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 pdb1m0v.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2741 ACE   ( 201-)  B  1
2743 ACE   ( 201-)  B  2
2745 ACE   ( 201-)  B  3
2747 ACE   ( 201-)  B  4
2749 ACE   ( 201-)  B  5
2751 ACE   ( 201-)  B  6
2753 ACE   ( 201-)  B  7
2755 ACE   ( 201-)  B  8
2757 ACE   ( 201-)  B  9
2759 ACE   ( 201-)  B 10
2761 ACE   ( 201-)  B 11
2763 ACE   ( 201-)  B 12
2765 ACE   ( 201-)  B 13
2767 ACE   ( 201-)  B 14
2769 ACE   ( 201-)  B 15
2771 ACE   ( 201-)  B 16
2773 ACE   ( 201-)  B 17
2775 ACE   ( 201-)  B 18
2777 ACE   ( 201-)  B 19
2779 ACE   ( 201-)  B 20

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 131 ASP   ( 202-)  B  1   N   bound to 2741 ACE   ( 201-)  B  1   C
 268 ASP   ( 202-)  B  2   N   bound to 2743 ACE   ( 201-)  B  2   C
 405 ASP   ( 202-)  B  3   N   bound to 2745 ACE   ( 201-)  B  3   C
 542 ASP   ( 202-)  B  4   N   bound to 2747 ACE   ( 201-)  B  4   C
 679 ASP   ( 202-)  B  5   N   bound to 2749 ACE   ( 201-)  B  5   C
 816 ASP   ( 202-)  B  6   N   bound to 2751 ACE   ( 201-)  B  6   C
 953 ASP   ( 202-)  B  7   N   bound to 2753 ACE   ( 201-)  B  7   C
1090 ASP   ( 202-)  B  8   N   bound to 2755 ACE   ( 201-)  B  8   C
1227 ASP   ( 202-)  B  9   N   bound to 2757 ACE   ( 201-)  B  9   C
1364 ASP   ( 202-)  B 10   N   bound to 2759 ACE   ( 201-)  B 10   C
1501 ASP   ( 202-)  B 11   N   bound to 2761 ACE   ( 201-)  B 11   C
1638 ASP   ( 202-)  B 12   N   bound to 2763 ACE   ( 201-)  B 12   C
1775 ASP   ( 202-)  B 13   N   bound to 2765 ACE   ( 201-)  B 13   C
1912 ASP   ( 202-)  B 14   N   bound to 2767 ACE   ( 201-)  B 14   C
2049 ASP   ( 202-)  B 15   N   bound to 2769 ACE   ( 201-)  B 15   C
2186 ASP   ( 202-)  B 16   N   bound to 2771 ACE   ( 201-)  B 16   C
2323 ASP   ( 202-)  B 17   N   bound to 2773 ACE   ( 201-)  B 17   C
2460 ASP   ( 202-)  B 18   N   bound to 2775 ACE   ( 201-)  B 18   C
2597 ASP   ( 202-)  B 19   N   bound to 2777 ACE   ( 201-)  B 19   C
2734 ASP   ( 202-)  B 20   N   bound to 2779 ACE   ( 201-)  B 20   C

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

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.

 133 PTR   ( 204-)  B
 270 PTR   ( 204-)  B
 407 PTR   ( 204-)  B
 544 PTR   ( 204-)  B
 681 PTR   ( 204-)  B
 818 PTR   ( 204-)  B
 955 PTR   ( 204-)  B
1092 PTR   ( 204-)  B
1229 PTR   ( 204-)  B
1366 PTR   ( 204-)  B 1
1503 PTR   ( 204-)  B 1
1640 PTR   ( 204-)  B 1
1777 PTR   ( 204-)  B 1
1914 PTR   ( 204-)  B 1
2051 PTR   ( 204-)  B 1
2188 PTR   ( 204-)  B 1
2325 PTR   ( 204-)  B 1
2462 PTR   ( 204-)  B 1
2599 PTR   ( 204-)  B 1
2689 ASN   (  86-)  A 2
2736 PTR   ( 204-)  B 2

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 MET   (   1-)  A    Zero
   2 ASN   (   2-)  A    Zero
   3 LEU   (   3-)  A    Zero
   4 SER   (   4-)  A    Zero
   5 LEU   (   5-)  A    Zero
   6 SER   (   6-)  A    Zero
   7 ASP   (   7-)  A    Zero
   8 LEU   (   8-)  A    Zero
   9 HIS   (   9-)  A    Zero
  10 ARG   (  10-)  A    Zero
  11 GLN   (  11-)  A    Zero
  12 VAL   (  12-)  A    Zero
  13 SER   (  13-)  A    Zero
  14 ARG   (  14-)  A    Zero
  15 LEU   (  15-)  A    Zero
  16 VAL   (  16-)  A    Zero
  17 GLN   (  17-)  A    Zero
  18 GLN   (  18-)  A    Zero
  19 GLU   (  19-)  A    Zero
  20 SER   (  20-)  A    Zero
  21 GLY   (  21-)  A    Zero
  22 ASP   (  22-)  A    Zero
  23 CYS   (  23-)  A    Zero
  24 THR   (  24-)  A    Zero
  25 GLY   (  25-)  A    Zero
And so on for a total of 2740 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 : 0.267
Model 2 : 0.308
Model 3 : 0.267
Model 4 : 0.265
Model 5 : 0.269
Model 6 : 0.287
Model 7 : 0.304
Model 8 : 0.297
Model 9 : 0.278
Model 10 : 0.279
Model 11 : 0.266
Model 12 : 0.275
Model 13 : 0.261
Model 14 : 0.273
Model 15 : 0.271
Model 16 : 0.288
Model 17 : 0.276
Model 18 : 0.273
Model 19 : 0.280
Model 20 : 0.261

Note: Per-model averages for bond-angle check

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

Model 1 : 0.499
Model 2 : 0.529
Model 3 : 0.494
Model 4 : 0.520
Model 5 : 0.486
Model 6 : 0.500
Model 7 : 0.523
Model 8 : 0.544
Model 9 : 0.492
Model 10 : 0.544
Model 11 : 0.503
Model 12 : 0.500
Model 13 : 0.505
Model 14 : 0.497
Model 15 : 0.505
Model 16 : 0.531
Model 17 : 0.528
Model 18 : 0.488
Model 19 : 0.500
Model 20 : 0.495

Note: Per-model averages for chirality check

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

Model 1 : 0.423
Model 2 : 0.429
Model 3 : 0.424
Model 4 : 0.439
Model 5 : 0.426
Model 6 : 0.434
Model 7 : 0.469
Model 8 : 0.531
Model 9 : 0.422
Model 10 : 0.457
Model 11 : 0.438
Model 12 : 0.473
Model 13 : 0.442
Model 14 : 0.420
Model 15 : 0.446
Model 16 : 0.460
Model 17 : 0.477
Model 18 : 0.430
Model 19 : 0.438
Model 20 : 0.409

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

1762 GLU   ( 118-)  A 1   4.07

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 : -6.000

Note: Per-model averages for Ramachandran check

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

Model 1 : -6.087
Model 2 : -6.242
Model 3 : -6.580
Model 4 : -6.300
Model 5 : -5.721
Model 6 : -5.734
Model 7 : -5.906
Model 8 : -6.311
Model 9 : -6.227
Model 10 : -5.480
Model 11 : -5.957
Model 12 : -6.312
Model 13 : -5.755
Model 14 : -5.877
Model 15 : -5.976
Model 16 : -6.082
Model 17 : -6.045
Model 18 : -5.692
Model 19 : -5.995
Model 20 : -5.728

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.

1271 THR   (  38-)  A 1   -3.7
  38 THR   (  38-)  A    -3.7
1272 PHE   (  39-)  A 1   -3.7
 317 THR   (  43-)  A    -3.6
 312 THR   (  38-)  A    -3.5
1276 THR   (  43-)  A 1   -3.5
  39 PHE   (  39-)  A    -3.5
2646 THR   (  43-)  A 2   -3.5
1139 THR   (  43-)  A    -3.4
1545 THR   (  38-)  A 1   -3.4
1824 THR   (  43-)  A 1   -3.4
 722 THR   (  37-)  A    -3.4
 998 PHE   (  39-)  A    -3.3
2275 HIS   (  83-)  A 1   -3.3
 861 PHE   (  39-)  A    -3.2
1409 PHE   (  39-)  A 1   -3.2
 576 ARG   (  28-)  A    -3.1
2412 HIS   (  83-)  A 1   -3.1
1809 ARG   (  28-)  A 1   -3.1
1124 ARG   (  28-)  A    -3.1
1956 THR   (  38-)  A 1   -3.0
1672 ARG   (  28-)  A 1   -3.0
2094 PHE   (  39-)  A 1   -3.0
2433 ARG   ( 104-)  A 1   -3.0
1946 ARG   (  28-)  A 1   -3.0
And so on for a total of 593 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.

   2 ASN   (   2-)  A  Poor phi/psi
  19 GLU   (  19-)  A  Poor phi/psi
  22 ASP   (  22-)  A  Poor phi/psi
  23 CYS   (  23-)  A  Poor phi/psi
  28 ARG   (  28-)  A  Poor phi/psi
  37 THR   (  37-)  A  Poor phi/psi
  38 THR   (  38-)  A  Poor phi/psi
  39 PHE   (  39-)  A  Poor phi/psi
  40 GLN   (  40-)  A  Poor phi/psi
  41 GLY   (  41-)  A  Poor phi/psi
  44 ILE   (  44-)  A  Poor phi/psi
  64 ALA   (  64-)  A  Poor phi/psi
  65 ASN   (  65-)  A  Poor phi/psi
  66 VAL   (  66-)  A  Poor phi/psi
  67 VAL   (  67-)  A  Poor phi/psi
  68 LEU   (  68-)  A  Poor phi/psi
  69 THR   (  69-)  A  Poor phi/psi
  83 HIS   (  83-)  A  Poor phi/psi
  84 ASN   (  84-)  A  Poor phi/psi
  85 LEU   (  85-)  A  Poor phi/psi
  93 VAL   (  93-)  A  Poor phi/psi
  94 GLY   (  94-)  A  Poor phi/psi
  95 ASN   (  95-)  A  Poor phi/psi
 103 LEU   ( 103-)  A  Poor phi/psi
 105 SER   ( 105-)  A  Poor phi/psi
And so on for a total of 466 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 : -8.024

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 : -8.067
Model 2 : -8.377
Model 3 : -8.148
Model 4 : -8.129
Model 5 : -7.963
Model 6 : -8.026
Model 7 : -8.192
Model 8 : -8.037
Model 9 : -7.894
Model 10 : -8.019
Model 11 : -8.130
Model 12 : -7.771
Model 13 : -7.540
Model 14 : -8.103
Model 15 : -7.707
Model 16 : -8.038
Model 17 : -8.184
Model 18 : -7.860
Model 19 : -7.920
Model 20 : -8.367

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.

2664 SER   (  61-)  A 2   0.33
 627 SER   (  79-)  A    0.36
 972 SER   (  13-)  A    0.37
 746 SER   (  61-)  A    0.37
 490 SER   (  79-)  A    0.38
1109 SER   (  13-)  A    0.38
1794 SER   (  13-)  A 1   0.38
1723 SER   (  79-)  A 1   0.39
1239 SER   (   6-)  A 1   0.39
2609 SER   (   6-)  A 2   0.39
1038 SER   (  79-)  A    0.39
  61 SER   (  61-)  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!

  17 GLN   (  17-)  A      0
  18 GLN   (  18-)  A      0
  19 GLU   (  19-)  A      0
  22 ASP   (  22-)  A      0
  23 CYS   (  23-)  A      0
  27 LEU   (  27-)  A      0
  28 ARG   (  28-)  A      0
  30 ASN   (  30-)  A      0
  34 ASN   (  34-)  A      0
  35 LYS   (  35-)  A      0
  36 GLU   (  36-)  A      0
  37 THR   (  37-)  A      0
  38 THR   (  38-)  A      0
  39 PHE   (  39-)  A      0
  40 GLN   (  40-)  A      0
  43 THR   (  43-)  A      0
  44 ILE   (  44-)  A      0
  46 SER   (  46-)  A      0
  63 VAL   (  63-)  A      0
  64 ALA   (  64-)  A      0
  65 ASN   (  65-)  A      0
  66 VAL   (  66-)  A      0
  67 VAL   (  67-)  A      0
  68 LEU   (  68-)  A      0
  70 GLN   (  70-)  A      0
And so on for a total of 1328 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 : 1.236

Note: Per-model averages for omega angle check

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

Model 1 : 1.272
Model 2 : 1.195
Model 3 : 1.220
Model 4 : 1.325
Model 5 : 1.215
Model 6 : 1.222
Model 7 : 1.328
Model 8 : 1.596
Model 9 : 1.200
Model 10 : 1.292
Model 11 : 1.214
Model 12 : 1.323
Model 13 : 1.212
Model 14 : 1.224
Model 15 : 1.286
Model 16 : 1.330
Model 17 : 1.375
Model 18 : 1.229
Model 19 : 1.235
Model 20 : 1.141

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!

1802 GLY   (  21-)  A 1  3.47   10
2487 GLY   (  21-)  A 1  3.38   14
 706 GLY   (  21-)  A   3.10   13
2350 GLY   (  21-)  A 1  2.82   11
 295 GLY   (  21-)  A   2.81   13
1528 GLY   (  21-)  A 1  2.49   12
 980 GLY   (  21-)  A   2.38   15
2624 GLY   (  21-)  A 2  2.38   13
 432 GLY   (  21-)  A   2.32   12
 569 GLY   (  21-)  A   2.29   17
 726 GLY   (  41-)  A   2.10   26
 178 GLY   (  41-)  A   1.83   12
1548 GLY   (  41-)  A 1  1.82   15

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].

 410 PRO   ( 207-)  B  -147.4 envelop C-delta (-144 degrees)
 547 PRO   ( 207-)  B  -112.1 envelop C-gamma (-108 degrees)
 684 PRO   ( 207-)  B  -118.3 half-chair C-delta/C-gamma (-126 degrees)
 821 PRO   ( 207-)  B  -114.8 envelop C-gamma (-108 degrees)
1095 PRO   ( 207-)  B  -133.1 half-chair C-delta/C-gamma (-126 degrees)
1232 PRO   ( 207-)  B  -140.8 envelop C-delta (-144 degrees)
1506 PRO   ( 207-)  B 1 -115.8 envelop C-gamma (-108 degrees)
1643 PRO   ( 207-)  B 1 -119.1 half-chair C-delta/C-gamma (-126 degrees)
1917 PRO   ( 207-)  B 1 -114.5 envelop C-gamma (-108 degrees)
2054 PRO   ( 207-)  B 1 -114.0 envelop C-gamma (-108 degrees)
2191 PRO   ( 207-)  B 1 -130.3 half-chair C-delta/C-gamma (-126 degrees)
2328 PRO   ( 207-)  B 1 -120.5 half-chair C-delta/C-gamma (-126 degrees)
2602 PRO   ( 207-)  B 1 -126.3 half-chair C-delta/C-gamma (-126 degrees)
2739 PRO   ( 207-)  B 2  -57.3 half-chair C-beta/C-alpha (-54 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.

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

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

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

1595 TYR   (  88-)  A 1    CA   <->  1609 SER   ( 102-)  A 1    OG   0.60    2.20
 176 PHE   (  39-)  A      C    <->   244 GLN   ( 107-)  A      NE2  0.57    2.53
1052 VAL   (  93-)  A      C    <->  1056 ASN   (  97-)  A      O    0.51    2.29
1409 PHE   (  39-)  A 1    C    <->  1477 GLN   ( 107-)  A 1    NE2  0.51    2.59
 438 LEU   (  27-)  A      CB   <->   441 ASN   (  30-)  A      O    0.50    2.30
1326 VAL   (  93-)  A 1    C    <->  1330 ASN   (  97-)  A 1    O    0.47    2.33
2281 ASP   (  89-)  A 1    C    <->  2293 VAL   ( 101-)  A 1    O    0.47    2.33
 616 LEU   (  68-)  A      N    <->   646 SER   (  98-)  A      O    0.46    2.24
 178 GLY   (  41-)  A      C    <->   244 GLN   ( 107-)  A      NE2  0.44    2.66
  89 ASP   (  89-)  A      CB   <->   101 VAL   ( 101-)  A      O    0.44    2.36
 121 LEU   ( 121-)  A      O    <->   126 GLY   ( 126-)  A      N    0.43    2.27
2313 LEU   ( 121-)  A 1    O    <->  2318 GLY   ( 126-)  A 1    N    0.43    2.27
 831 HIS   (   9-)  A      CD2  <->   939 LEU   ( 117-)  A      CD2  0.43    2.77
 861 PHE   (  39-)  A      C    <->   929 GLN   ( 107-)  A      NE2  0.43    2.67
2555 ASP   (  89-)  A 1    CB   <->  2567 VAL   ( 101-)  A 1    O    0.42    2.38
 500 ASP   (  89-)  A      CB   <->   512 VAL   ( 101-)  A      O    0.41    2.39
 897 LYS   (  75-)  A      CG   <->   937 VAL   ( 115-)  A      CG1  0.41    2.79
1185 ASP   (  89-)  A      CB   <->  1197 VAL   ( 101-)  A      O    0.41    2.39
2285 VAL   (  93-)  A 1    C    <->  2289 ASN   (  97-)  A 1    O    0.40    2.40
 212 LYS   (  75-)  A      CG   <->   252 VAL   ( 115-)  A      CG1  0.40    2.80
 831 HIS   (   9-)  A      ND1  <->   939 LEU   ( 117-)  A      O    0.40    2.30
2692 ASP   (  89-)  A 2    CB   <->  2704 VAL   ( 101-)  A 2    O    0.40    2.40
1598 ARG   (  91-)  A 1    O    <->  1605 SER   (  98-)  A 1    CB   0.40    2.40
1322 ASP   (  89-)  A 1    CB   <->  1334 VAL   ( 101-)  A 1    O    0.40    2.40
1080 LEU   ( 121-)  A      O    <->  1085 GLY   ( 126-)  A      N    0.40    2.30
And so on for a total of 3117 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

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

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

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