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 pdb1nwd.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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; 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: C; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Note: Ramachandran plot

Chain identifier: B; Model number 20

Note: Ramachandran plot

Chain identifier: C; 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 ALA   (   1-)  A    Zero
   2 ASP   (   2-)  A    Zero
   3 GLN   (   3-)  A    Zero
   4 LEU   (   4-)  A    Zero
   5 THR   (   5-)  A    Zero
   6 GLU   (   6-)  A    Zero
   7 GLU   (   7-)  A    Zero
   8 GLN   (   8-)  A    Zero
   9 ILE   (   9-)  A    Zero
  10 ALA   (  10-)  A    Zero
  11 GLU   (  11-)  A    Zero
  12 PHE   (  12-)  A    Zero
  13 LYS   (  13-)  A    Zero
  14 GLU   (  14-)  A    Zero
  15 ALA   (  15-)  A    Zero
  16 PHE   (  16-)  A    Zero
  17 SER   (  17-)  A    Zero
  18 LEU   (  18-)  A    Zero
  19 PHE   (  19-)  A    Zero
  20 ASP   (  20-)  A    Zero
  21 LYS   (  21-)  A    Zero
  22 ASP   (  22-)  A    Zero
  23 GLY   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 GLY   (  25-)  A    Zero
And so on for a total of 4080 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 : 0.629
Model 2 : 0.627
Model 3 : 0.625
Model 4 : 0.623
Model 5 : 0.620
Model 6 : 0.617
Model 7 : 0.625
Model 8 : 0.625
Model 9 : 0.627
Model 10 : 0.622
Model 11 : 0.626
Model 12 : 0.627
Model 13 : 0.626
Model 14 : 0.631
Model 15 : 0.625
Model 16 : 0.628
Model 17 : 0.627
Model 18 : 0.622
Model 19 : 0.630
Model 20 : 0.623

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.

  60 ASN   (  60-)  A      CA   CB   CG  118.31    5.7
  89 PHE   (  89-)  A      CA   CB   CG  118.24    4.4
 169 PHE   (  21-)  B      CA   CB   CG  119.17    5.4
 197 PHE   (  21-)  C      CA   CB   CG  117.82    4.0
 216 PHE   (  12-)  A      CA   CB   CG  117.84    4.0
 296 PHE   (  92-)  A      CA   CB   CG  118.75    4.9
 373 PHE   (  21-)  B      CA   CB   CG  118.03    4.2
 401 PHE   (  21-)  C      CA   CB   CG  118.71    4.9
 466 ASP   (  58-)  A      CA   CB   CG  117.10    4.5
 497 PHE   (  89-)  A      CA   CB   CG  118.24    4.4
 577 PHE   (  21-)  B      CA   CB   CG  118.73    4.9
 605 PHE   (  21-)  C      CA   CB   CG  119.73    5.9
 670 ASP   (  58-)  A      CA   CB   CG  116.63    4.0
 701 PHE   (  89-)  A      CA   CB   CG  117.87    4.1
 781 PHE   (  21-)  B      CA   CB   CG  118.92    5.1
 908 PHE   (  92-)  A      CA   CB   CG  118.30    4.5
1013 PHE   (  21-)  C      CA   CB   CG  118.04    4.2
1091 MET   (  71-)  A     -C    N    CA  128.96    4.0
1095 LYS   (  75-)  A     -C    N    CA  129.10    4.1
1112 PHE   (  92-)  A      CA   CB   CG  117.91    4.1
1189 PHE   (  21-)  B      CA   CB   CG  118.00    4.2
1217 PHE   (  21-)  C      CA   CB   CG  118.38    4.6
1299 LYS   (  75-)  A     -C    N    CA  129.75    4.5
1393 PHE   (  21-)  B      CA   CB   CG  118.87    5.1
1421 PHE   (  21-)  C      CA   CB   CG  118.72    4.9
And so on for a total of 66 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.942
Model 2 : 0.954
Model 3 : 0.929
Model 4 : 0.943
Model 5 : 0.933
Model 6 : 0.950
Model 7 : 0.940
Model 8 : 0.952
Model 9 : 0.936
Model 10 : 0.940
Model 11 : 0.940
Model 12 : 0.935
Model 13 : 0.955
Model 14 : 0.941
Model 15 : 0.941
Model 16 : 0.938
Model 17 : 0.942
Model 18 : 0.951
Model 19 : 0.953
Model 20 : 0.944

Note: Per-model averages for chirality check

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

Model 1 : 0.727
Model 2 : 0.675
Model 3 : 0.734
Model 4 : 0.644
Model 5 : 0.674
Model 6 : 0.744
Model 7 : 0.722
Model 8 : 0.740
Model 9 : 0.661
Model 10 : 0.705
Model 11 : 0.702
Model 12 : 0.685
Model 13 : 0.753
Model 14 : 0.746
Model 15 : 0.721
Model 16 : 0.663
Model 17 : 0.688
Model 18 : 0.741
Model 19 : 0.737
Model 20 : 0.702

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

2108 PHE   (  68-)  A 1    CB   5.53
3480 PHE   (  12-)  A 1    CB   5.50
2741 PHE   (  89-)  A 1    CB   4.88
1527 TYR   (  99-)  A      CB   4.83
1597 PHE   (  21-)  B      CB   4.82
 138 TYR   ( 138-)  A      CB   4.65
2537 PHE   (  89-)  A 1    CB   4.60
3895 PHE   (  19-)  A 2    CB   4.39
2586 TYR   ( 138-)  A 1    CB   4.38
1039 PHE   (  19-)  A      CB   4.11
1935 TYR   (  99-)  A 1    CB   4.09
 420 PHE   (  12-)  A      CB   4.08
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.671

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.671

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.874
Model 2 : -3.745
Model 3 : -3.373
Model 4 : -3.331
Model 5 : -3.885
Model 6 : -4.047
Model 7 : -4.195
Model 8 : -4.489
Model 9 : -3.407
Model 10 : -3.125
Model 11 : -3.530
Model 12 : -3.997
Model 13 : -3.494
Model 14 : -3.862
Model 15 : -3.562
Model 16 : -3.824
Model 17 : -3.117
Model 18 : -3.256
Model 19 : -3.779
Model 20 : -3.524

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.

1935 TYR   (  99-)  A 1   -3.2
 401 PHE   (  21-)  C    -3.1
 473 PHE   (  65-)  A    -2.8
2715 ILE   (  63-)  A 1   -2.8
1166 THR   ( 146-)  A    -2.8
1581 LYS   (   5-)  B    -2.6
  65 PHE   (  65-)  A    -2.6
2248 LEU   (   4-)  A 1   -2.5
3268 LEU   (   4-)  A 1   -2.5
1024 LEU   (   4-)  A    -2.5
 267 ILE   (  63-)  A    -2.5
 471 ILE   (  63-)  A    -2.5
 208 LEU   (   4-)  A    -2.5
 385 LYS   (   5-)  C    -2.5
 610 LYS   (  26-)  C    -2.4
2601 LYS   (   5-)  B 1   -2.4
2105 PHE   (  65-)  A 1   -2.4
1660 THR   (  28-)  A    -2.4
 462 GLU   (  54-)  A    -2.4
1287 ILE   (  63-)  A    -2.4
  95 ASP   (  95-)  A    -2.3
2656 LEU   (   4-)  A 1   -2.3
2186 THR   ( 146-)  A 1   -2.3
1083 ILE   (  63-)  A    -2.3
  99 TYR   (  99-)  A    -2.3
And so on for a total of 109 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.

  75 LYS   (  75-)  A  Poor phi/psi
  76 MET   (  76-)  A  Poor phi/psi
  77 LYS   (  77-)  A  Poor phi/psi
  79 THR   (  79-)  A  Poor phi/psi
  80 ASP   (  80-)  A  omega poor
 124 MET   ( 124-)  A  omega poor
 126 ARG   ( 126-)  A  omega poor
 173 LYS   (  25-)  B  omega poor
 229 GLY   (  25-)  A  Poor phi/psi
 279 LYS   (  75-)  A  Poor phi/psi
 280 MET   (  76-)  A  Poor phi/psi
 282 ASP   (  78-)  A  Poor phi/psi
 328 MET   ( 124-)  A  omega poor
 355 HIS   (   3-)  B  omega poor
 428 ASP   (  20-)  A  Poor phi/psi
 433 GLY   (  25-)  A  Poor phi/psi
 482 ARG   (  74-)  A  Poor phi/psi
 483 LYS   (  75-)  A  Poor phi/psi
 487 THR   (  79-)  A  Poor phi/psi
 555 ALA   ( 147-)  A  omega poor
 558 SER   (   2-)  B  Poor phi/psi
 687 LYS   (  75-)  A  Poor phi/psi
 688 MET   (  76-)  A  Poor phi/psi
 736 MET   ( 124-)  A  omega poor
 762 SER   (   2-)  B  Poor phi/psi
And so on for a total of 167 lines.

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 : -2.666
Model 2 : -3.103
Model 3 : -2.986
Model 4 : -2.908
Model 5 : -2.790
Model 6 : -3.252
Model 7 : -2.876
Model 8 : -2.945
Model 9 : -3.482
Model 10 : -3.425
Model 11 : -2.454
Model 12 : -2.679
Model 13 : -2.704
Model 14 : -3.570
Model 15 : -2.200
Model 16 : -3.465
Model 17 : -3.056
Model 18 : -2.932
Model 19 : -1.975
Model 20 : -3.432

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.

1409 GLU   (   9-)  C    0.33
2282 SER   (  38-)  A 1   0.34
1535 HIS   ( 107-)  A    0.36
1874 SER   (  38-)  A 1   0.36
2078 SER   (  38-)  A 1   0.36
2690 SER   (  38-)  A 1   0.36
3506 SER   (  38-)  A 1   0.36
2429 GLU   (   9-)  C 1   0.36
2759 HIS   ( 107-)  A 1   0.36
1816 SER   (   8-)  C    0.37
2604 SER   (   8-)  B 1   0.37
 242 SER   (  38-)  A    0.37
 458 ASP   (  50-)  A    0.38
1992 SER   (   8-)  B 1   0.38
2894 SER   (  38-)  A 1   0.38
 446 SER   (  38-)  A    0.38
 492 GLU   (  84-)  A    0.38
 695 GLU   (  83-)  A    0.38
1670 SER   (  38-)  A    0.38
3167 HIS   ( 107-)  A 1   0.38
 388 SER   (   8-)  C    0.39
1262 SER   (  38-)  A    0.39
2196 SER   (   8-)  B 1   0.40

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 GLN   (   3-)  A      0
   6 GLU   (   6-)  A      0
  21 LYS   (  21-)  A      0
  22 ASP   (  22-)  A      0
  39 LEU   (  39-)  A      0
  41 GLN   (  41-)  A      0
  60 ASN   (  60-)  A      0
  72 MET   (  72-)  A      0
  74 ARG   (  74-)  A      0
  75 LYS   (  75-)  A      0
  76 MET   (  76-)  A      0
  77 LYS   (  77-)  A      0
  81 SER   (  81-)  A      0
  94 LYS   (  94-)  A      0
  95 ASP   (  95-)  A      0
  97 ASN   (  97-)  A      0
  99 TYR   (  99-)  A      0
 112 LEU   ( 112-)  A      0
 114 GLU   ( 114-)  A      0
 126 ARG   ( 126-)  A      0
 127 GLU   ( 127-)  A      0
 128 ALA   ( 128-)  A      0
 129 ASP   ( 129-)  A      0
 130 ILE   ( 130-)  A      0
 131 ASP   ( 131-)  A      0
And so on for a total of 1302 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 5.997
Model 2 : 5.554
Model 3 : 5.660
Model 4 : 5.446
Model 5 : 5.537
Model 6 : 5.784
Model 7 : 5.647
Model 8 : 5.817
Model 9 : 5.450
Model 10 : 4.991
Model 11 : 5.666
Model 12 : 5.500
Model 13 : 5.730
Model 14 : 5.239
Model 15 : 5.774
Model 16 : 5.387
Model 17 : 5.215
Model 18 : 4.857
Model 19 : 5.563
Model 20 : 5.877

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!

2101 GLY   (  61-)  A 1  2.30   21
2305 GLY   (  61-)  A 1  2.03   18
3581 GLY   ( 113-)  A 1  1.96   42
3937 GLY   (  61-)  A 2  1.95   17
1672 GLY   (  40-)  A   1.93   31
 113 GLY   ( 113-)  A   1.91   63
3325 GLY   (  61-)  A 1  1.90   23
2791 GLU   ( 139-)  A 1  1.88   18
 955 GLU   ( 139-)  A   1.75   21
3811 GLU   ( 139-)  A 1  1.74   24
1745 GLY   ( 113-)  A   1.70   80
 227 GLY   (  23-)  A   1.69   20
3085 GLY   (  25-)  A 1  1.69   17
 652 GLY   (  40-)  A   1.66   64
 469 GLY   (  61-)  A   1.65   35
1897 GLY   (  61-)  A 1  1.65   52
3974 GLY   (  98-)  A 2  1.64   16
3100 GLY   (  40-)  A 1  1.61   57
2748 GLY   (  96-)  A 1  1.59   20
2969 GLY   ( 113-)  A 1  1.58   57
 521 GLY   ( 113-)  A   1.57   30
 244 GLY   (  40-)  A   1.55   80
3733 GLY   (  61-)  A 1  1.55   35
3199 GLU   ( 139-)  A 1  1.54   20
1337 GLY   ( 113-)  A   1.54   80
1693 GLY   (  61-)  A   1.52   28
 856 GLY   (  40-)  A   1.50   64

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.

3796 MET   ( 124-)  A 1    SD   <->  3838 TRP   (  18-)  B 1    CE3  0.23    3.17
1552 MET   ( 124-)  A      SD   <->  1594 TRP   (  18-)  B      CE3  0.20    3.20
3184 MET   ( 124-)  A 1    SD   <->  3226 TRP   (  18-)  B 1    CE3  0.18    3.22
3603 GLN   ( 135-)  A 1    C    <->  4206  CA   ( 152-)  A 1   CA    0.18    3.02
3399 GLN   ( 135-)  A 1    C    <->  4199  CA   ( 152-)  A 1   CA    0.18    3.02
 224 ASP   (  20-)  A      CG   <->  4091  CA   ( 149-)  A     CA    0.18    3.02
1348 MET   ( 124-)  A      SD   <->  1390 TRP   (  18-)  B      CE3  0.18    3.22
3388 MET   ( 124-)  A 1    SD   <->  3430 TRP   (  18-)  B 1    CE3  0.17    3.23
2672 ASP   (  20-)  A 1    CG   <->  4175  CA   ( 149-)  A 1   CA    0.15    3.05
4000 MET   ( 124-)  A 2    SD   <->  4042 TRP   (  18-)  B 2    CE3  0.15    3.25
2980 MET   ( 124-)  A 1    SD   <->  3022 TRP   (  18-)  B 1    CE3  0.15    3.25
1960 MET   ( 124-)  A 1    SD   <->  2002 TRP   (  18-)  B 1    CZ3  0.14    3.26
 940 MET   ( 124-)  A      SD   <->   982 TRP   (  18-)  B      CE3  0.13    3.27
1040 ASP   (  20-)  A      CG   <->  4119  CA   ( 149-)  A     CA    0.12    3.08
2164 MET   ( 124-)  A 1    SD   <->  2206 TRP   (  18-)  B 1    CE3  0.12    3.28
 124 MET   ( 124-)  A      SD   <->   166 TRP   (  18-)  B      CE3  0.12    3.28
3395 ASP   ( 131-)  A 1    CB   <->  4199  CA   ( 152-)  A 1   CA    0.11    3.09
2368 MET   ( 124-)  A 1    SD   <->  2410 TRP   (  18-)  B 1    CE3  0.11    3.29
2772 GLU   ( 120-)  A 1    C    <->  2776 MET   ( 124-)  A 1    SD   0.11    3.29
 802 MET   (  14-)  C      SD   <->   806 TRP   (  18-)  C      CZ2  0.10    3.30
 543 GLN   ( 135-)  A      C    <->  4101  CA   ( 152-)  A     CA    0.10    3.10
1248 ASP   (  24-)  A      CG   <->  4126  CA   ( 149-)  A     CA    0.10    3.10
 940 MET   ( 124-)  A      SD   <->   982 TRP   (  18-)  B      CD2  0.10    3.30
1756 MET   ( 124-)  A      SD   <->  1798 TRP   (  18-)  B      CE3  0.10    3.30
 124 MET   ( 124-)  A      SD   <->   166 TRP   (  18-)  B      CD2  0.09    3.31
And so on for a total of 67 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: B; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 20

Note: Inside/Outside RMS Z-score plot

Chain identifier: C; 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: B; Model number 1

Note: Quality value plot

Chain identifier: C; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: B; Model number 2

Note: Quality value plot

Chain identifier: C; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: B; Model number 3

Note: Quality value plot

Chain identifier: C; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: B; Model number 4

Note: Quality value plot

Chain identifier: C; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: B; Model number 5

Note: Quality value plot

Chain identifier: C; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: B; Model number 6

Note: Quality value plot

Chain identifier: C; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: B; Model number 7

Note: Quality value plot

Chain identifier: C; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: B; Model number 8

Note: Quality value plot

Chain identifier: C; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: B; Model number 9

Note: Quality value plot

Chain identifier: C; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: B; Model number 10

Note: Quality value plot

Chain identifier: C; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: B; Model number 11

Note: Quality value plot

Chain identifier: C; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: B; Model number 12

Note: Quality value plot

Chain identifier: C; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: B; Model number 13

Note: Quality value plot

Chain identifier: C; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: B; Model number 14

Note: Quality value plot

Chain identifier: C; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: B; Model number 15

Note: Quality value plot

Chain identifier: C; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: B; Model number 16

Note: Quality value plot

Chain identifier: C; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: B; Model number 17

Note: Quality value plot

Chain identifier: C; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: B; Model number 18

Note: Quality value plot

Chain identifier: C; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: B; Model number 19

Note: Quality value plot

Chain identifier: C; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Note: Quality value plot

Chain identifier: B; Model number 20

Note: Quality value plot

Chain identifier: C; 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: B; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: C; 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: B; Model number 20

Note: Second generation quality Z-score plot

Chain identifier: C; 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: Unusual ion packing


Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure