WHAT IF Check report

This file was created 2011-12-21 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 pdb1bo9.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

Note: Ramachandran plot

Chain identifier: A; Model number 21

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 THR   (   1-)  A    Zero
   2 PHE   (   2-)  A    Zero
   3 ASN   (   3-)  A    Zero
   4 PRO   (   4-)  A    Zero
   5 SER   (   5-)  A    Zero
   6 SER   (   6-)  A    Zero
   7 ASP   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 ALA   (   9-)  A    Zero
  10 ALA   (  10-)  A    Zero
  11 LEU   (  11-)  A    Zero
  12 HIS   (  12-)  A    Zero
  13 LYS   (  13-)  A    Zero
  14 ALA   (  14-)  A    Zero
  15 ILE   (  15-)  A    Zero
  16 MET   (  16-)  A    Zero
  17 VAL   (  17-)  A    Zero
  18 LYS   (  18-)  A    Zero
  19 GLY   (  19-)  A    Zero
  20 VAL   (  20-)  A    Zero
  21 ASP   (  21-)  A    Zero
  22 GLU   (  22-)  A    Zero
  23 ALA   (  23-)  A    Zero
  24 THR   (  24-)  A    Zero
  25 ILE   (  25-)  A    Zero
And so on for a total of 1460 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 : 0.929
Model 2 : 0.915
Model 3 : 0.923
Model 4 : 0.912
Model 5 : 0.918
Model 6 : 0.923
Model 7 : 0.918
Model 8 : 0.919
Model 9 : 0.924
Model 10 : 0.920
Model 11 : 0.924
Model 12 : 0.914
Model 13 : 0.927
Model 14 : 0.918
Model 15 : 0.914
Model 16 : 0.918
Model 17 : 0.926
Model 18 : 0.942
Model 19 : 0.925
Model 20 : 0.928
Model 21 : 0.917

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.

  63 HIS   (  63-)  A      CA   CB   CG  109.49   -4.3
 136 HIS   (  63-)  A      CA   CB   CG  109.44   -4.4
 209 HIS   (  63-)  A      CA   CB   CG  109.49   -4.3
 282 HIS   (  63-)  A      CA   CB   CG  109.46   -4.3
 355 HIS   (  63-)  A      CA   CB   CG  109.45   -4.4
 367 PHE   (   2-)  A      CA   CB   CG  109.76   -4.0
 428 HIS   (  63-)  A      CA   CB   CG  109.67   -4.1
 450 HIS   (  12-)  A      CA   CB   CG  108.28   -5.5
 501 HIS   (  63-)  A      CA   CB   CG  109.50   -4.3
 574 HIS   (  63-)  A      CA   CB   CG  109.45   -4.4
 647 HIS   (  63-)  A      CA   CB   CG  109.55   -4.3
 659 PHE   (   2-)  A 1    CA   CB   CG  109.58   -4.2
 720 HIS   (  63-)  A 1    CA   CB   CG  109.67   -4.1
 793 HIS   (  63-)  A 1    CA   CB   CG  109.38   -4.4
 866 HIS   (  63-)  A 1    CA   CB   CG  109.42   -4.4
 939 HIS   (  63-)  A 1    CA   CB   CG  109.60   -4.2
1012 HIS   (  63-)  A 1    CA   CB   CG  109.44   -4.4
1085 HIS   (  63-)  A 1    CA   CB   CG  109.49   -4.3
1158 HIS   (  63-)  A 1    CA   CB   CG  109.44   -4.4
1231 HIS   (  63-)  A 1    CA   CB   CG  109.49   -4.3
1243 PHE   (   2-)  A 1    CA   CB   CG  108.98   -4.8
1389 PHE   (   2-)  A 2    CA   CB   CG  109.41   -4.4
1450 HIS   (  63-)  A 2    CA   CB   CG  109.69   -4.1
1462 PHE   (   2-)  A 2    CA   CB   CG  109.46   -4.3
1523 HIS   (  63-)  A 2    CA   CB   CG  109.43   -4.4

Note: Per-model averages for bond-angle check

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

Model 1 : 0.932
Model 2 : 0.949
Model 3 : 0.925
Model 4 : 0.940
Model 5 : 0.942
Model 6 : 0.942
Model 7 : 0.951
Model 8 : 0.931
Model 9 : 0.939
Model 10 : 0.948
Model 11 : 0.940
Model 12 : 0.945
Model 13 : 0.924
Model 14 : 0.932
Model 15 : 0.950
Model 16 : 0.924
Model 17 : 0.942
Model 18 : 0.955
Model 19 : 0.942
Model 20 : 0.940
Model 21 : 0.942

Note: Per-model averages for chirality check

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

Model 1 : 0.817
Model 2 : 0.835
Model 3 : 0.813
Model 4 : 0.798
Model 5 : 0.820
Model 6 : 0.817
Model 7 : 0.833
Model 8 : 0.817
Model 9 : 0.821
Model 10 : 0.819
Model 11 : 0.827
Model 12 : 0.823
Model 13 : 0.814
Model 14 : 0.808
Model 15 : 0.809
Model 16 : 0.826
Model 17 : 0.833
Model 18 : 0.842
Model 19 : 0.816
Model 20 : 0.830
Model 21 : 0.824

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.

1273 ARG   (  32-)  A 1   8.44
 981 ARG   (  32-)  A 1   7.83
1419 ARG   (  32-)  A 2   7.77
 913 ARG   (  37-)  A 1   7.64
 178 ARG   (  32-)  A    7.62
  32 ARG   (  32-)  A    7.62
1127 ARG   (  32-)  A 1   7.38
 470 ARG   (  32-)  A    6.99
1497 ARG   (  37-)  A 2   6.98
1059 ARG   (  37-)  A 1   6.97
 183 ARG   (  37-)  A    6.95
1200 ARG   (  32-)  A 1   6.94
 251 ARG   (  32-)  A    6.80
1492 ARG   (  32-)  A 2   6.76
 324 ARG   (  32-)  A    6.67
1424 ARG   (  37-)  A 2   6.62
 110 ARG   (  37-)  A    6.41
 689 ARG   (  32-)  A 1   6.27
 256 ARG   (  37-)  A    5.96
 835 ARG   (  32-)  A 1   5.91
 621 ARG   (  37-)  A    5.85
  37 ARG   (  37-)  A    5.78
 543 ARG   (  32-)  A    5.77
 840 ARG   (  37-)  A 1   5.76
 986 ARG   (  37-)  A 1   5.75
 762 ARG   (  32-)  A 1   5.74
 548 ARG   (  37-)  A    5.64
 767 ARG   (  37-)  A 1   5.62
 616 ARG   (  32-)  A    5.60
 694 ARG   (  37-)  A 1   5.59
 105 ARG   (  32-)  A    5.59
 402 ARG   (  37-)  A    5.46
1278 ARG   (  37-)  A 1   5.30
 329 ARG   (  37-)  A    5.22
 908 ARG   (  32-)  A 1   5.15
1132 ARG   (  37-)  A 1   5.04
1351 ARG   (  37-)  A 1   5.04
1346 ARG   (  32-)  A 1   4.95

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 : -6.791

Note: Per-model averages for Ramachandran check

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

Model 1 : -6.473
Model 2 : -6.218
Model 3 : -6.535
Model 4 : -6.757
Model 5 : -6.582
Model 6 : -6.208
Model 7 : -7.120
Model 8 : -7.301
Model 9 : -7.332
Model 10 : -5.813
Model 11 : -6.513
Model 12 : -6.866
Model 13 : -7.569
Model 14 : -7.058
Model 15 : -6.791
Model 16 : -6.813
Model 17 : -7.178
Model 18 : -7.182
Model 19 : -7.072
Model 20 : -7.021
Model 21 : -6.207

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.

1229 THR   (  61-)  A 1   -3.5
 732 PHE   (   2-)  A 1   -3.2
 294 PHE   (   2-)  A    -3.2
 878 PHE   (   2-)  A 1   -3.1
   2 PHE   (   2-)  A    -3.1
 720 HIS   (  63-)  A 1   -3.0
1170 PHE   (   2-)  A 1   -3.0
1389 PHE   (   2-)  A 2   -2.9
1448 THR   (  61-)  A 2   -2.8
 486 THR   (  48-)  A    -2.8
1304 HIS   (  63-)  A 1   -2.7
1478 LYS   (  18-)  A 2   -2.7
1450 HIS   (  63-)  A 2   -2.7
1346 ARG   (  32-)  A 1   -2.7
 355 HIS   (  63-)  A    -2.7
 662 SER   (   5-)  A 1   -2.7
1319 SER   (   5-)  A 1   -2.7
 218 LEU   (  72-)  A    -2.7
1167 LEU   (  72-)  A 1   -2.6
1302 THR   (  61-)  A 1   -2.6
1100 SER   (   5-)  A 1   -2.6
 151 SER   (   5-)  A    -2.6
1316 PHE   (   2-)  A 1   -2.6
 224 SER   (   5-)  A    -2.6
 729 LEU   (  72-)  A 1   -2.6
And so on for a total of 161 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.

   2 PHE   (   2-)  A  Poor phi/psi
   5 SER   (   5-)  A  Poor phi/psi
  18 LYS   (  18-)  A  Poor phi/psi
  19 GLY   (  19-)  A  Poor phi/psi
  20 VAL   (  20-)  A  Poor phi/psi
  22 GLU   (  22-)  A  Poor phi/psi
  33 ASN   (  33-)  A  Poor phi/psi
  47 GLU   (  47-)  A  Poor phi/psi
  52 LEU   (  52-)  A  Poor phi/psi
  77 PRO   (   4-)  A  Poor phi/psi
  78 SER   (   5-)  A  Poor phi/psi
  91 LYS   (  18-)  A  Poor phi/psi
  92 GLY   (  19-)  A  Poor phi/psi
  93 VAL   (  20-)  A  Poor phi/psi
  95 GLU   (  22-)  A  Poor phi/psi
 106 ASN   (  33-)  A  Poor phi/psi
 120 GLU   (  47-)  A  Poor phi/psi
 151 SER   (   5-)  A  Poor phi/psi
 165 GLY   (  19-)  A  Poor phi/psi
 166 VAL   (  20-)  A  Poor phi/psi
 168 GLU   (  22-)  A  Poor phi/psi
 193 GLU   (  47-)  A  Poor phi/psi
 198 LEU   (  52-)  A  Poor phi/psi
 224 SER   (   5-)  A  Poor phi/psi
 237 LYS   (  18-)  A  Poor phi/psi
And so on for a total of 156 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 : -6.995

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 : -7.418
Model 2 : -6.565
Model 3 : -7.456
Model 4 : -6.290
Model 5 : -7.073
Model 6 : -7.687
Model 7 : -6.812
Model 8 : -6.447
Model 9 : -6.695
Model 10 : -7.326
Model 11 : -7.138
Model 12 : -7.109
Model 13 : -7.288
Model 14 : -6.700
Model 15 : -6.838
Model 16 : -7.494
Model 17 : -6.886
Model 18 : -6.526
Model 19 : -6.861
Model 20 : -7.427
Model 21 : -6.864

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.

 358 GLU   (  66-)  A    0.33

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 SER   (   5-)  A      0
  16 MET   (  16-)  A      0
  17 VAL   (  17-)  A      0
  18 LYS   (  18-)  A      0
  20 VAL   (  20-)  A      0
  22 GLU   (  22-)  A      0
  23 ALA   (  23-)  A      0
  24 THR   (  24-)  A      0
  33 ASN   (  33-)  A      0
  48 THR   (  48-)  A      0
  52 LEU   (  52-)  A      0
  59 ALA   (  59-)  A      0
  60 LEU   (  60-)  A      0
  61 THR   (  61-)  A      0
  63 HIS   (  63-)  A      0
  67 VAL   (  67-)  A      0
  71 LEU   (  71-)  A      0
  72 LEU   (  72-)  A      0
  73 LYS   (  73-)  A      0
  74 THR   (   1-)  A      0
  75 PHE   (   2-)  A      0
  77 PRO   (   4-)  A      0
  78 SER   (   5-)  A      0
  89 MET   (  16-)  A      0
And so on for a total of 554 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.347

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 : 0.754

Note: Per-model averages for omega angle check

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

Model 1 : 0.736
Model 2 : 0.646
Model 3 : 0.704
Model 4 : 0.670
Model 5 : 0.838
Model 6 : 0.759
Model 7 : 0.697
Model 8 : 0.689
Model 9 : 0.707
Model 10 : 0.740
Model 11 : 0.803
Model 12 : 0.705
Model 13 : 0.828
Model 14 : 0.734
Model 15 : 0.766
Model 16 : 0.673
Model 17 : 0.823
Model 18 : 0.982
Model 19 : 0.806
Model 20 : 0.806
Model 21 : 0.682

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!

1303 GLY   (  62-)  A 1  3.01   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].

   4 PRO   (   4-)  A   -65.8 envelop C-beta (-72 degrees)
  51 PRO   (  51-)  A   -60.8 half-chair C-beta/C-alpha (-54 degrees)
  77 PRO   (   4-)  A   -51.0 half-chair C-beta/C-alpha (-54 degrees)
 150 PRO   (   4-)  A   -66.0 envelop C-beta (-72 degrees)
 197 PRO   (  51-)  A   -62.8 half-chair C-beta/C-alpha (-54 degrees)
 223 PRO   (   4-)  A   -64.3 envelop C-beta (-72 degrees)
 296 PRO   (   4-)  A   -52.0 half-chair C-beta/C-alpha (-54 degrees)
 343 PRO   (  51-)  A   -58.2 half-chair C-beta/C-alpha (-54 degrees)
 416 PRO   (  51-)  A   -64.1 envelop C-beta (-72 degrees)
 442 PRO   (   4-)  A   -51.5 half-chair C-beta/C-alpha (-54 degrees)
 489 PRO   (  51-)  A   -62.8 half-chair C-beta/C-alpha (-54 degrees)
 588 PRO   (   4-)  A   -51.4 half-chair C-beta/C-alpha (-54 degrees)
 635 PRO   (  51-)  A   -59.0 half-chair C-beta/C-alpha (-54 degrees)
 661 PRO   (   4-)  A 1  -61.7 half-chair C-beta/C-alpha (-54 degrees)
 708 PRO   (  51-)  A 1  -61.5 half-chair C-beta/C-alpha (-54 degrees)
 734 PRO   (   4-)  A 1  -51.7 half-chair C-beta/C-alpha (-54 degrees)
 781 PRO   (  51-)  A 1  -58.1 half-chair C-beta/C-alpha (-54 degrees)
 807 PRO   (   4-)  A 1  -51.2 half-chair C-beta/C-alpha (-54 degrees)
 927 PRO   (  51-)  A 1  -56.8 half-chair C-beta/C-alpha (-54 degrees)
 953 PRO   (   4-)  A 1  -55.0 half-chair C-beta/C-alpha (-54 degrees)
1026 PRO   (   4-)  A 1  -63.7 envelop C-beta (-72 degrees)
1172 PRO   (   4-)  A 1  -52.3 half-chair C-beta/C-alpha (-54 degrees)
1219 PRO   (  51-)  A 1  -64.8 envelop C-beta (-72 degrees)
1245 PRO   (   4-)  A 1  -53.7 half-chair C-beta/C-alpha (-54 degrees)
1318 PRO   (   4-)  A 1  -64.6 envelop C-beta (-72 degrees)
1365 PRO   (  51-)  A 1  -64.0 envelop C-beta (-72 degrees)
1438 PRO   (  51-)  A 2  -64.0 envelop C-beta (-72 degrees)
1464 PRO   (   4-)  A 2  -53.1 half-chair C-beta/C-alpha (-54 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. 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.

 613 LEU   (  29-)  A      CD2 <->  621 ARG   (  37-)  A      NE     0.29    2.81
1258 VAL   (  17-)  A 1    CG1 <-> 1261 VAL   (  20-)  A 1    N      0.27    2.83
1273 ARG   (  32-)  A 1    CB  <-> 1277 GLN   (  36-)  A 1    NE2    0.26    2.84
 733 ASN   (   3-)  A 1    ND2 <->  736 SER   (   6-)  A 1    CB     0.26    2.84
1171 ASN   (   3-)  A 1    ND2 <-> 1174 SER   (   6-)  A 1    CB     0.26    2.84
 295 ASN   (   3-)  A      ND2 <->  298 SER   (   6-)  A      CB     0.26    2.84
 844 LYS   (  41-)  A 1    NZ  <->  875 LEU   (  72-)  A 1    CD1    0.25    2.85
   2 PHE   (   2-)  A      CD2 <->   36 GLN   (  36-)  A      CD     0.25    2.95
1398 LEU   (  11-)  A 2    CD1 <-> 1431 TYR   (  44-)  A 2    CE1    0.24    2.96
1431 TYR   (  44-)  A 2    CE1 <-> 1435 THR   (  48-)  A 2    CG2    0.24    2.96
1132 ARG   (  37-)  A 1    NH2 <-> 1166 LEU   (  71-)  A 1    C      0.24    2.86
1243 PHE   (   2-)  A 1    CE2 <-> 1277 GLN   (  36-)  A 1    CB     0.24    2.96
1170 PHE   (   2-)  A 1    CD2 <-> 1204 GLN   (  36-)  A 1    CD     0.24    2.96
 586 PHE   (   2-)  A      CE1 <->  620 GLN   (  36-)  A      CB     0.23    2.97
 908 ARG   (  32-)  A 1    NH2 <->  916 ILE   (  40-)  A 1    CG2    0.23    2.87
 805 PHE   (   2-)  A 1    CD1 <->  839 GLN   (  36-)  A 1    CB     0.23    2.97
 981 ARG   (  32-)  A 1    CB  <->  985 GLN   (  36-)  A 1    CD     0.23    2.97
 513 PHE   (   2-)  A      CD2 <->  547 GLN   (  36-)  A      CB     0.23    2.97
 221 PHE   (   2-)  A      CD1 <->  255 GLN   (  36-)  A      CB     0.23    2.97
1024 PHE   (   2-)  A 1    CE2 <-> 1058 GLN   (  36-)  A 1    CB     0.23    2.97
1097 PHE   (   2-)  A 1    CD2 <-> 1131 GLN   (  36-)  A 1    CD     0.23    2.97
1416 LEU   (  29-)  A 2    CD2 <-> 1424 ARG   (  37-)  A 2    CG     0.23    2.97
 586 PHE   (   2-)  A      CE1 <->  624 ILE   (  40-)  A      CD1    0.23    2.97
 951 PHE   (   2-)  A 1    CD2 <->  985 GLN   (  36-)  A 1    CB     0.22    2.98
  29 LEU   (  29-)  A      CD2 <->   37 ARG   (  37-)  A      CG     0.22    2.98
And so on for a total of 506 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 21

Warning: Abnormal packing environment for some 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

Note: Quality value plot

Chain identifier: A; Model number 21

Warning: Low packing Z-score for some residues


Note: Per-model averages for NQA





















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 21

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