -2.6
 552 GLU   (  72-)  A    -2.6
 163 MET   (   3-)  A    -2.6
 874 SER   (  74-)  A 1   -2.6
 187 LEU   (  27-)  A    -2.6
 943 GLU   (  63-)  A 1   -2.6
And so on for a total of 312 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.

  15 GLY   (  15-)  A  Poor phi/psi
  20 VAL   (  20-)  A  Poor phi/psi
  55 GLY   (  55-)  A  Poor phi/psi
  92 GLN   (  12-)  A  Poor phi/psi
 116 GLY   (  36-)  A  Poor phi/psi
 131 GLY   (  51-)  A  Poor phi/psi
 152 GLU   (  72-)  A  Poor phi/psi
 163 MET   (   3-)  A  Poor phi/psi
 175 GLY   (  15-)  A  Poor phi/psi
 196 GLY   (  36-)  A  Poor phi/psi
 210 GLY   (  50-)  A  Poor phi/psi
 215 GLY   (  55-)  A  Poor phi/psi
 246 GLU   (   6-)  A  Poor phi/psi
 260 VAL   (  20-)  A  Poor phi/psi
 264 GLY   (  24-)  A  Poor phi/psi
 290 GLY   (  50-)  A  Poor phi/psi
 293 GLY   (  53-)  A  Poor phi/psi
 312 GLU   (  72-)  A  Poor phi/psi
 330 ARG   (  10-)  A  Poor phi/psi
 335 GLY   (  15-)  A  Poor phi/psi
 342 GLN   (  22-)  A  Poor phi/psi
 345 GLY   (  25-)  A  Poor phi/psi
 352 GLY   (  32-)  A  Poor phi/psi
 356 GLY   (  36-)  A  Poor phi/psi
 371 GLY   (  51-)  A  Poor phi/psi
And so on for a total of 118 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 : -7.513

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 : -6.255
Model 2 : -7.490
Model 3 : -7.683
Model 4 : -7.759
Model 5 : -7.446
Model 6 : -7.484
Model 7 : -7.606
Model 8 : -7.311
Model 9 : -8.006
Model 10 : -7.366
Model 11 : -7.487
Model 12 : -7.873
Model 13 : -7.275
Model 14 : -7.527
Model 15 : -7.740
Model 16 : -8.030
Model 17 : -7.605
Model 18 : -7.041
Model 19 : -7.191
Model 20 : -8.079

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.

 474 SER   (  74-)  A    0.39

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 MET   (   3-)  A      0
   5 GLU   (   5-)  A      0
   7 GLN   (   7-)  A      0
   8 TYR   (   8-)  A      0
   9 ASN   (   9-)  A      0
  10 ARG   (  10-)  A      0
  11 TYR   (  11-)  A      0
  12 GLN   (  12-)  A      0
  13 GLN   (  13-)  A      0
  16 ALA   (  16-)  A      0
  18 GLU   (  18-)  A      0
  20 VAL   (  20-)  A      0
  21 LEU   (  21-)  A      0
  22 GLN   (  22-)  A      0
  23 MET   (  23-)  A      0
  28 CYS   (  28-)  A      0
  29 PRO   (  29-)  A      0
  31 PRO   (  31-)  A      0
  33 CYS   (  33-)  A      0
  35 ALA   (  35-)  A      0
  43 GLN   (  43-)  A      0
  44 ARG   (  44-)  A      0
  45 LYS   (  45-)  A      0
  48 CYS   (  48-)  A      0
  49 GLU   (  49-)  A      0
And so on for a total of 1037 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 : 0.177

Note: Per-model averages for omega angle check

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

Model 1 : 0.139
Model 2 : 0.018
Model 3 : 0.000
Model 4 : 0.051
Model 5 : 0.000
Model 6 : 0.000
Model 7 : 0.083
Model 8 : 0.027
Model 9 : 0.152
Model 10 : 0.000
Model 11 : 0.046
Model 12 : 0.000
Model 13 : 0.107
Model 14 : 0.115
Model 15 : 0.043
Model 16 : 0.126
Model 17 : 0.089
Model 18 : 0.000
Model 19 : 0.084
Model 20 : 0.095

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!

1250 GLY   (  50-)  A 1  2.49   26
 815 GLY   (  15-)  A 1  2.30   14
 255 GLY   (  15-)  A   2.04   12
1173 GLY   (  53-)  A 1  2.00   30
 533 GLY   (  53-)  A   1.84   10
1465 GLY   (  25-)  A 1  1.81   19
  51 GLY   (  51-)  A   1.79   12
1392 GLY   (  32-)  A 1  1.77   43
 192 GLY   (  32-)  A   1.73   46
  32 GLY   (  32-)  A   1.61   22
 512 GLY   (  32-)  A   1.60   10
 825 GLY   (  25-)  A 1  1.54   16

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.

1001 PRO   (  41-)  A 1    C   <-> 1022 ARG   (  62-)  A 1    NH2    0.46    2.64
1083 GLN   (  43-)  A 1    CD  <-> 1101 CYS   (  61-)  A 1    SG     0.46    2.94
1083 GLN   (  43-)  A 1    NE2 <-> 1101 CYS   (  61-)  A 1    SG     0.44    2.86
1559 PRO   (  39-)  A 2    CD  <-> 1582 ARG   (  62-)  A 2    CZ     0.41    2.79
 423 MET   (  23-)  A      SD  <->  462 ARG   (  62-)  A      NH1    0.40    2.90
1315 ALA   (  35-)  A 1    CB  <-> 1328 CYS   (  48-)  A 1    SG     0.40    3.00
1143 MET   (  23-)  A 1    SD  <-> 1144 GLY   (  24-)  A 1    N      0.37    2.83
1468 CYS   (  28-)  A 1    SG  <-> 1475 ALA   (  35-)  A 1    CB     0.36    3.04
1406 VAL   (  46-)  A 1    CG1 <-> 1420 PHE   (  60-)  A 1    CZ     0.36    2.84
 263 MET   (  23-)  A      SD  <->  264 GLY   (  24-)  A      N      0.36    2.84
 621 CYS   (  61-)  A      O   <->  625 LYS   (  65-)  A      N      0.35    2.35
 743 MET   (  23-)  A 1    SD  <->  785 LYS   (  65-)  A 1    CD     0.35    3.05
1233 CYS   (  33-)  A 1    SG  <-> 1254 LEU   (  54-)  A 1    CD2    0.34    3.06
 753 CYS   (  33-)  A 1    SG  <->  754 GLY   (  34-)  A 1    N      0.34    2.86
1163 GLN   (  43-)  A 1    N   <-> 1182 ARG   (  62-)  A 1    NH2    0.33    2.52
1021 CYS   (  61-)  A 1    O   <-> 1025 LYS   (  65-)  A 1    N      0.33    2.37
 781 CYS   (  61-)  A 1    O   <->  785 LYS   (  65-)  A 1    N      0.33    2.37
1341 CYS   (  61-)  A 1    O   <-> 1345 LYS   (  65-)  A 1    N      0.33    2.37
 221 CYS   (  61-)  A      O   <->  225 LYS   (  65-)  A      N      0.33    2.37
1501 CYS   (  61-)  A 1    O   <-> 1505 LYS   (  65-)  A 1    N      0.33    2.37
 301 CYS   (  61-)  A      O   <->  305 LYS   (  65-)  A      N      0.32    2.38
1181 CYS   (  61-)  A 1    O   <-> 1185 LYS   (  65-)  A 1    N      0.32    2.38
1424 CYS   (  64-)  A 1    SG  <-> 1429 HIS   (  69-)  A 1    CE1    0.32    3.08
 941 CYS   (  61-)  A 1    O   <->  945 LYS   (  65-)  A 1    N      0.32    2.38
1101 CYS   (  61-)  A 1    O   <-> 1105 LYS   (  65-)  A 1    N      0.32    2.38
And so on for a total of 568 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