WHAT IF Check report

This file was created 2012-01-12 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 pdb1qyp.ent

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

 490 ALA   (  35-)  A  9              489 THR   (  33-)  A  9           3.0

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

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 620 HIS   (  51-)  A 1
 644 CYS   (  18-)  A 1

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 GLU   (   5-)  A    Zero
   6 GLN   (   6-)  A    Zero
   7 ASP   (   7-)  A    Zero
   8 LEU   (   8-)  A    Zero
   9 LYS   (   9-)  A    Zero
  10 THR   (  10-)  A    Zero
  11 LEU   (  11-)  A    Zero
  12 PRO   (  12-)  A    Zero
  13 THR   (  13-)  A    Zero
  14 THR   (  14-)  A    Zero
  15 LYS   (  15-)  A    Zero
  16 ILE   (  16-)  A    Zero
  17 THR   (  17-)  A    Zero
  18 CYS   (  18-)  A    Zero
  19 PRO   (  19-)  A    Zero
  20 LYS   (  20-)  A    Zero
  21 CYS   (  21-)  A    Zero
  22 GLY   (  22-)  A    Zero
  23 ASN   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 THR   (  25-)  A    Zero
And so on for a total of 1424 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 : 0.954
Model 2 : 0.952
Model 3 : 0.950
Model 4 : 0.949
Model 5 : 0.949
Model 6 : 0.951
Model 7 : 0.950
Model 8 : 0.956
Model 9 : 0.944
Model 10 : 0.948
Model 11 : 0.951
Model 12 : 0.953
Model 13 : 0.952
Model 14 : 0.953
Model 15 : 0.951
Model 16 : 0.949
Model 17 : 0.950
Model 18 : 0.954
Model 19 : 0.948
Model 20 : 0.953
Model 21 : 0.949
Model 22 : 0.953
Model 23 : 0.949
Model 24 : 0.953
Model 25 : 0.952

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.

   3 HIS   (   3-)  A      CA   CB   CG  109.56   -4.2
  43 PHE   (  43-)  A      CA   CB   CG  109.36   -4.4
  46 CYS   (  46-)  A      N    CA   CB  103.65   -4.0
  51 HIS   (  51-)  A      CA   CB   CG  109.41   -4.4
  60 HIS   (   3-)  A      CA   CB   CG  109.34   -4.5
 100 PHE   (  43-)  A      CA   CB   CG  109.23   -4.6
 108 HIS   (  51-)  A      CA   CB   CG  109.53   -4.3
 117 HIS   (   3-)  A      CA   CB   CG  109.36   -4.4
 132 CYS   (  18-)  A      N    CA   CB  103.64   -4.0
 157 PHE   (  43-)  A      CA   CB   CG  109.40   -4.4
 165 HIS   (  51-)  A      CA   CB   CG  109.68   -4.1
 174 HIS   (   3-)  A      CA   CB   CG  109.45   -4.3
 214 PHE   (  43-)  A      CA   CB   CG  109.47   -4.3
 222 HIS   (  51-)  A      CA   CB   CG  109.32   -4.5
 231 HIS   (   3-)  A      CA   CB   CG  109.46   -4.3
 246 CYS   (  18-)  A      N    CA   CB  103.66   -4.0
 271 PHE   (  43-)  A      CA   CB   CG  109.41   -4.4
 279 HIS   (  51-)  A      CA   CB   CG  109.41   -4.4
 288 HIS   (   3-)  A      CA   CB   CG  109.36   -4.4
 303 CYS   (  18-)  A      N    CA   CB  103.63   -4.0
 336 HIS   (  51-)  A      CA   CB   CG  109.52   -4.3
 345 HIS   (   3-)  A      CA   CB   CG  109.49   -4.3
 360 CYS   (  18-)  A      N    CA   CB  103.51   -4.1
 385 PHE   (  43-)  A      CA   CB   CG  109.58   -4.2
 393 HIS   (  51-)  A      CA   CB   CG  109.55   -4.2
And so on for a total of 89 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.394
Model 2 : 1.401
Model 3 : 1.391
Model 4 : 1.394
Model 5 : 1.396
Model 6 : 1.388
Model 7 : 1.383
Model 8 : 1.394
Model 9 : 1.392
Model 10 : 1.386
Model 11 : 1.398
Model 12 : 1.390
Model 13 : 1.399
Model 14 : 1.388
Model 15 : 1.389
Model 16 : 1.387
Model 17 : 1.389
Model 18 : 1.392
Model 19 : 1.385
Model 20 : 1.383
Model 21 : 1.382
Model 22 : 1.389
Model 23 : 1.393
Model 24 : 1.397
Model 25 : 1.389

Note: Per-model averages for chirality check

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

Model 1 : 1.256
Model 2 : 1.271
Model 3 : 1.259
Model 4 : 1.260
Model 5 : 1.266
Model 6 : 1.263
Model 7 : 1.262
Model 8 : 1.257
Model 9 : 1.264
Model 10 : 1.265
Model 11 : 1.268
Model 12 : 1.268
Model 13 : 1.277
Model 14 : 1.252
Model 15 : 1.254
Model 16 : 1.252
Model 17 : 1.258
Model 18 : 1.279
Model 19 : 1.259
Model 20 : 1.270
Model 21 : 1.252
Model 22 : 1.263
Model 23 : 1.265
Model 24 : 1.272
Model 25 : 1.265

Error: Side chain planarity problems

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

1230 ARG   (  34-)  A 2   8.41
 205 ARG   (  34-)  A    8.35
 774 ARG   (  34-)  A 1   8.13
 851 ARG   (  54-)  A 1   8.06
1364 ARG   (  54-)  A 2   7.96
 908 ARG   (  54-)  A 1   7.91
 453 ARG   (  54-)  A    7.86
 546 ARG   (  34-)  A 1   7.82
 319 ARG   (  34-)  A    7.81
 680 ARG   (  54-)  A 1   7.80
 965 ARG   (  54-)  A 1   7.76
  91 ARG   (  34-)  A    7.75
 225 ARG   (  54-)  A    7.67
 888 ARG   (  34-)  A 1   7.59
 945 ARG   (  34-)  A 1   7.58
1287 ARG   (  34-)  A 2   7.39
 623 ARG   (  54-)  A 1   7.36
1079 ARG   (  54-)  A 1   7.34
 831 ARG   (  34-)  A 1   7.16
 660 ARG   (  34-)  A 1   7.13
 339 ARG   (  54-)  A    6.95
 794 ARG   (  54-)  A 1   6.85
 433 ARG   (  34-)  A    6.84
1022 ARG   (  54-)  A 1   6.66
 168 ARG   (  54-)  A    6.62
1421 ARG   (  54-)  A 2   6.43
 603 ARG   (  34-)  A 1   6.26
1250 ARG   (  54-)  A 2   6.19
1002 ARG   (  34-)  A 1   6.17
1344 ARG   (  34-)  A 2   6.15
 376 ARG   (  34-)  A    6.10
 717 ARG   (  34-)  A 1   6.02
 566 ARG   (  54-)  A 1   5.64
1307 ARG   (  54-)  A 2   5.54
1173 ARG   (  34-)  A 2   5.52
1401 ARG   (  34-)  A 2   5.43
1116 ARG   (  34-)  A 2   5.39
1136 ARG   (  54-)  A 2   5.35
1193 ARG   (  54-)  A 2   5.34
  34 ARG   (  34-)  A    5.31
  54 ARG   (  54-)  A    5.23
 148 ARG   (  34-)  A    5.19
1059 ARG   (  34-)  A 1   5.06
 396 ARG   (  54-)  A    4.74
 111 ARG   (  54-)  A    4.32

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 : -5.441

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.411
Model 2 : -5.268
Model 3 : -5.068
Model 4 : -4.494
Model 5 : -4.826
Model 6 : -5.091
Model 7 : -5.236
Model 8 : -5.382
Model 9 : -5.167
Model 10 : -4.828
Model 11 : -5.977
Model 12 : -5.147
Model 13 : -6.304
Model 14 : -5.282
Model 15 : -5.735
Model 16 : -5.405
Model 17 : -6.224
Model 18 : -5.415
Model 19 : -6.392
Model 20 : -5.618
Model 21 : -5.607
Model 22 : -5.975
Model 23 : -5.289
Model 24 : -5.543
Model 25 : -5.317

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.

 511 TYR   (  56-)  A    -3.7
 807 THR   (  10-)  A 1   -3.5
 910 TYR   (  56-)  A 1   -3.4
1172 THR   (  33-)  A 2   -3.3
 796 TYR   (  56-)  A 1   -3.1
 261 THR   (  33-)  A    -3.0
 572 HIS   (   3-)  A 1   -3.0
 642 ILE   (  16-)  A 1   -2.9
  73 ILE   (  16-)  A    -2.8
 187 ILE   (  16-)  A    -2.8
  16 ILE   (  16-)  A    -2.8
 528 ILE   (  16-)  A 1   -2.8
 870 ILE   (  16-)  A 1   -2.8
 472 ILE   (  16-)  A    -2.8
 984 ILE   (  16-)  A 1   -2.8
 301 ILE   (  16-)  A    -2.8
 699 ILE   (  16-)  A 1   -2.8
 585 ILE   (  16-)  A 1   -2.8
 244 ILE   (  16-)  A    -2.8
1378 LEU   (  11-)  A 2   -2.8
 739 TYR   (  56-)  A 1   -2.8
 148 ARG   (  34-)  A    -2.8
 625 TYR   (  56-)  A 1   -2.7
 179 LEU   (   8-)  A    -2.7
1383 ILE   (  16-)  A 2   -2.7
And so on for a total of 288 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.

  11 LEU   (  11-)  A  Poor phi/psi
  33 THR   (  33-)  A  Poor phi/psi
  34 ARG   (  34-)  A  Poor phi/psi
  35 ALA   (  35-)  A  Poor phi/psi
  36 GLY   (  36-)  A  Poor phi/psi
  37 ASP   (  37-)  A  Poor phi/psi
  40 SER   (  40-)  A  Poor phi/psi
  53 TRP   (  53-)  A  Poor phi/psi
  55 SER   (  55-)  A  Poor phi/psi
  59 SER   (   2-)  A  Poor phi/psi
  60 HIS   (   3-)  A  Poor phi/psi
  63 GLN   (   6-)  A  Poor phi/psi
  68 LEU   (  11-)  A  Poor phi/psi
  90 THR   (  33-)  A  Poor phi/psi
  91 ARG   (  34-)  A  Poor phi/psi
  97 SER   (  40-)  A  Poor phi/psi
 110 TRP   (  53-)  A  Poor phi/psi
 113 TYR   (  56-)  A  Poor phi/psi
 116 SER   (   2-)  A  Poor phi/psi
 118 MET   (   4-)  A  Poor phi/psi
 122 LEU   (   8-)  A  Poor phi/psi
 123 LYS   (   9-)  A  Poor phi/psi
 148 ARG   (  34-)  A  Poor phi/psi
 154 SER   (  40-)  A  Poor phi/psi
 167 TRP   (  53-)  A  Poor phi/psi
And so on for a total of 176 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -6.992

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 : -6.577
Model 2 : -7.038
Model 3 : -7.102
Model 4 : -7.067
Model 5 : -7.632
Model 6 : -7.183
Model 7 : -6.062
Model 8 : -7.248
Model 9 : -6.508
Model 10 : -7.752
Model 11 : -7.408
Model 12 : -6.494
Model 13 : -7.149
Model 14 : -7.110
Model 15 : -7.257
Model 16 : -7.054
Model 17 : -6.652
Model 18 : -6.953
Model 19 : -6.973
Model 20 : -7.275
Model 21 : -6.575
Model 22 : -6.705
Model 23 : -6.822
Model 24 : -7.058
Model 25 : -7.142

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 GLU   (   5-)  A      0
   6 GLN   (   6-)  A      0
   7 ASP   (   7-)  A      0
   8 LEU   (   8-)  A      0
  10 THR   (  10-)  A      0
  11 LEU   (  11-)  A      0
  15 LYS   (  15-)  A      0
  16 ILE   (  16-)  A      0
  21 CYS   (  21-)  A      0
  23 ASN   (  23-)  A      0
  24 ASP   (  24-)  A      0
  25 THR   (  25-)  A      0
  27 TYR   (  27-)  A      0
  28 TRP   (  28-)  A      0
  34 ARG   (  34-)  A      0
  35 ALA   (  35-)  A      0
  37 ASP   (  37-)  A      0
  38 GLU   (  38-)  A      0
  39 PRO   (  39-)  A      0
  40 SER   (  40-)  A      0
  46 CYS   (  46-)  A      0
  47 THR   (  47-)  A      0
  48 LYS   (  48-)  A      0
And so on for a total of 986 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 : 0.574

Note: Per-model averages for omega angle check

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

Model 1 : 0.616
Model 2 : 0.591
Model 3 : 0.571
Model 4 : 0.672
Model 5 : 0.588
Model 6 : 0.558
Model 7 : 0.515
Model 8 : 0.614
Model 9 : 0.627
Model 10 : 0.606
Model 11 : 0.657
Model 12 : 0.672
Model 13 : 0.600
Model 14 : 0.582
Model 15 : 0.548
Model 16 : 0.638
Model 17 : 0.577
Model 18 : 0.632
Model 19 : 0.533
Model 20 : 0.573
Model 21 : 0.593
Model 22 : 0.684
Model 23 : 0.568
Model 24 : 0.680
Model 25 : 0.626

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!

1403 GLY   (  36-)  A 2  1.84   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  12 PRO   (  12-)  A    0.03 LOW
  19 PRO   (  19-)  A    0.06 LOW
  39 PRO   (  39-)  A    0.02 LOW
  69 PRO   (  12-)  A    0.07 LOW
  76 PRO   (  19-)  A    0.09 LOW
  96 PRO   (  39-)  A    0.00 LOW
 126 PRO   (  12-)  A    0.01 LOW
 133 PRO   (  19-)  A    0.01 LOW
 153 PRO   (  39-)  A    0.00 LOW
 183 PRO   (  12-)  A    0.02 LOW
 190 PRO   (  19-)  A    0.06 LOW
 210 PRO   (  39-)  A    0.01 LOW
 240 PRO   (  12-)  A    0.03 LOW
 247 PRO   (  19-)  A    0.04 LOW
 267 PRO   (  39-)  A    0.02 LOW
 297 PRO   (  12-)  A    0.00 LOW
 304 PRO   (  19-)  A    0.03 LOW
 324 PRO   (  39-)  A    0.02 LOW
 354 PRO   (  12-)  A    0.01 LOW
 361 PRO   (  19-)  A    0.04 LOW
 381 PRO   (  39-)  A    0.00 LOW
 411 PRO   (  12-)  A    0.03 LOW
 418 PRO   (  19-)  A    0.06 LOW
 438 PRO   (  39-)  A    0.02 LOW
 468 PRO   (  12-)  A    0.03 LOW
And so on for a total of 75 lines.

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.

 763 ASN   (  23-)  A 1    CB  <->  786 CYS   (  46-)  A 1    SG     0.43    2.97
 771 MET   (  31-)  A 1    SD  <->  783 PHE   (  43-)  A 1    CZ     0.42    2.98
1048 ASN   (  23-)  A 1    CB  <-> 1071 CYS   (  46-)  A 1    SG     0.42    2.98
 308 ASN   (  23-)  A      CB  <->  331 CYS   (  46-)  A      SG     0.42    2.98
1227 MET   (  31-)  A 2    SD  <-> 1239 PHE   (  43-)  A 2    CD1    0.42    2.98
 270 ILE   (  42-)  A      CG2 <->  272 TYR   (  44-)  A      CE1    0.41    2.79
 327 ILE   (  42-)  A      CG2 <->  329 TYR   (  44-)  A      CE1    0.41    2.79
1181 ILE   (  42-)  A 2    CG2 <-> 1183 TYR   (  44-)  A 2    CE1    0.40    2.80
 753 THR   (  13-)  A 1    CG2 <->  767 TYR   (  27-)  A 1    CD1    0.40    2.80
 127 THR   (  13-)  A      CG2 <->  141 TYR   (  27-)  A      CD1    0.40    2.80
 384 ILE   (  42-)  A      CG2 <->  386 TYR   (  44-)  A      CE1    0.39    2.81
 582 THR   (  13-)  A 1    CG2 <->  596 TYR   (  27-)  A 1    CD1    0.39    2.81
1038 THR   (  13-)  A 1    CG2 <-> 1052 TYR   (  27-)  A 1    CD1    0.39    2.81
 896 ILE   (  42-)  A 1    CG2 <->  898 TYR   (  44-)  A 1    CE1    0.39    2.81
 981 THR   (  13-)  A 1    CG2 <->  995 TYR   (  27-)  A 1    CD1    0.38    2.82
 696 THR   (  13-)  A 1    CG2 <->  710 TYR   (  27-)  A 1    CD1    0.38    2.82
 924 THR   (  13-)  A 1    CG2 <->  938 TYR   (  27-)  A 1    CD1    0.38    2.82
 525 THR   (  13-)  A 1    CG2 <->  539 TYR   (  27-)  A 1    CD1    0.38    2.82
 365 ASN   (  23-)  A      CG  <->  388 CYS   (  46-)  A      SG     0.38    3.02
 422 ASN   (  23-)  A      CB  <->  445 CYS   (  46-)  A      SG     0.37    3.03
  23 ASN   (  23-)  A      CB  <->   46 CYS   (  46-)  A      SG     0.37    3.03
 810 THR   (  13-)  A 1    CG2 <->  824 TYR   (  27-)  A 1    CD1    0.37    2.83
 706 ASN   (  23-)  A 1    CB  <->  729 CYS   (  46-)  A 1    SG     0.37    3.03
 137 ASN   (  23-)  A      CB  <->  160 CYS   (  46-)  A      SG     0.36    3.04
 412 THR   (  13-)  A      CG2 <->  426 TYR   (  27-)  A      CD1    0.36    2.84
And so on for a total of 962 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

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

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

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

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