WHAT IF Check report

This file was created 2011-12-16 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 pdb2kkw.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

Note: Ramachandran plot

Chain identifier: A; Model number 31

Note: Ramachandran plot

Chain identifier: A; Model number 32

Note: Ramachandran plot

Chain identifier: A; Model number 33

Note: Ramachandran plot

Chain identifier: A; Model number 34

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.

  22 THR   (  22-)  A    Zero
  26 VAL   (  26-)  A    Zero
  37 VAL   (  37-)  A    Zero
  44 THR   (  44-)  A    Zero
  48 VAL   (  48-)  A    Zero
  52 VAL   (  52-)  A    Zero
  63 VAL   (  63-)  A    Zero
  70 VAL   (  70-)  A    Zero
  81 THR   (  81-)  A    Zero
 162 THR   (  22-)  A    Zero
 166 VAL   (  26-)  A    Zero
 177 VAL   (  37-)  A    Zero
 184 THR   (  44-)  A    Zero
 188 VAL   (  48-)  A    Zero
 192 VAL   (  52-)  A    Zero
 203 VAL   (  63-)  A    Zero
 210 VAL   (  70-)  A    Zero
 221 THR   (  81-)  A    Zero
 302 THR   (  22-)  A    Zero
 306 VAL   (  26-)  A    Zero
 317 VAL   (  37-)  A    Zero
 324 THR   (  44-)  A    Zero
 328 VAL   (  48-)  A    Zero
 332 VAL   (  52-)  A    Zero
 343 VAL   (  63-)  A    Zero
And so on for a total of 306 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 : 0.505
Model 2 : 0.498
Model 3 : 0.510
Model 4 : 0.490
Model 5 : 0.505
Model 6 : 0.491
Model 7 : 0.503
Model 8 : 0.506
Model 9 : 0.490
Model 10 : 0.488
Model 11 : 0.496
Model 12 : 0.497
Model 13 : 0.501
Model 14 : 0.483
Model 15 : 0.488
Model 16 : 0.500
Model 17 : 0.506
Model 18 : 0.508
Model 19 : 0.493
Model 20 : 0.492
Model 21 : 0.503
Model 22 : 0.495
Model 23 : 0.528
Model 24 : 0.496
Model 25 : 0.499
Model 26 : 0.504
Model 27 : 0.505
Model 28 : 0.511
Model 29 : 0.508
Model 30 : 0.499
Model 31 : 0.508
Model 32 : 0.501
Model 33 : 0.509
Model 34 : 0.511

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.

   4 PHE   (   4-)  A      CA   CB   CG  109.37   -4.4
  50 HIS   (  50-)  A      CA   CB   CG  109.56   -4.2
  94 PHE   (  94-)  A      CA   CB   CG  109.58   -4.2
 144 PHE   (   4-)  A      CA   CB   CG  109.47   -4.3
 190 HIS   (  50-)  A      CA   CB   CG  109.76   -4.0
 234 PHE   (  94-)  A      CA   CB   CG  109.53   -4.3
 284 PHE   (   4-)  A      CA   CB   CG  108.95   -4.8
 330 HIS   (  50-)  A      CA   CB   CG  109.53   -4.3
 374 PHE   (  94-)  A      CA   CB   CG  109.48   -4.3
 424 PHE   (   4-)  A      CA   CB   CG  109.42   -4.4
 470 HIS   (  50-)  A      CA   CB   CG  109.80   -4.0
 514 PHE   (  94-)  A      CA   CB   CG  109.50   -4.3
 564 PHE   (   4-)  A      CA   CB   CG  109.75   -4.1
 610 HIS   (  50-)  A      CA   CB   CG  109.48   -4.3
 654 PHE   (  94-)  A      CA   CB   CG  109.45   -4.4
 704 PHE   (   4-)  A      CA   CB   CG  109.48   -4.3
 750 HIS   (  50-)  A      CA   CB   CG  109.51   -4.3
 794 PHE   (  94-)  A      CA   CB   CG  109.68   -4.1
 844 PHE   (   4-)  A      CA   CB   CG  109.55   -4.3
 890 HIS   (  50-)  A      CA   CB   CG  109.48   -4.3
 903 VAL   (  63-)  A      N    CA   CB  121.39    6.4
 934 PHE   (  94-)  A      CA   CB   CG  109.50   -4.3
 984 PHE   (   4-)  A      CA   CB   CG  109.59   -4.2
1028 VAL   (  48-)  A      N    CA   CB  118.82    4.9
1030 HIS   (  50-)  A      CA   CB   CG  109.45   -4.3
And so on for a total of 109 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.734
Model 2 : 0.729
Model 3 : 0.743
Model 4 : 0.725
Model 5 : 0.735
Model 6 : 0.732
Model 7 : 0.752
Model 8 : 0.746
Model 9 : 0.730
Model 10 : 0.727
Model 11 : 0.746
Model 12 : 0.739
Model 13 : 0.744
Model 14 : 0.733
Model 15 : 0.723
Model 16 : 0.742
Model 17 : 0.748
Model 18 : 0.747
Model 19 : 0.737
Model 20 : 0.726
Model 21 : 0.729
Model 22 : 0.731
Model 23 : 0.761
Model 24 : 0.737
Model 25 : 0.732
Model 26 : 0.751
Model 27 : 0.745
Model 28 : 0.755
Model 29 : 0.746
Model 30 : 0.731
Model 31 : 0.749
Model 32 : 0.737
Model 33 : 0.736
Model 34 : 0.760

Note: Per-model averages for chirality check

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

Model 1 : 0.678
Model 2 : 0.673
Model 3 : 0.675
Model 4 : 0.669
Model 5 : 0.674
Model 6 : 0.668
Model 7 : 0.679
Model 8 : 0.682
Model 9 : 0.678
Model 10 : 0.663
Model 11 : 0.710
Model 12 : 0.670
Model 13 : 0.679
Model 14 : 0.679
Model 15 : 0.671
Model 16 : 0.671
Model 17 : 0.692
Model 18 : 0.693
Model 19 : 0.690
Model 20 : 0.676
Model 21 : 0.680
Model 22 : 0.658
Model 23 : 0.704
Model 24 : 0.680
Model 25 : 0.685
Model 26 : 0.699
Model 27 : 0.678
Model 28 : 0.681
Model 29 : 0.687
Model 30 : 0.692
Model 31 : 0.693
Model 32 : 0.698
Model 33 : 0.678
Model 34 : 0.673

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : 3.374
Model 2 : 3.880
Model 3 : 3.016
Model 4 : 2.217
Model 5 : 2.569
Model 6 : 3.750
Model 7 : 2.807
Model 8 : 3.304
Model 9 : 2.327
Model 10 : 2.972
Model 11 : 3.688
Model 12 : 3.552
Model 13 : 2.974
Model 14 : 3.149
Model 15 : 3.505
Model 16 : 2.810
Model 17 : 2.866
Model 18 : 4.225
Model 19 : 3.366
Model 20 : 2.132
Model 21 : 2.953
Model 22 : 2.627
Model 23 : 2.651
Model 24 : 3.074
Model 25 : 3.488
Model 26 : 4.072
Model 27 : 2.743
Model 28 : 3.815
Model 29 : 3.192
Model 30 : 3.569
Model 31 : 2.456
Model 32 : 3.713
Model 33 : 3.642
Model 34 : 3.293

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.

1019 TYR   (  39-)  A    -3.5
1017 VAL   (  37-)  A    -2.7
4609 SER   ( 129-)  A 3   -2.7
 829 SER   ( 129-)  A    -2.7
1809 SER   ( 129-)  A 1   -2.6
2913 LEU   ( 113-)  A 2   -2.6
1109 SER   ( 129-)  A    -2.5
4749 SER   ( 129-)  A 3   -2.5
1997 VAL   (  37-)  A 1   -2.4
1857 VAL   (  37-)  A 1   -2.4
3632 GLY   ( 132-)  A 2   -2.3
 532 ILE   ( 112-)  A    -2.3
2216 MET   ( 116-)  A 1   -2.3
3339 ASP   ( 119-)  A 2   -2.3
3896 MET   ( 116-)  A 2   -2.2
 816 MET   ( 116-)  A    -2.2
3759 ASP   ( 119-)  A 2   -2.2
4036 MET   ( 116-)  A 2   -2.2
2071 GLY   ( 111-)  A 1   -2.2
2636 MET   ( 116-)  A 1   -2.2
1936 MET   ( 116-)  A 1   -2.2
 181 GLY   (  41-)  A    -2.2
 536 MET   ( 116-)  A    -2.2
 676 MET   ( 116-)  A    -2.1
1516 MET   ( 116-)  A 1   -2.1
3681 GLY   (  41-)  A 2   -2.1
 601 GLY   (  41-)  A    -2.1
4039 ASP   ( 119-)  A 2   -2.1
1161 GLY   (  41-)  A    -2.1
2219 ASP   ( 119-)  A 1   -2.1
 794 PHE   (  94-)  A    -2.1
4241 GLY   (  41-)  A 3   -2.1
3479 ASP   ( 119-)  A 2   -2.1
1799 ASP   ( 119-)  A 1   -2.1
3117 VAL   (  37-)  A 2   -2.1
4240 VAL   (  40-)  A 3   -2.1
2837 VAL   (  37-)  A 2   -2.1
1297 VAL   (  37-)  A 1   -2.0
3817 VAL   (  37-)  A 2   -2.0
 461 GLY   (  41-)  A    -2.0
3616 MET   ( 116-)  A 2   -2.0
2773 LEU   ( 113-)  A 2   -2.0
4459 ASP   ( 119-)  A 3   -2.0

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.

  40 VAL   (  40-)  A  Poor phi/psi
  41 GLY   (  41-)  A  Poor phi/psi
 107 ALA   ( 107-)  A  Poor phi/psi
 119 ASP   ( 119-)  A  Poor phi/psi
 126 GLU   ( 126-)  A  Poor phi/psi
 177 VAL   (  37-)  A  Poor phi/psi
 321 GLY   (  41-)  A  Poor phi/psi
 386 GLY   ( 106-)  A  Poor phi/psi
 413 TYR   ( 133-)  A  Poor phi/psi
 415 ASP   ( 135-)  A  Poor phi/psi
 461 GLY   (  41-)  A  Poor phi/psi
 514 PHE   (  94-)  A  Poor phi/psi
 519 GLN   (  99-)  A  Poor phi/psi
 524 GLU   ( 104-)  A  Poor phi/psi
 525 GLU   ( 105-)  A  Poor phi/psi
 533 LEU   ( 113-)  A  Poor phi/psi
 535 ASP   ( 115-)  A  Poor phi/psi
 553 TYR   ( 133-)  A  Poor phi/psi
 554 GLN   ( 134-)  A  Poor phi/psi
 599 TYR   (  39-)  A  Poor phi/psi
 654 PHE   (  94-)  A  Poor phi/psi
 675 ASP   ( 115-)  A  Poor phi/psi
 684 ALA   ( 124-)  A  Poor phi/psi
 739 TYR   (  39-)  A  Poor phi/psi
 741 GLY   (  41-)  A  Poor phi/psi
And so on for a total of 150 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 : 5.008
Model 2 : 3.912
Model 3 : 5.499
Model 4 : 4.754
Model 5 : 5.194
Model 6 : 4.408
Model 7 : 3.900
Model 8 : 4.657
Model 9 : 3.996
Model 10 : 5.301
Model 11 : 5.596
Model 12 : 5.845
Model 13 : 4.052
Model 14 : 4.974
Model 15 : 4.333
Model 16 : 5.014
Model 17 : 3.682
Model 18 : 5.543
Model 19 : 5.036
Model 20 : 4.582
Model 21 : 4.626
Model 22 : 6.355
Model 23 : 4.422
Model 24 : 5.084
Model 25 : 5.319
Model 26 : 5.479
Model 27 : 4.531
Model 28 : 4.010
Model 29 : 5.425
Model 30 : 4.334
Model 31 : 6.127
Model 32 : 4.665
Model 33 : 3.927
Model 34 : 5.036

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.

 462 SER   (  42-)  A    0.33
1582 SER   (  42-)  A 1   0.36
2842 SER   (  42-)  A 2   0.36
1862 SER   (  42-)  A 1   0.38
   9 SER   (   9-)  A    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!

  33 THR   (  33-)  A      0
  34 LYS   (  34-)  A      0
  39 TYR   (  39-)  A      0
  40 VAL   (  40-)  A      0
  42 SER   (  42-)  A      0
  92 THR   (  92-)  A      0
  94 PHE   (  94-)  A      0
 100 LEU   ( 100-)  A      0
 107 ALA   ( 107-)  A      0
 114 GLU   ( 114-)  A      0
 118 VAL   ( 118-)  A      0
 119 ASP   ( 119-)  A      0
 120 PRO   ( 120-)  A      0
 125 TYR   ( 125-)  A      0
 126 GLU   ( 126-)  A      0
 127 MET   ( 127-)  A      0
 131 GLU   ( 131-)  A      0
 133 TYR   ( 133-)  A      0
 137 GLU   ( 137-)  A      0
 139 GLU   ( 139-)  A      0
 140 ALA   ( 140-)  A      0
 141 MET   (   1-)  A      0
 142 ASP   (   2-)  A      0
 177 VAL   (  37-)  A      0
 178 LEU   (  38-)  A      0
And so on for a total of 1359 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 : 0.410

Note: Per-model averages for omega angle check

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

Model 1 : 0.500
Model 2 : 0.492
Model 3 : 0.481
Model 4 : 0.430
Model 5 : 0.453
Model 6 : 0.439
Model 7 : 0.509
Model 8 : 0.464
Model 9 : 0.439
Model 10 : 0.416
Model 11 : 0.462
Model 12 : 0.472
Model 13 : 0.432
Model 14 : 0.397
Model 15 : 0.426
Model 16 : 0.479
Model 17 : 0.418
Model 18 : 0.415
Model 19 : 0.416
Model 20 : 0.377
Model 21 : 0.446
Model 22 : 0.392
Model 23 : 0.465
Model 24 : 0.465
Model 25 : 0.418
Model 26 : 0.384
Model 27 : 0.486
Model 28 : 0.509
Model 29 : 0.372
Model 30 : 0.452
Model 31 : 0.430
Model 32 : 0.362
Model 33 : 0.419
Model 34 : 0.385

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!

2486 GLY   ( 106-)  A 1  2.57   10
3606 GLY   ( 106-)  A 2  2.15   28
1506 GLY   ( 106-)  A 1  1.64   15

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]

 268 PRO   ( 128-)  A    0.19 LOW
1088 PRO   ( 108-)  A    0.13 LOW
1818 PRO   ( 138-)  A 1   0.19 LOW
1948 PRO   ( 128-)  A 1   0.19 LOW
2368 PRO   ( 128-)  A 1   0.19 LOW
3068 PRO   ( 128-)  A 2   0.18 LOW
3208 PRO   ( 128-)  A 2   0.19 LOW
4058 PRO   ( 138-)  A 2   0.19 LOW

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].

 548 PRO   ( 128-)  A   106.5 envelop C-beta (108 degrees)
1118 PRO   ( 138-)  A   105.5 envelop C-beta (108 degrees)
1958 PRO   ( 138-)  A 1  104.7 envelop C-beta (108 degrees)
2788 PRO   ( 128-)  A 2  102.4 envelop C-beta (108 degrees)
3078 PRO   ( 138-)  A 2  104.8 envelop C-beta (108 degrees)
3348 PRO   ( 128-)  A 2  104.4 envelop C-beta (108 degrees)
3778 PRO   ( 138-)  A 2  104.8 envelop C-beta (108 degrees)
4748 PRO   ( 128-)  A 3  107.7 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 708 LEU   (   8-)  A      CD1 <->  712 LYS   (  12-)  A      NZ     0.35    2.75
 807 ALA   ( 107-)  A      N   <->  808 PRO   ( 108-)  A      CD     0.34    2.66
2079 ASP   ( 119-)  A 1    N   <-> 2080 PRO   ( 120-)  A 1    CD     0.34    2.66
 256 MET   ( 116-)  A      N   <->  257 PRO   ( 117-)  A      CD     0.34    2.66
4736 MET   ( 116-)  A 3    N   <-> 4737 PRO   ( 117-)  A 3    CD     0.33    2.67
 532 ILE   ( 112-)  A      O   <->  534 GLU   ( 114-)  A      N      0.32    2.38
3336 MET   ( 116-)  A 2    N   <-> 3337 PRO   ( 117-)  A 2    CD     0.32    2.68
3187 ALA   ( 107-)  A 2    N   <-> 3188 PRO   ( 108-)  A 2    CD     0.32    2.68
1787 ALA   ( 107-)  A 1    N   <-> 1788 PRO   ( 108-)  A 1    CD     0.31    2.69
4115 VAL   (  55-)  A 3    O   <-> 4119 THR   (  59-)  A 3    N      0.30    2.40
1813 TYR   ( 133-)  A 1    O   <-> 1815 ASP   ( 135-)  A 1    N      0.30    2.40
3680 VAL   (  40-)  A 2    O   <-> 3684 THR   (  44-)  A 2    N      0.29    2.41
2155 VAL   (  55-)  A 1    O   <-> 2159 THR   (  59-)  A 1    N      0.29    2.41
2776 MET   ( 116-)  A 2    N   <-> 2777 PRO   ( 117-)  A 2    CD     0.29    2.71
 247 ALA   ( 107-)  A      N   <->  248 PRO   ( 108-)  A      CD     0.28    2.72
4508 GLU   (  28-)  A 3    OE2 <-> 4512 LYS   (  32-)  A 3    NZ     0.28    2.42
 825 TYR   ( 125-)  A      CE1 <->  830 GLU   ( 130-)  A      CD     0.28    2.92
 195 VAL   (  55-)  A      O   <->  199 THR   (  59-)  A      N      0.28    2.42
3888 PRO   ( 108-)  A 2    O   <-> 3890 GLU   ( 110-)  A 2    N      0.28    2.42
4596 MET   ( 116-)  A 3    N   <-> 4597 PRO   ( 117-)  A 3    CD     0.28    2.72
2789 SER   ( 129-)  A 2    O   <-> 2791 GLU   ( 131-)  A 2    N      0.28    2.42
2647 MET   ( 127-)  A 1    SD  <-> 2650 GLU   ( 130-)  A 1    OE2    0.28    2.72
2015 VAL   (  55-)  A 1    O   <-> 2019 THR   (  59-)  A 1    N      0.28    2.42
1716 GLY   (  36-)  A 1    O   <-> 1718 LEU   (  38-)  A 1    N      0.28    2.42
 755 VAL   (  55-)  A      O   <->  759 THR   (  59-)  A      N      0.28    2.42
And so on for a total of 544 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.260

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 31

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 32

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 33

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 34

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

Note: Quality value plot

Chain identifier: A; Model number 31

Note: Quality value plot

Chain identifier: A; Model number 32

Note: Quality value plot

Chain identifier: A; Model number 33

Note: Quality value plot

Chain identifier: A; Model number 34

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: 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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 31

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 32

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 33

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 34

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