WHAT IF Check report

This file was created 2012-01-04 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 pdb1l1p.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

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 GLY   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 HIS   (   3-)  A    Zero
   4 MET   (   4-)  A    Zero
   5 GLN   (   5-)  A    Zero
   6 ALA   (   6-)  A    Zero
   7 THR   (   7-)  A    Zero
   8 TRP   (   8-)  A    Zero
   9 LYS   (   9-)  A    Zero
  10 GLU   (  10-)  A    Zero
  11 LYS   (  11-)  A    Zero
  12 ASP   (  12-)  A    Zero
  13 GLY   (  13-)  A    Zero
  14 ALA   (  14-)  A    Zero
  15 VAL   (  15-)  A    Zero
  16 GLU   (  16-)  A    Zero
  17 ALA   (  17-)  A    Zero
  18 GLU   (  18-)  A    Zero
  19 ASP   (  19-)  A    Zero
  20 ARG   (  20-)  A    Zero
  21 VAL   (  21-)  A    Zero
  22 THR   (  22-)  A    Zero
  23 ILE   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 PHE   (  25-)  A    Zero
And so on for a total of 3180 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 : 0.242
Model 2 : 0.241
Model 3 : 0.246
Model 4 : 0.242
Model 5 : 0.243
Model 6 : 0.239
Model 7 : 0.238
Model 8 : 0.241
Model 9 : 0.240
Model 10 : 0.245
Model 11 : 0.235
Model 12 : 0.238
Model 13 : 0.236
Model 14 : 0.254
Model 15 : 0.246
Model 16 : 0.243
Model 17 : 0.241
Model 18 : 0.240
Model 19 : 0.244
Model 20 : 0.241
Model 21 : 0.241
Model 22 : 0.249
Model 23 : 0.242
Model 24 : 0.234
Model 25 : 0.245
Model 26 : 0.242
Model 27 : 0.241
Model 28 : 0.251
Model 29 : 0.236
Model 30 : 0.239

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.

  62 HIS   (  62-)  A      CG   ND1  CE1 109.60    4.0
  90 PHE   (  90-)  A      CA   CB   CG  118.00    4.2
 380 HIS   (  62-)  A      CG   ND1  CE1 109.63    4.0
 698 HIS   (  62-)  A      CG   ND1  CE1 109.63    4.0
1228 HIS   (  62-)  A 1    CG   ND1  CE1 109.66    4.1
1440 HIS   (  62-)  A 1    CG   ND1  CE1 109.64    4.0
1468 PHE   (  90-)  A 1    CA   CB   CG  117.95    4.1
1652 HIS   (  62-)  A 1    CG   ND1  CE1 109.66    4.1
1758 HIS   (  62-)  A 1    CG   ND1  CE1 109.63    4.0
1970 HIS   (  62-)  A 1    CG   ND1  CE1 109.66    4.1
2123 HIS   (   3-)  A 2    CG   ND1  CE1 109.61    4.0
2182 HIS   (  62-)  A 2    CG   ND1  CE1 109.63    4.0
2288 HIS   (  62-)  A 2    CG   ND1  CE1 109.63    4.0
2422 PHE   (  90-)  A 2    CA   CB   CG  117.87    4.1
2500 HIS   (  62-)  A 2    CG   ND1  CE1 109.63    4.0
2606 HIS   (  62-)  A 2    CG   ND1  CE1 109.66    4.1
2818 HIS   (  62-)  A 2    CG   ND1  CE1 109.63    4.0
2924 HIS   (  62-)  A 2    CG   ND1  CE1 109.71    4.1
3030 HIS   (  62-)  A 2    CG   ND1  CE1 109.65    4.1

Note: Per-model averages for bond-angle check

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

Model 1 : 0.502
Model 2 : 0.489
Model 3 : 0.490
Model 4 : 0.497
Model 5 : 0.497
Model 6 : 0.494
Model 7 : 0.490
Model 8 : 0.487
Model 9 : 0.487
Model 10 : 0.486
Model 11 : 0.482
Model 12 : 0.478
Model 13 : 0.491
Model 14 : 0.511
Model 15 : 0.485
Model 16 : 0.502
Model 17 : 0.491
Model 18 : 0.484
Model 19 : 0.503
Model 20 : 0.497
Model 21 : 0.476
Model 22 : 0.496
Model 23 : 0.506
Model 24 : 0.469
Model 25 : 0.483
Model 26 : 0.490
Model 27 : 0.492
Model 28 : 0.495
Model 29 : 0.476
Model 30 : 0.490

Note: Per-model averages for chirality check

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

Model 1 : 0.497
Model 2 : 0.471
Model 3 : 0.469
Model 4 : 0.474
Model 5 : 0.456
Model 6 : 0.482
Model 7 : 0.471
Model 8 : 0.460
Model 9 : 0.470
Model 10 : 0.471
Model 11 : 0.459
Model 12 : 0.472
Model 13 : 0.475
Model 14 : 0.476
Model 15 : 0.463
Model 16 : 0.461
Model 17 : 0.477
Model 18 : 0.464
Model 19 : 0.466
Model 20 : 0.473
Model 21 : 0.455
Model 22 : 0.465
Model 23 : 0.480
Model 24 : 0.455
Model 25 : 0.481
Model 26 : 0.464
Model 27 : 0.467
Model 28 : 0.465
Model 29 : 0.473
Model 30 : 0.461

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 : -6.169

Note: Per-model averages for Ramachandran check

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

Model 1 : -6.343
Model 2 : -6.434
Model 3 : -5.996
Model 4 : -6.304
Model 5 : -5.757
Model 6 : -5.762
Model 7 : -6.168
Model 8 : -6.579
Model 9 : -6.111
Model 10 : -6.403
Model 11 : -6.326
Model 12 : -6.331
Model 13 : -6.405
Model 14 : -5.838
Model 15 : -5.720
Model 16 : -6.058
Model 17 : -5.945
Model 18 : -6.071
Model 19 : -5.525
Model 20 : -6.429
Model 21 : -6.541
Model 22 : -6.068
Model 23 : -6.115
Model 24 : -6.175
Model 25 : -6.148
Model 26 : -6.146
Model 27 : -6.634
Model 28 : -6.106
Model 29 : -6.260
Model 30 : -6.370

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.

1563 HIS   (  79-)  A 1   -3.0
1852 ARG   (  50-)  A 1   -3.0
1958 ARG   (  50-)  A 1   -2.9
2594 ARG   (  50-)  A 2   -2.9
1216 ARG   (  50-)  A 1   -2.9
 156 ARG   (  50-)  A    -2.9
1322 ARG   (  50-)  A 1   -2.9
 792 ARG   (  50-)  A    -2.9
2700 ARG   (  50-)  A 2   -2.9
 262 ARG   (  50-)  A    -2.9
2276 ARG   (  50-)  A 2   -2.9
 474 ARG   (  50-)  A    -2.9
1428 ARG   (  50-)  A 1   -2.9
1004 ARG   (  50-)  A 1   -2.9
3018 ARG   (  50-)  A 2   -2.8
 580 ARG   (  50-)  A    -2.8
1746 ARG   (  50-)  A 1   -2.8
2382 ARG   (  50-)  A 2   -2.8
 368 ARG   (  50-)  A    -2.8
2912 ARG   (  50-)  A 2   -2.8
1928 ARG   (  20-)  A 1   -2.8
2472 PHE   (  34-)  A 2   -2.8
 988 PHE   (  34-)  A 1   -2.8
2170 ARG   (  50-)  A 2   -2.8
 645 LYS   (   9-)  A    -2.8
And so on for a total of 565 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.

   4 MET   (   4-)  A  Poor phi/psi
  11 LYS   (  11-)  A  Poor phi/psi
  17 ALA   (  17-)  A  Poor phi/psi
  29 VAL   (  29-)  A  Poor phi/psi
  34 PHE   (  34-)  A  Poor phi/psi
  57 ASP   (  57-)  A  Poor phi/psi
  62 HIS   (  62-)  A  Poor phi/psi
  78 TYR   (  78-)  A  Poor phi/psi
  85 GLY   (  85-)  A  Poor phi/psi
  95 LYS   (  95-)  A  Poor phi/psi
 109 HIS   (   3-)  A  Poor phi/psi
 117 LYS   (  11-)  A  Poor phi/psi
 123 ALA   (  17-)  A  Poor phi/psi
 135 VAL   (  29-)  A  Poor phi/psi
 140 PHE   (  34-)  A  Poor phi/psi
 156 ARG   (  50-)  A  Poor phi/psi
 201 LYS   (  95-)  A  Poor phi/psi
 223 LYS   (  11-)  A  Poor phi/psi
 229 ALA   (  17-)  A  Poor phi/psi
 246 PHE   (  34-)  A  Poor phi/psi
 262 ARG   (  50-)  A  Poor phi/psi
 269 ASP   (  57-)  A  Poor phi/psi
 307 LYS   (  95-)  A  Poor phi/psi
 329 LYS   (  11-)  A  Poor phi/psi
 335 ALA   (  17-)  A  Poor phi/psi
And so on for a total of 229 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 : -7.603

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 : -7.585
Model 2 : -7.741
Model 3 : -7.195
Model 4 : -7.847
Model 5 : -7.905
Model 6 : -7.472
Model 7 : -7.089
Model 8 : -7.711
Model 9 : -7.323
Model 10 : -7.272
Model 11 : -7.430
Model 12 : -7.622
Model 13 : -7.615
Model 14 : -7.427
Model 15 : -7.594
Model 16 : -7.922
Model 17 : -7.385
Model 18 : -7.690
Model 19 : -7.341
Model 20 : -7.813
Model 21 : -7.465
Model 22 : -7.581
Model 23 : -7.807
Model 24 : -7.673
Model 25 : -7.577
Model 26 : -7.404
Model 27 : -7.912
Model 28 : -7.678
Model 29 : -8.010
Model 30 : -8.004

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.

1434 GLU   (  56-)  A 1   0.38
2494 GLU   (  56-)  A 2   0.38
2918 GLU   (  56-)  A 2   0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 HIS   (   3-)  A      0
   4 MET   (   4-)  A      0
   5 GLN   (   5-)  A      0
   6 ALA   (   6-)  A      0
   8 TRP   (   8-)  A      0
   9 LYS   (   9-)  A      0
  11 LYS   (  11-)  A      0
  12 ASP   (  12-)  A      0
  14 ALA   (  14-)  A      0
  15 VAL   (  15-)  A      0
  18 GLU   (  18-)  A      0
  19 ASP   (  19-)  A      0
  24 ASP   (  24-)  A      0
  26 THR   (  26-)  A      0
  29 VAL   (  29-)  A      0
  30 ASP   (  30-)  A      0
  34 PHE   (  34-)  A      0
  35 GLU   (  35-)  A      0
  38 LYS   (  38-)  A      0
  40 SER   (  40-)  A      0
  46 MET   (  46-)  A      0
  48 GLN   (  48-)  A      0
  50 ARG   (  50-)  A      0
  51 MET   (  51-)  A      0
  52 ILE   (  52-)  A      0
And so on for a total of 1764 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.389

Note: Per-model averages for omega angle check

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

Model 1 : 1.468
Model 2 : 1.394
Model 3 : 1.372
Model 4 : 1.380
Model 5 : 1.382
Model 6 : 1.424
Model 7 : 1.394
Model 8 : 1.359
Model 9 : 1.360
Model 10 : 1.398
Model 11 : 1.359
Model 12 : 1.443
Model 13 : 1.407
Model 14 : 1.396
Model 15 : 1.345
Model 16 : 1.405
Model 17 : 1.381
Model 18 : 1.394
Model 19 : 1.394
Model 20 : 1.395
Model 21 : 1.370
Model 22 : 1.390
Model 23 : 1.437
Model 24 : 1.420
Model 25 : 1.453
Model 26 : 1.362
Model 27 : 1.376
Model 28 : 1.378
Model 29 : 1.399
Model 30 : 1.389

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!

 259 GLY   (  47-)  A   2.05   10
3015 GLY   (  47-)  A 2  1.86   17
2803 GLY   (  47-)  A 2  1.78   21
2061 GLY   (  47-)  A 2  1.75   13
 683 GLY   (  47-)  A   1.74   11
1319 GLY   (  47-)  A 1  1.72   19
2167 GLY   (  47-)  A 2  1.68   32
 471 GLY   (  47-)  A   1.65   26
1531 GLY   (  47-)  A 1  1.63   45
 365 GLY   (  47-)  A   1.63   28
1425 GLY   (  47-)  A 1  1.62   51
 895 GLY   (  47-)  A   1.61   19
 153 GLY   (  47-)  A   1.61   30
2485 GLY   (  47-)  A 2  1.60   25
1849 GLY   (  47-)  A 1  1.60   19
1001 GLY   (  47-)  A 1  1.56   28
3121 GLY   (  47-)  A 3  1.53   24
1743 GLY   (  47-)  A 1  1.50   30

Warning: Unusual PRO puckering phases

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

  53 PRO   (  53-)  A  -128.5 half-chair C-delta/C-gamma (-126 degrees)
1431 PRO   (  53-)  A 1 -116.6 envelop C-gamma (-108 degrees)
1643 PRO   (  53-)  A 1 -118.1 half-chair C-delta/C-gamma (-126 degrees)
2279 PRO   (  53-)  A 2 -120.1 half-chair C-delta/C-gamma (-126 degrees)
2915 PRO   (  53-)  A 2 -118.2 half-chair C-delta/C-gamma (-126 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.

1293 VAL   (  21-)  A 1    CG2 <-> 1331 ILE   (  59-)  A 1    CG2    0.33    2.87
 975 VAL   (  21-)  A 1    CG2 <-> 1013 ILE   (  59-)  A 1    CG2    0.31    2.89
1081 VAL   (  21-)  A 1    CG2 <-> 1119 ILE   (  59-)  A 1    CG2    0.31    2.89
 445 VAL   (  21-)  A      CG2 <->  483 ILE   (  59-)  A      CG2    0.30    2.90
2141 VAL   (  21-)  A 2    CG2 <-> 2179 ILE   (  59-)  A 2    CG2    0.29    2.91
1717 VAL   (  21-)  A 1    CG2 <-> 1755 ILE   (  59-)  A 1    CG2    0.29    2.91
2353 VAL   (  21-)  A 2    CG2 <-> 2391 ILE   (  59-)  A 2    CG2    0.29    2.91
2636 ILE   (  92-)  A 2    CG2 <-> 2637 ASN   (  93-)  A 2    N      0.29    2.71
 233 VAL   (  21-)  A      CG2 <->  271 ILE   (  59-)  A      CG2    0.28    2.92
 869 VAL   (  21-)  A      CG2 <->  907 ILE   (  59-)  A      CG2    0.28    2.92
1187 VAL   (  21-)  A 1    CG2 <-> 1225 ILE   (  59-)  A 1    CG2    0.28    2.92
 657 VAL   (  21-)  A      CG2 <->  695 ILE   (  59-)  A      CG2    0.27    2.93
2247 VAL   (  21-)  A 2    CG2 <-> 2285 ILE   (  59-)  A 2    CG2    0.27    2.93
1823 VAL   (  21-)  A 1    CG2 <-> 1861 ILE   (  59-)  A 1    CG2    0.27    2.93
 339 VAL   (  21-)  A      CG2 <->  377 ILE   (  59-)  A      CG2    0.27    2.93
1611 VAL   (  21-)  A 1    CG2 <-> 1649 ILE   (  59-)  A 1    CG2    0.27    2.93
 988 PHE   (  34-)  A 1    CE1 <-> 1040 LYS   (  86-)  A 1    NZ     0.26    2.84
 551 VAL   (  21-)  A      CG2 <->  589 ILE   (  59-)  A      CG2    0.26    2.94
3097 ILE   (  23-)  A 3    CG2 <-> 3168 LEU   (  94-)  A 3    CD1    0.26    2.94
2037 ILE   (  23-)  A 2    CG2 <-> 2108 LEU   (  94-)  A 2    CD1    0.26    2.94
2560 GLU   (  16-)  A 2    N   <-> 2563 ASP   (  19-)  A 2    CG     0.26    2.84
2035 VAL   (  21-)  A 2    CG2 <-> 2073 ILE   (  59-)  A 2    CG2    0.26    2.94
2024 GLU   (  10-)  A 2    CB  <-> 2112 GLU   (  98-)  A 2    CB     0.26    2.94
 867 ASP   (  19-)  A      O   <->  894 MET   (  46-)  A      N      0.25    2.45
2030 GLU   (  16-)  A 2    N   <-> 2033 ASP   (  19-)  A 2    CG     0.25    2.85
And so on for a total of 1639 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