WHAT IF Check report

This file was created 2012-01-05 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 pdb1om2.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: B; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: B; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: B; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: B; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: B; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: B; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: B; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: B; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: B; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: B; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: B; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: B; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: B; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: B; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: B; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: B; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: B; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: B; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: B; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Note: Ramachandran plot

Chain identifier: B; 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 ARG   (   1-)  A    Zero
   2 ALA   (   2-)  A    Zero
   3 GLY   (   3-)  A    Zero
   4 LEU   (   4-)  A    Zero
   5 SER   (   5-)  A    Zero
   6 LYS   (   6-)  A    Zero
   7 LEU   (   7-)  A    Zero
   8 PRO   (   8-)  A    Zero
   9 ASP   (   9-)  A    Zero
  10 LEU   (  10-)  A    Zero
  11 LYS   (  11-)  A    Zero
  12 ASP   (  12-)  A    Zero
  13 ALA   (  13-)  A    Zero
  14 GLU   (  14-)  A    Zero
  15 ALA   (  15-)  A    Zero
  16 VAL   (  16-)  A    Zero
  17 GLN   (  17-)  A    Zero
  18 LYS   (  18-)  A    Zero
  19 PHE   (  19-)  A    Zero
  20 PHE   (  20-)  A    Zero
  21 LEU   (  21-)  A    Zero
  22 GLU   (  22-)  A    Zero
  23 GLU   (  23-)  A    Zero
  24 ILE   (  24-)  A    Zero
  25 GLN   (  25-)  A    Zero
And so on for a total of 2120 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 : 0.480
Model 2 : 0.505
Model 3 : 0.491
Model 4 : 0.492
Model 5 : 0.490
Model 6 : 0.491
Model 7 : 0.493
Model 8 : 0.493
Model 9 : 0.488
Model 10 : 0.491
Model 11 : 0.489
Model 12 : 0.496
Model 13 : 0.497
Model 14 : 0.500
Model 15 : 0.483
Model 16 : 0.493
Model 17 : 0.500
Model 18 : 0.496
Model 19 : 0.491
Model 20 : 0.485

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  20 PHE   (  20-)  A      CA   CB   CG  119.55    5.7
  42 HIS   (  42-)  A      NE2  CD2  CG  110.73    4.2
  59 VAL   (  59-)  A      CA   CB   CG1 117.62    4.2
 126 PHE   (  20-)  A      CA   CB   CG  119.13    5.3
 148 HIS   (  42-)  A      NE2  CD2  CG  110.73    4.2
 175 PHE   (  69-)  A      CA   CB   CG  118.35    4.5
 232 PHE   (  20-)  A      CA   CB   CG  118.59    4.8
 254 HIS   (  42-)  A      NE2  CD2  CG  110.79    4.3
 271 VAL   (  59-)  A      CA   CB   CG1 120.14    5.7
 338 PHE   (  20-)  A      CA   CB   CG  118.26    4.5
 342 ILE   (  24-)  A      CA   CB   CG2 117.57    4.2
 360 HIS   (  42-)  A      NE2  CD2  CG  111.09    4.6
 364 ALA   (  46-)  A      C    CA   CB  117.49    4.7
 406 SER   (  88-)  A     -C    N    CA  129.22    4.2
 430 LYS   (   6-)  A     -C    N    CA  130.27    4.8
 466 HIS   (  42-)  A      NE2  CD2  CG  110.81    4.3
 469 ASN   (  45-)  A      CA   CB   CG  119.38    6.8
 483 VAL   (  59-)  A      CA   CB   CG1 119.68    5.4
 493 PHE   (  69-)  A      CA   CB   CG  118.43    4.6
 502 THR   (  78-)  A      CA   CB   CG2 118.41    4.7
 512 SER   (  88-)  A     -C    N    CA  129.30    4.2
 523 LEU   (   4-)  B     -C    N    CA  129.20    4.2
 550 PHE   (  20-)  A      CA   CB   CG  118.26    4.5
 572 HIS   (  42-)  A      NE2  CD2  CG  110.82    4.3
 589 VAL   (  59-)  A      CA   CB   CG1 117.94    4.4
And so on for a total of 93 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.017
Model 2 : 1.026
Model 3 : 1.033
Model 4 : 1.033
Model 5 : 1.085
Model 6 : 1.066
Model 7 : 1.068
Model 8 : 1.061
Model 9 : 1.050
Model 10 : 1.059
Model 11 : 1.068
Model 12 : 1.066
Model 13 : 1.083
Model 14 : 1.061
Model 15 : 1.063
Model 16 : 1.082
Model 17 : 1.095
Model 18 : 1.081
Model 19 : 1.025
Model 20 : 1.050

Note: Per-model averages for chirality check

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

Model 1 : 0.932
Model 2 : 0.954
Model 3 : 0.935
Model 4 : 0.983
Model 5 : 0.993
Model 6 : 0.918
Model 7 : 0.946
Model 8 : 0.968
Model 9 : 0.964
Model 10 : 0.941
Model 11 : 1.017
Model 12 : 1.006
Model 13 : 0.977
Model 14 : 0.926
Model 15 : 0.966
Model 16 : 1.041
Model 17 : 0.972
Model 18 : 1.042
Model 19 : 0.905
Model 20 : 1.062

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 467 LEU   (  43-)  A    4.24
1026 LEU   (  72-)  A 1   4.23
 279 PRO   (  67-)  A    4.21
1845 LEU   (  43-)  A 1   4.11
2081 PRO   (  67-)  A 2   4.02

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1811 ASP   (   9-)  A 1   4.11

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 : -4.131

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.906
Model 2 : -4.081
Model 3 : -3.667
Model 4 : -4.128
Model 5 : -3.423
Model 6 : -4.713
Model 7 : -4.403
Model 8 : -4.113
Model 9 : -4.049
Model 10 : -3.890
Model 11 : -4.280
Model 12 : -4.623
Model 13 : -4.256
Model 14 : -4.545
Model 15 : -3.859
Model 16 : -4.472
Model 17 : -3.365
Model 18 : -4.240
Model 19 : -4.797
Model 20 : -3.802

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.

1762 PRO   (  66-)  A 1   -3.0
1020 PRO   (  66-)  A 1   -3.0
1338 PRO   (  66-)  A 1   -3.0
 914 PRO   (  66-)  A    -2.9
 596 PRO   (  66-)  A    -2.9
  66 PRO   (  66-)  A    -2.9
1444 PRO   (  66-)  A 1   -2.9
 172 PRO   (  66-)  A    -2.9
1974 PRO   (  66-)  A 1   -2.8
 808 PRO   (  66-)  A    -2.8
1232 PRO   (  66-)  A 1   -2.7
 534 LEU   (   4-)  A    -2.7
1915 LEU   (   7-)  A 1   -2.7
1265 LEU   (   4-)  B 1   -2.7
 113 LEU   (   7-)  A    -2.7
1385 LEU   (   7-)  A 1   -2.7
  89 LEU   (  89-)  A    -2.6
1154 VAL   (  94-)  A 1   -2.6
 384 PRO   (  66-)  A    -2.6
 852 LEU   (   4-)  A    -2.6
2018 LEU   (   4-)  A 2   -2.6
1656 PRO   (  66-)  A 1   -2.6
1276 LEU   (   4-)  A 1   -2.6
 195 LEU   (  89-)  A    -2.6
1891 LEU   (  89-)  A 1   -2.6
And so on for a total of 110 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.

   9 ASP   (   9-)  A  Poor phi/psi
  10 LEU   (  10-)  A  Poor phi/psi
  97 PRO   (   2-)  B  Poor phi/psi
 100 SER   (   5-)  B  Poor phi/psi
 110 LEU   (   4-)  A  Poor phi/psi
 196 GLY   (  90-)  A  Poor phi/psi
 204 ARG   (   3-)  B  Poor phi/psi
 205 LEU   (   4-)  B  Poor phi/psi
 206 SER   (   5-)  B  Poor phi/psi
 220 PRO   (   8-)  A  Poor phi/psi
 222 LEU   (  10-)  A  Poor phi/psi
 276 LEU   (  64-)  A  Poor phi/psi
 299 GLN   (  87-)  A  Poor phi/psi
 300 SER   (  88-)  A  Poor phi/psi
 311 LEU   (   4-)  B  Poor phi/psi
 312 SER   (   5-)  B  Poor phi/psi
 326 PRO   (   8-)  A  Poor phi/psi
 328 LEU   (  10-)  A  Poor phi/psi
 353 ASP   (  35-)  A  Poor phi/psi
 403 SER   (  85-)  A  Poor phi/psi
 405 GLN   (  87-)  A  Poor phi/psi
 406 SER   (  88-)  A  Poor phi/psi
 418 SER   (   5-)  B  Poor phi/psi
 429 SER   (   5-)  A  Poor phi/psi
 430 LYS   (   6-)  A  Poor phi/psi
And so on for a total of 132 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 : -5.937

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 : -5.502
Model 2 : -5.830
Model 3 : -5.657
Model 4 : -5.743
Model 5 : -6.884
Model 6 : -6.032
Model 7 : -6.342
Model 8 : -5.385
Model 9 : -6.327
Model 10 : -6.676
Model 11 : -5.685
Model 12 : -5.921
Model 13 : -5.390
Model 14 : -6.044
Model 15 : -6.322
Model 16 : -5.808
Model 17 : -5.849
Model 18 : -5.351
Model 19 : -5.545
Model 20 : -6.451

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.

 492 VAL   (  68-)  A    0.35
1552 VAL   (  68-)  A 1   0.36
1658 VAL   (  68-)  A 1   0.38

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!

   5 SER   (   5-)  A      0
   7 LEU   (   7-)  A      0
   8 PRO   (   8-)  A      0
   9 ASP   (   9-)  A      0
  10 LEU   (  10-)  A      0
  11 LYS   (  11-)  A      0
  33 GLN   (  33-)  A      0
  35 ASP   (  35-)  A      0
  50 CYS   (  50-)  A      0
  63 THR   (  63-)  A      0
  64 LEU   (  64-)  A      0
  66 PRO   (  66-)  A      0
  77 PRO   (  77-)  A      0
  85 SER   (  85-)  A      0
  86 ALA   (  86-)  A      0
  87 GLN   (  87-)  A      0
  88 SER   (  88-)  A      0
  89 LEU   (  89-)  A      0
  92 ASP   (  92-)  A      0
  94 VAL   (  94-)  A      0
  95 GLU   (  95-)  A      0
  96 GLY   (   1-)  B      0
  97 PRO   (   2-)  B      0
  98 ARG   (   3-)  B      0
  99 LEU   (   4-)  B      0
And so on for a total of 785 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 : 1.890

Note: Per-model averages for omega angle check

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

Model 1 : 1.837
Model 2 : 1.873
Model 3 : 1.868
Model 4 : 1.777
Model 5 : 1.884
Model 6 : 1.953
Model 7 : 1.897
Model 8 : 1.971
Model 9 : 2.001
Model 10 : 1.944
Model 11 : 1.788
Model 12 : 1.957
Model 13 : 1.823
Model 14 : 2.069
Model 15 : 1.945
Model 16 : 1.966
Model 17 : 2.006
Model 18 : 1.964
Model 19 : 1.883
Model 20 : 1.960

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!

 533 GLY   (   3-)  A   1.86   11
 196 GLY   (  90-)  A   1.69   11

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. 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].

  53 PRO   (  53-)  A  -115.7 envelop C-gamma (-108 degrees)
  66 PRO   (  66-)  A   -47.3 half-chair C-beta/C-alpha (-54 degrees)
 159 PRO   (  53-)  A  -118.3 half-chair C-delta/C-gamma (-126 degrees)
 172 PRO   (  66-)  A   -50.8 half-chair C-beta/C-alpha (-54 degrees)
 203 PRO   (   2-)  B  -112.4 envelop C-gamma (-108 degrees)
 265 PRO   (  53-)  A  -114.9 envelop C-gamma (-108 degrees)
 278 PRO   (  66-)  A    41.1 envelop C-delta (36 degrees)
 371 PRO   (  53-)  A  -117.7 half-chair C-delta/C-gamma (-126 degrees)
 384 PRO   (  66-)  A   -58.7 half-chair C-beta/C-alpha (-54 degrees)
 477 PRO   (  53-)  A  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 583 PRO   (  53-)  A  -113.9 envelop C-gamma (-108 degrees)
 596 PRO   (  66-)  A   -44.8 envelop C-alpha (-36 degrees)
 689 PRO   (  53-)  A  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 702 PRO   (  66-)  A   -66.0 envelop C-beta (-72 degrees)
 795 PRO   (  53-)  A  -116.7 envelop C-gamma (-108 degrees)
 808 PRO   (  66-)  A   -59.9 half-chair C-beta/C-alpha (-54 degrees)
 901 PRO   (  53-)  A  -117.5 half-chair C-delta/C-gamma (-126 degrees)
 914 PRO   (  66-)  A   -48.5 half-chair C-beta/C-alpha (-54 degrees)
 925 PRO   (  77-)  A   -62.1 half-chair C-beta/C-alpha (-54 degrees)
1007 PRO   (  53-)  A 1 -119.7 half-chair C-delta/C-gamma (-126 degrees)
1020 PRO   (  66-)  A 1  -45.1 half-chair C-beta/C-alpha (-54 degrees)
1113 PRO   (  53-)  A 1 -114.6 envelop C-gamma (-108 degrees)
1126 PRO   (  66-)  A 1  -64.3 envelop C-beta (-72 degrees)
1219 PRO   (  53-)  A 1 -115.0 envelop C-gamma (-108 degrees)
1232 PRO   (  66-)  A 1    2.3 envelop N (0 degrees)
1325 PRO   (  53-)  A 1 -117.7 half-chair C-delta/C-gamma (-126 degrees)
1338 PRO   (  66-)  A 1  -46.9 half-chair C-beta/C-alpha (-54 degrees)
1431 PRO   (  53-)  A 1 -120.4 half-chair C-delta/C-gamma (-126 degrees)
1444 PRO   (  66-)  A 1  -47.3 half-chair C-beta/C-alpha (-54 degrees)
1537 PRO   (  53-)  A 1 -119.1 half-chair C-delta/C-gamma (-126 degrees)
1643 PRO   (  53-)  A 1 -121.5 half-chair C-delta/C-gamma (-126 degrees)
1656 PRO   (  66-)  A 1  -59.7 half-chair C-beta/C-alpha (-54 degrees)
1749 PRO   (  53-)  A 1 -120.6 half-chair C-delta/C-gamma (-126 degrees)
1762 PRO   (  66-)  A 1  -49.0 half-chair C-beta/C-alpha (-54 degrees)
1855 PRO   (  53-)  A 1 -118.2 half-chair C-delta/C-gamma (-126 degrees)
1868 PRO   (  66-)  A 1   27.6 envelop C-delta (36 degrees)
1961 PRO   (  53-)  A 1 -113.5 envelop C-gamma (-108 degrees)
1974 PRO   (  66-)  A 1  -59.0 half-chair C-beta/C-alpha (-54 degrees)
2067 PRO   (  53-)  A 2 -117.9 half-chair C-delta/C-gamma (-126 degrees)
2080 PRO   (  66-)  A 2   21.3 half-chair N/C-delta (18 degrees)

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.

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).

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

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.

1811 ASP   (   9-)  A 1    CG   <->  1813 LYS   (  11-)  A 1    NZ   0.16    2.94
1085 GLN   (  25-)  A 1    NE2  <->  1158 ARG   (   3-)  B 1    C    0.16    2.94
 801 VAL   (  59-)  A      CG1  <->   844 LEU   (   7-)  B      CD2  0.16    3.04
1798 LEU   (   7-)  B 1    CD1  <->  1799 LEU   (   8-)  B 1    CD2  0.16    3.04
 377 VAL   (  59-)  A      CG1  <->   420 LEU   (   7-)  B      CD2  0.15    3.05
2073 VAL   (  59-)  A 2    CG1  <->  2116 LEU   (   7-)  B 2    CD2  0.15    3.05
1649 VAL   (  59-)  A 1    CG1  <->  1692 LEU   (   7-)  B 1    CD2  0.14    3.06
1543 VAL   (  59-)  A 1    CG1  <->  1586 LEU   (   7-)  B 1    CD2  0.14    3.06
  59 VAL   (  59-)  A      CG1  <->   102 LEU   (   7-)  B      CD2  0.14    3.06
 165 VAL   (  59-)  A      CG1  <->   208 LEU   (   7-)  B      CD2  0.14    3.06
1861 VAL   (  59-)  A 1    CG1  <->  1904 LEU   (   7-)  B 1    CD2  0.13    3.07
1119 VAL   (  59-)  A 1    CG1  <->  1162 LEU   (   7-)  B 1    CD2  0.13    3.07
 632 LEU   (   7-)  B      CD1  <->   633 LEU   (   8-)  B      CD2  0.13    3.07
1437 VAL   (  59-)  A 1    CG1  <->  1480 LEU   (   7-)  B 1    CD2  0.12    3.08
   9 ASP   (   9-)  A      CG   <->    11 LYS   (  11-)  A      NZ   0.12    2.98
 898 CYS   (  50-)  A      SG   <->   900 GLN   (  52-)  A      CG   0.12    3.28
1225 VAL   (  59-)  A 1    CG1  <->  1268 LEU   (   7-)  B 1    CD2  0.12    3.08
 674 LYS   (  38-)  A      NZ   <->   678 HIS   (  42-)  A      NE2  0.11    2.89
1937 GLU   (  29-)  A 1    CD   <->  2004 GLY   (   1-)  B 1    N    0.11    2.99
 854 LYS   (   6-)  A      NZ   <->   870 GLU   (  22-)  A      CD   0.11    2.99
2010 LEU   (   7-)  B 1    CD1  <->  2011 LEU   (   8-)  B 1    CD2  0.11    3.09
2093 ILE   (  79-)  A 2    CG2  <->  2094 SER   (  80-)  A 2    N    0.10    2.90
1056 LEU   (   7-)  B 1    CD1  <->  1057 LEU   (   8-)  B 1    CD2  0.10    3.10
1734 LYS   (  38-)  A 1    NZ   <->  1738 HIS   (  42-)  A 1    NE2  0.10    2.90
 360 HIS   (  42-)  A      CG   <->   361 LEU   (  43-)  A      N    0.10    2.90
And so on for a total of 157 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


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: 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