WHAT IF Check report

This file was created 2012-01-31 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 pdb3pdz.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

Note: Ramachandran plot

Chain identifier: A; Model number 22

Note: Ramachandran plot

Chain identifier: A; Model number 23

Note: Ramachandran plot

Chain identifier: A; Model number 24

Note: Ramachandran plot

Chain identifier: A; Model number 25

Note: Ramachandran plot

Chain identifier: A; Model number 26

Note: Ramachandran plot

Chain identifier: A; Model number 27

Note: Ramachandran plot

Chain identifier: A; Model number 28

Note: Ramachandran plot

Chain identifier: A; Model number 29

Note: Ramachandran plot

Chain identifier: A; Model number 30

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.253
Model 2 : 0.255
Model 3 : 0.255
Model 4 : 0.254
Model 5 : 0.258
Model 6 : 0.254
Model 7 : 0.257
Model 8 : 0.254
Model 9 : 0.258
Model 10 : 0.254
Model 11 : 0.257
Model 12 : 0.258
Model 13 : 0.255
Model 14 : 0.257
Model 15 : 0.255
Model 16 : 0.256
Model 17 : 0.256
Model 18 : 0.255
Model 19 : 0.253
Model 20 : 0.256
Model 21 : 0.258
Model 22 : 0.253
Model 23 : 0.259
Model 24 : 0.256
Model 25 : 0.253
Model 26 : 0.255
Model 27 : 0.255
Model 28 : 0.256
Model 29 : 0.258
Model 30 : 0.260

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.

   1 PRO   (   1-)  A      N    CA   CB  107.50    4.1
  97 PRO   (   1-)  A      N    CA   CB  107.55    4.1
 193 PRO   (   1-)  A      N    CA   CB  107.63    4.2
 289 PRO   (   1-)  A      N    CA   CB  107.49    4.1
 385 PRO   (   1-)  A      N    CA   CB  107.57    4.2
 481 PRO   (   1-)  A      N    CA   CB  107.52    4.1
 577 PRO   (   1-)  A      N    CA   CB  107.55    4.1
 673 PRO   (   1-)  A      N    CA   CB  107.58    4.2
 769 PRO   (   1-)  A      N    CA   CB  107.59    4.2
 865 PRO   (   1-)  A 1    N    CA   CB  107.64    4.2
 961 PRO   (   1-)  A 1    N    CA   CB  107.56    4.1
1057 PRO   (   1-)  A 1    N    CA   CB  107.51    4.1
1153 PRO   (   1-)  A 1    N    CA   CB  107.59    4.2
1249 PRO   (   1-)  A 1    N    CA   CB  107.57    4.2
1345 PRO   (   1-)  A 1    N    CA   CB  107.62    4.2
1441 PRO   (   1-)  A 1    N    CA   CB  107.53    4.1
1537 PRO   (   1-)  A 1    N    CA   CB  107.54    4.1
1633 PRO   (   1-)  A 1    N    CA   CB  107.54    4.1
1729 PRO   (   1-)  A 1    N    CA   CB  107.58    4.2
1825 PRO   (   1-)  A 2    N    CA   CB  107.57    4.2
1921 PRO   (   1-)  A 2    N    CA   CB  107.55    4.1
2017 PRO   (   1-)  A 2    N    CA   CB  107.54    4.1
2113 PRO   (   1-)  A 2    N    CA   CB  107.51    4.1
2209 PRO   (   1-)  A 2    N    CA   CB  107.60    4.2
2305 PRO   (   1-)  A 2    N    CA   CB  107.56    4.1
2401 PRO   (   1-)  A 2    N    CA   CB  107.55    4.1
2497 PRO   (   1-)  A 2    N    CA   CB  107.50    4.1
2593 PRO   (   1-)  A 2    N    CA   CB  107.56    4.1
2689 PRO   (   1-)  A 2    N    CA   CB  107.53    4.1
2785 PRO   (   1-)  A 3    N    CA   CB  107.62    4.2

Note: Per-model averages for bond-angle check

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

Model 1 : 0.506
Model 2 : 0.508
Model 3 : 0.505
Model 4 : 0.513
Model 5 : 0.518
Model 6 : 0.506
Model 7 : 0.514
Model 8 : 0.514
Model 9 : 0.523
Model 10 : 0.508
Model 11 : 0.510
Model 12 : 0.508
Model 13 : 0.513
Model 14 : 0.519
Model 15 : 0.516
Model 16 : 0.511
Model 17 : 0.521
Model 18 : 0.517
Model 19 : 0.511
Model 20 : 0.514
Model 21 : 0.524
Model 22 : 0.511
Model 23 : 0.518
Model 24 : 0.520
Model 25 : 0.509
Model 26 : 0.522
Model 27 : 0.509
Model 28 : 0.514
Model 29 : 0.516
Model 30 : 0.520

Note: Per-model averages for chirality check

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

Model 1 : 0.381
Model 2 : 0.373
Model 3 : 0.375
Model 4 : 0.380
Model 5 : 0.396
Model 6 : 0.380
Model 7 : 0.377
Model 8 : 0.382
Model 9 : 0.389
Model 10 : 0.386
Model 11 : 0.385
Model 12 : 0.373
Model 13 : 0.401
Model 14 : 0.400
Model 15 : 0.390
Model 16 : 0.378
Model 17 : 0.377
Model 18 : 0.395
Model 19 : 0.378
Model 20 : 0.384
Model 21 : 0.415
Model 22 : 0.378
Model 23 : 0.392
Model 24 : 0.396
Model 25 : 0.376
Model 26 : 0.394
Model 27 : 0.385
Model 28 : 0.379
Model 29 : 0.405
Model 30 : 0.390

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 : -6.118

Note: Per-model averages for Ramachandran check

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

Model 1 : -6.101
Model 2 : -5.650
Model 3 : -6.154
Model 4 : -6.069
Model 5 : -6.088
Model 6 : -5.894
Model 7 : -6.095
Model 8 : -6.394
Model 9 : -6.131
Model 10 : -6.156
Model 11 : -5.879
Model 12 : -6.250
Model 13 : -6.436
Model 14 : -6.063
Model 15 : -5.981
Model 16 : -6.440
Model 17 : -5.822
Model 18 : -5.546
Model 19 : -6.280
Model 20 : -5.964
Model 21 : -6.401
Model 22 : -6.085
Model 23 : -6.323
Model 24 : -6.070
Model 25 : -6.323
Model 26 : -5.975
Model 27 : -6.128
Model 28 : -6.180
Model 29 : -6.578
Model 30 : -6.086

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.

  28 THR   (  28-)  A    -3.3
 896 HIS   (  32-)  A 1   -3.3
 796 THR   (  28-)  A    -3.3
 316 THR   (  28-)  A    -3.3
2140 THR   (  28-)  A 2   -3.3
 892 THR   (  28-)  A 1   -3.3
1660 THR   (  28-)  A 1   -3.3
 604 THR   (  28-)  A    -3.2
1756 THR   (  28-)  A 1   -3.2
1084 THR   (  28-)  A 1   -3.2
  23 THR   (  23-)  A    -3.2
2716 THR   (  28-)  A 2   -3.2
1372 THR   (  28-)  A 1   -3.1
2711 THR   (  23-)  A 2   -3.1
1079 THR   (  23-)  A 1   -3.1
1175 THR   (  23-)  A 1   -3.1
 119 THR   (  23-)  A    -3.1
2039 THR   (  23-)  A 2   -3.1
1463 THR   (  23-)  A 1   -3.0
 503 THR   (  23-)  A    -3.0
1468 THR   (  28-)  A 1   -3.0
2423 THR   (  23-)  A 2   -3.0
 983 THR   (  23-)  A 1   -3.0
2519 THR   (  23-)  A 2   -3.0
1367 THR   (  23-)  A 1   -3.0
And so on for a total of 446 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.

   3 PRO   (   3-)  A  Poor phi/psi
  15 ASP   (  15-)  A  Poor phi/psi
  17 SER   (  17-)  A  Poor phi/psi
  27 ASN   (  27-)  A  Poor phi/psi
  33 GLY   (  33-)  A  Poor phi/psi
  42 PRO   (  42-)  A  Poor phi/psi
  62 ASN   (  62-)  A  Poor phi/psi
  80 ASN   (  80-)  A  Poor phi/psi
  83 GLN   (  83-)  A  Poor phi/psi
  89 LEU   (  89-)  A  Poor phi/psi
 100 GLY   (   4-)  A  Poor phi/psi
 110 ASN   (  14-)  A  Poor phi/psi
 111 ASP   (  15-)  A  Poor phi/psi
 123 ASN   (  27-)  A  Poor phi/psi
 129 GLY   (  33-)  A  Poor phi/psi
 138 PRO   (  42-)  A  Poor phi/psi
 158 ASN   (  62-)  A  Poor phi/psi
 176 ASN   (  80-)  A  Poor phi/psi
 179 GLN   (  83-)  A  Poor phi/psi
 185 LEU   (  89-)  A  Poor phi/psi
 195 PRO   (   3-)  A  Poor phi/psi
 207 ASP   (  15-)  A  Poor phi/psi
 209 SER   (  17-)  A  Poor phi/psi
 217 GLY   (  25-)  A  Poor phi/psi
 224 HIS   (  32-)  A  Poor phi/psi
And so on for a total of 293 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 : -7.468

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 : -7.390
Model 2 : -7.441
Model 3 : -7.430
Model 4 : -7.426
Model 5 : -7.910
Model 6 : -7.202
Model 7 : -7.603
Model 8 : -7.830
Model 9 : -7.717
Model 10 : -7.582
Model 11 : -7.206
Model 12 : -7.874
Model 13 : -6.987
Model 14 : -7.438
Model 15 : -7.361
Model 16 : -6.489
Model 17 : -7.656
Model 18 : -7.429
Model 19 : -7.963
Model 20 : -6.873
Model 21 : -7.730
Model 22 : -7.791
Model 23 : -7.431
Model 24 : -7.941
Model 25 : -7.627
Model 26 : -7.128
Model 27 : -7.393
Model 28 : -7.594
Model 29 : -7.318
Model 30 : -7.283

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 PRO   (   3-)  A      0
  10 GLU   (  10-)  A      0
  14 ASN   (  14-)  A      0
  15 ASP   (  15-)  A      0
  16 ASN   (  16-)  A      0
  18 LEU   (  18-)  A      0
  23 THR   (  23-)  A      0
  26 VAL   (  26-)  A      0
  27 ASN   (  27-)  A      0
  28 THR   (  28-)  A      0
  29 SER   (  29-)  A      0
  31 ARG   (  31-)  A      0
  32 HIS   (  32-)  A      0
  38 LYS   (  38-)  A      0
  39 ALA   (  39-)  A      0
  41 ILE   (  41-)  A      0
  42 PRO   (  42-)  A      0
  43 GLN   (  43-)  A      0
  49 ASP   (  49-)  A      0
  51 ARG   (  51-)  A      0
  52 ILE   (  52-)  A      0
  54 LYS   (  54-)  A      0
  59 LEU   (  59-)  A      0
  61 VAL   (  61-)  A      0
  62 ASN   (  62-)  A      0
And so on for a total of 1441 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 : 0.866

Note: Per-model averages for omega angle check

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

Model 1 : 0.909
Model 2 : 0.857
Model 3 : 0.848
Model 4 : 0.906
Model 5 : 0.870
Model 6 : 0.866
Model 7 : 0.902
Model 8 : 0.883
Model 9 : 0.891
Model 10 : 0.932
Model 11 : 0.898
Model 12 : 0.839
Model 13 : 0.916
Model 14 : 0.875
Model 15 : 0.933
Model 16 : 0.835
Model 17 : 0.901
Model 18 : 0.931
Model 19 : 0.904
Model 20 : 0.842
Model 21 : 1.040
Model 22 : 0.887
Model 23 : 0.900
Model 24 : 0.913
Model 25 : 0.869
Model 26 : 0.958
Model 27 : 0.881
Model 28 : 0.848
Model 29 : 0.929
Model 30 : 0.864

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!

2756 GLY   (  68-)  A 2  2.11   16
1700 GLY   (  68-)  A 1  2.10   12
1412 GLY   (  68-)  A 1  2.10   21
2084 GLY   (  68-)  A 2  2.10   16
 260 GLY   (  68-)  A   2.09   16
2660 GLY   (  68-)  A 2  2.09   22
 836 GLY   (  68-)  A   2.09   34
2180 GLY   (  68-)  A 2  2.08   18
 548 GLY   (  68-)  A   2.08   18
 932 GLY   (  68-)  A 1  2.07   14
1988 GLY   (  68-)  A 2  2.07   27
  68 GLY   (  68-)  A   2.07   41
1796 GLY   (  68-)  A 1  2.07   31
 740 GLY   (  68-)  A   2.06   32
2564 GLY   (  68-)  A 2  2.04   30
2372 GLY   (  68-)  A 2  2.04   60
 452 GLY   (  68-)  A   2.04   12
1220 GLY   (  68-)  A 1  2.02   29
 164 GLY   (  68-)  A   2.01   28
1508 GLY   (  68-)  A 1  2.01   18
1604 GLY   (  68-)  A 1  2.00   18
1028 GLY   (  68-)  A 1  2.00   17
 644 GLY   (  68-)  A   1.99   19
  92 GLY   (  92-)  A   1.95   19
2468 GLY   (  68-)  A 2  1.95   37
1124 GLY   (  68-)  A 1  1.94   14
1724 GLY   (  92-)  A 1  1.80   11
1436 GLY   (  92-)  A 1  1.76   13
2588 GLY   (  92-)  A 2  1.70   15
 572 GLY   (  92-)  A   1.67   13
1666 GLY   (  34-)  A 1  1.63   17
 668 GLY   (  92-)  A   1.56   15
 226 GLY   (  34-)  A   1.55   18
 514 GLY   (  34-)  A   1.54   14
1186 GLY   (  34-)  A 1  1.53   14

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].

   1 PRO   (   1-)  A    49.9 half-chair C-delta/C-gamma (54 degrees)
  97 PRO   (   1-)  A    50.5 half-chair C-delta/C-gamma (54 degrees)
 193 PRO   (   1-)  A  -130.7 half-chair C-delta/C-gamma (-126 degrees)
 289 PRO   (   1-)  A  -132.6 half-chair C-delta/C-gamma (-126 degrees)
 385 PRO   (   1-)  A    47.5 half-chair C-delta/C-gamma (54 degrees)
 481 PRO   (   1-)  A    51.3 half-chair C-delta/C-gamma (54 degrees)
 577 PRO   (   1-)  A    49.2 half-chair C-delta/C-gamma (54 degrees)
 579 PRO   (   3-)  A   105.4 envelop C-beta (108 degrees)
 673 PRO   (   1-)  A  -132.1 half-chair C-delta/C-gamma (-126 degrees)
 769 PRO   (   1-)  A    48.0 half-chair C-delta/C-gamma (54 degrees)
 865 PRO   (   1-)  A 1 -128.8 half-chair C-delta/C-gamma (-126 degrees)
 961 PRO   (   1-)  A 1 -134.0 half-chair C-delta/C-gamma (-126 degrees)
 963 PRO   (   3-)  A 1  109.8 envelop C-beta (108 degrees)
1057 PRO   (   1-)  A 1 -133.7 half-chair C-delta/C-gamma (-126 degrees)
1153 PRO   (   1-)  A 1 -131.5 half-chair C-delta/C-gamma (-126 degrees)
1155 PRO   (   3-)  A 1 -113.8 envelop C-gamma (-108 degrees)
1249 PRO   (   1-)  A 1 -130.6 half-chair C-delta/C-gamma (-126 degrees)
1345 PRO   (   1-)  A 1 -130.4 half-chair C-delta/C-gamma (-126 degrees)
1441 PRO   (   1-)  A 1   45.5 half-chair C-delta/C-gamma (54 degrees)
1537 PRO   (   1-)  A 1   48.7 half-chair C-delta/C-gamma (54 degrees)
1539 PRO   (   3-)  A 1 -113.7 envelop C-gamma (-108 degrees)
1633 PRO   (   1-)  A 1 -130.5 half-chair C-delta/C-gamma (-126 degrees)
1729 PRO   (   1-)  A 1   46.6 half-chair C-delta/C-gamma (54 degrees)
1825 PRO   (   1-)  A 2 -130.1 half-chair C-delta/C-gamma (-126 degrees)
1921 PRO   (   1-)  A 2 -131.3 half-chair C-delta/C-gamma (-126 degrees)
2017 PRO   (   1-)  A 2   44.8 envelop C-delta (36 degrees)
2113 PRO   (   1-)  A 2 -133.2 half-chair C-delta/C-gamma (-126 degrees)
2209 PRO   (   1-)  A 2 -129.0 half-chair C-delta/C-gamma (-126 degrees)
2305 PRO   (   1-)  A 2 -133.3 half-chair C-delta/C-gamma (-126 degrees)
2401 PRO   (   1-)  A 2   47.0 half-chair C-delta/C-gamma (54 degrees)
2497 PRO   (   1-)  A 2   46.1 half-chair C-delta/C-gamma (54 degrees)
2593 PRO   (   1-)  A 2 -130.5 half-chair C-delta/C-gamma (-126 degrees)
2689 PRO   (   1-)  A 2 -131.3 half-chair C-delta/C-gamma (-126 degrees)
2785 PRO   (   1-)  A 3   50.6 half-chair C-delta/C-gamma (54 degrees)
2787 PRO   (   3-)  A 3  111.8 envelop C-beta (108 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.

2051 ILE   (  35-)  A 2    CG2 <-> 2074 VAL   (  58-)  A 2    CG2    0.33    2.87
2243 ILE   (  35-)  A 2    CG2 <-> 2266 VAL   (  58-)  A 2    CG2    0.32    2.88
2531 ILE   (  35-)  A 2    CG2 <-> 2554 VAL   (  58-)  A 2    CG2    0.32    2.88
2629 VAL   (  37-)  A 2    O   <-> 2647 GLY   (  55-)  A 2    N      0.31    2.39
 425 ILE   (  41-)  A      C   <->  431 GLU   (  47-)  A      CB     0.30    2.90
 997 VAL   (  37-)  A 1    O   <-> 1015 GLY   (  55-)  A 1    N      0.30    2.40
2341 VAL   (  37-)  A 2    O   <-> 2359 GLY   (  55-)  A 2    N      0.30    2.40
2821 VAL   (  37-)  A 3    O   <-> 2839 GLY   (  55-)  A 3    N      0.29    2.41
 133 VAL   (  37-)  A      O   <->  151 GLY   (  55-)  A      N      0.29    2.41
1669 VAL   (  37-)  A 1    O   <-> 1687 GLY   (  55-)  A 1    N      0.29    2.41
2245 VAL   (  37-)  A 2    O   <-> 2263 GLY   (  55-)  A 2    N      0.28    2.42
 901 VAL   (  37-)  A 1    O   <->  919 GLY   (  55-)  A 1    N      0.28    2.42
1381 VAL   (  37-)  A 1    O   <-> 1399 GLY   (  55-)  A 1    N      0.28    2.42
 776 GLU   (   8-)  A      CB  <->  856 LEU   (  88-)  A      CD1    0.28    2.92
1765 VAL   (  37-)  A 1    O   <-> 1783 GLY   (  55-)  A 1    N      0.28    2.42
1957 VAL   (  37-)  A 2    O   <-> 1975 GLY   (  55-)  A 2    N      0.28    2.42
2820 TYR   (  36-)  A 3    CE2 <-> 2841 ARG   (  57-)  A 3    CG     0.28    2.92
1352 GLU   (   8-)  A 1    CB  <-> 1432 LEU   (  88-)  A 1    CD1    0.28    2.92
2679 LEU   (  87-)  A 2    CD2 <-> 2681 LEU   (  89-)  A 2    CD2    0.28    2.92
 968 GLU   (   8-)  A 1    CB  <-> 1048 LEU   (  88-)  A 1    CD1    0.28    2.92
1289 ILE   (  41-)  A 1    C   <-> 1295 GLU   (  47-)  A 1    CB     0.28    2.92
2249 ILE   (  41-)  A 2    C   <-> 2255 GLU   (  47-)  A 2    CB     0.28    2.92
1982 ASN   (  62-)  A 2    ND2 <-> 2001 THR   (  81-)  A 2    CG2    0.27    2.83
 517 VAL   (  37-)  A      O   <->  535 GLY   (  55-)  A      N      0.27    2.43
1189 VAL   (  37-)  A 1    O   <-> 1207 GLY   (  55-)  A 1    N      0.27    2.43
And so on for a total of 1607 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 22

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 23

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 24

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 25

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 26

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 27

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 28

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 29

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 30

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Warning: Structural average packing environment a bit worrysome

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

Note: Quality value plot

Chain identifier: A; Model number 22

Note: Quality value plot

Chain identifier: A; Model number 23

Note: Quality value plot

Chain identifier: A; Model number 24

Note: Quality value plot

Chain identifier: A; Model number 25

Note: Quality value plot

Chain identifier: A; Model number 26

Note: Quality value plot

Chain identifier: A; Model number 27

Note: Quality value plot

Chain identifier: A; Model number 28

Note: Quality value plot

Chain identifier: A; Model number 29

Note: Quality value plot

Chain identifier: A; Model number 30

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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 22

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 23

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 24

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 25

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 26

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 27

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 28

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 29

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 30

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