WHAT IF Check report

This file was created 2013-12-26 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 pdb2m55.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.

3342 ACE   ( 200-)  B  1
3349 ACE   ( 200-)  B  2
3356 ACE   ( 200-)  B  3
3363 ACE   ( 200-)  B  4
3370 ACE   ( 200-)  B  5
3377 ACE   ( 200-)  B  6
3384 ACE   ( 200-)  B  7
3391 ACE   ( 200-)  B  8
3398 ACE   ( 200-)  B  9
3405 ACE   ( 200-)  B 10
3412 ACE   ( 200-)  B 11
3419 ACE   ( 200-)  B 12
3426 ACE   ( 200-)  B 13
3433 ACE   ( 200-)  B 14
3440 ACE   ( 200-)  B 15
3447 ACE   ( 200-)  B 16
3454 ACE   ( 200-)  B 17
3461 ACE   ( 200-)  B 18
3468 ACE   ( 200-)  B 19
3475 ACE   ( 200-)  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.

 149 MET   ( 201-)  B  1   N   bound to 3342 ACE   ( 200-)  B  1   C
 316 MET   ( 201-)  B  2   N   bound to 3349 ACE   ( 200-)  B  2   C
 483 MET   ( 201-)  B  3   N   bound to 3356 ACE   ( 200-)  B  3   C
 650 MET   ( 201-)  B  4   N   bound to 3363 ACE   ( 200-)  B  4   C
 817 MET   ( 201-)  B  5   N   bound to 3370 ACE   ( 200-)  B  5   C
 984 MET   ( 201-)  B  6   N   bound to 3377 ACE   ( 200-)  B  6   C
1151 MET   ( 201-)  B  7   N   bound to 3384 ACE   ( 200-)  B  7   C
1318 MET   ( 201-)  B  8   N   bound to 3391 ACE   ( 200-)  B  8   C
1485 MET   ( 201-)  B  9   N   bound to 3398 ACE   ( 200-)  B  9   C
1652 MET   ( 201-)  B 10   N   bound to 3405 ACE   ( 200-)  B 10   C
1819 MET   ( 201-)  B 11   N   bound to 3412 ACE   ( 200-)  B 11   C
1986 MET   ( 201-)  B 12   N   bound to 3419 ACE   ( 200-)  B 12   C
2153 MET   ( 201-)  B 13   N   bound to 3426 ACE   ( 200-)  B 13   C
2320 MET   ( 201-)  B 14   N   bound to 3433 ACE   ( 200-)  B 14   C
2487 MET   ( 201-)  B 15   N   bound to 3440 ACE   ( 200-)  B 15   C
2654 MET   ( 201-)  B 16   N   bound to 3447 ACE   ( 200-)  B 16   C
2821 MET   ( 201-)  B 17   N   bound to 3454 ACE   ( 200-)  B 17   C
2988 MET   ( 201-)  B 18   N   bound to 3461 ACE   ( 200-)  B 18   C
3155 MET   ( 201-)  B 19   N   bound to 3468 ACE   ( 200-)  B 19   C
3322 MET   ( 201-)  B 20   N   bound to 3475 ACE   ( 200-)  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: B; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: B; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: B; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: B; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: B; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: B; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: B; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: B; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: B; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: B; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: B; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: B; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: B; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: B; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: B; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: B; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: B; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: B; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: B; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Note: Ramachandran plot

Chain identifier: B; Model number 20

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 ALA   (   1-)  A    Zero
   2 ASP   (   2-)  A    Zero
   3 GLN   (   3-)  A    Zero
   4 LEU   (   4-)  A    Zero
   5 THR   (   5-)  A    Zero
   6 GLU   (   6-)  A    Zero
   7 GLU   (   7-)  A    Zero
   8 GLN   (   8-)  A    Zero
   9 ILE   (   9-)  A    Zero
  10 ALA   (  10-)  A    Zero
  11 GLU   (  11-)  A    Zero
  12 PHE   (  12-)  A    Zero
  13 LYS   (  13-)  A    Zero
  14 GLU   (  14-)  A    Zero
  15 ALA   (  15-)  A    Zero
  16 PHE   (  16-)  A    Zero
  17 SER   (  17-)  A    Zero
  18 LEU   (  18-)  A    Zero
  19 PHE   (  19-)  A    Zero
  20 ASP   (  20-)  A    Zero
  21 LYS   (  21-)  A    Zero
  22 ASP   (  22-)  A    Zero
  23 GLY   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 GLY   (  25-)  A    Zero
And so on for a total of 3340 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 : 1.025
Model 2 : 1.027
Model 3 : 1.027
Model 4 : 1.032
Model 5 : 1.028
Model 6 : 1.025
Model 7 : 1.029
Model 8 : 1.028
Model 9 : 1.034
Model 10 : 1.029
Model 11 : 1.024
Model 12 : 1.028
Model 13 : 1.025
Model 14 : 1.026
Model 15 : 1.024
Model 16 : 1.027
Model 17 : 1.034
Model 18 : 1.030
Model 19 : 1.028
Model 20 : 1.029

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.

  19 PHE   (  19-)  A      CA   CB   CG  109.01   -4.8
  65 PHE   (  65-)  A      CA   CB   CG  108.95   -4.8
 152 PHE   ( 204-)  B      CA   CB   CG  109.32   -4.5
 186 PHE   (  19-)  A      CA   CB   CG  108.86   -4.9
 232 PHE   (  65-)  A      CA   CB   CG  108.93   -4.9
 274 HIS   ( 107-)  A      CA   CB   CG  109.48   -4.3
 353 PHE   (  19-)  A      CA   CB   CG  109.65   -4.2
 399 PHE   (  65-)  A      CA   CB   CG  109.15   -4.6
 441 HIS   ( 107-)  A      CA   CB   CG  109.65   -4.2
 486 PHE   ( 204-)  B      CA   CB   CG  109.75   -4.0
 520 PHE   (  19-)  A      CA   CB   CG  109.12   -4.7
 566 PHE   (  65-)  A      CA   CB   CG  108.83   -5.0
 687 PHE   (  19-)  A      CA   CB   CG  109.30   -4.5
 733 PHE   (  65-)  A      CA   CB   CG  109.65   -4.1
 775 HIS   ( 107-)  A      CA   CB   CG  109.54   -4.3
 854 PHE   (  19-)  A      CA   CB   CG  109.21   -4.6
 900 PHE   (  65-)  A      CA   CB   CG  109.13   -4.7
 942 HIS   ( 107-)  A      CA   CB   CG  109.57   -4.2
 987 PHE   ( 204-)  B      CA   CB   CG  109.36   -4.4
1021 PHE   (  19-)  A      CA   CB   CG  109.08   -4.7
1067 PHE   (  65-)  A      CA   CB   CG  109.39   -4.4
1109 HIS   ( 107-)  A      CA   CB   CG  109.67   -4.1
1188 PHE   (  19-)  A      CA   CB   CG  109.08   -4.7
1234 PHE   (  65-)  A      CA   CB   CG  108.88   -4.9
1355 PHE   (  19-)  A      CA   CB   CG  109.13   -4.7
And so on for a total of 56 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.001
Model 2 : 0.998
Model 3 : 0.997
Model 4 : 0.988
Model 5 : 0.986
Model 6 : 0.991
Model 7 : 0.981
Model 8 : 0.990
Model 9 : 1.000
Model 10 : 0.992
Model 11 : 1.001
Model 12 : 0.981
Model 13 : 0.994
Model 14 : 0.986
Model 15 : 0.994
Model 16 : 0.979
Model 17 : 0.993
Model 18 : 0.988
Model 19 : 0.985
Model 20 : 1.000

Note: Per-model averages for chirality check

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

Model 1 : 0.752
Model 2 : 0.748
Model 3 : 0.751
Model 4 : 0.757
Model 5 : 0.752
Model 6 : 0.725
Model 7 : 0.747
Model 8 : 0.740
Model 9 : 0.730
Model 10 : 0.740
Model 11 : 0.744
Model 12 : 0.755
Model 13 : 0.767
Model 14 : 0.754
Model 15 : 0.771
Model 16 : 0.747
Model 17 : 0.745
Model 18 : 0.750
Model 19 : 0.749
Model 20 : 0.756

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : 1.977
Model 2 : 1.176
Model 3 : 1.601
Model 4 : 1.508
Model 5 : 1.541
Model 6 : 1.863
Model 7 : 1.605
Model 8 : 1.985
Model 9 : 1.678
Model 10 : 1.908
Model 11 : 1.834
Model 12 : 1.419
Model 13 : 1.760
Model 14 : 1.414
Model 15 : 1.213
Model 16 : 1.280
Model 17 : 1.853
Model 18 : 1.572
Model 19 : 1.308
Model 20 : 1.689

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.

2584 THR   (  79-)  A 1   -3.3
1081 THR   (  79-)  A    -2.9
 413 THR   (  79-)  A    -2.8
 914 THR   (  79-)  A    -2.7
2918 THR   (  79-)  A 1   -2.7
1248 THR   (  79-)  A    -2.7
1916 THR   (  79-)  A 1   -2.7
2250 THR   (  79-)  A 1   -2.7
2751 THR   (  79-)  A 1   -2.7
 747 THR   (  79-)  A    -2.7
2818 THR   ( 146-)  A 1   -2.7
 246 THR   (  79-)  A    -2.6
3319 THR   ( 146-)  A 2   -2.6
1749 THR   (  79-)  A 1   -2.6
 146 THR   ( 146-)  A    -2.6
 313 THR   ( 146-)  A    -2.6
 580 THR   (  79-)  A    -2.6
1582 THR   (  79-)  A 1   -2.6
 814 THR   ( 146-)  A    -2.6
1315 THR   ( 146-)  A    -2.6
2083 THR   (  79-)  A 1   -2.6
 480 THR   ( 146-)  A    -2.5
3167 GLU   ( 213-)  B 1   -2.5
2417 THR   (  79-)  A 1   -2.5
2985 THR   ( 146-)  A 1   -2.5
And so on for a total of 66 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.

 160 LYS   ( 212-)  B  Poor phi/psi
 327 LYS   ( 212-)  B  Poor phi/psi
 412 ASP   (  78-)  A  Poor phi/psi
 504 GLN   (   3-)  A  Poor phi/psi
 661 LYS   ( 212-)  B  Poor phi/psi
 746 ASP   (  78-)  A  Poor phi/psi
 829 GLU   ( 213-)  B  Poor phi/psi
 913 ASP   (  78-)  A  Poor phi/psi
 981 THR   ( 146-)  A  Poor phi/psi
 996 GLU   ( 213-)  B  Poor phi/psi
1148 THR   ( 146-)  A  Poor phi/psi
1163 GLU   ( 213-)  B  Poor phi/psi
1247 ASP   (  78-)  A  Poor phi/psi
1482 THR   ( 146-)  A  Poor phi/psi
1497 GLU   ( 213-)  B  Poor phi/psi
1501 ALA   ( 217-)  B  Poor phi/psi
1581 ASP   (  78-)  A 1 Poor phi/psi
1582 THR   (  79-)  A 1 Poor phi/psi
1649 THR   ( 146-)  A 1 Poor phi/psi
1748 ASP   (  78-)  A 1 Poor phi/psi
1816 THR   ( 146-)  A 1 Poor phi/psi
1915 ASP   (  78-)  A 1 Poor phi/psi
1970 ASP   ( 133-)  A 1 Poor phi/psi
1983 THR   ( 146-)  A 1 Poor phi/psi
1997 LYS   ( 212-)  B 1 Poor phi/psi
2002 ALA   ( 217-)  B 1 Poor phi/psi
2150 THR   ( 146-)  A 1 Poor phi/psi
2251 ASP   (  80-)  A 1 Poor phi/psi
2317 THR   ( 146-)  A 1 Poor phi/psi
2336 ALA   ( 217-)  B 1 Poor phi/psi
2416 ASP   (  78-)  A 1 Poor phi/psi
2484 THR   ( 146-)  A 1 Poor phi/psi
2498 LYS   ( 212-)  B 1 Poor phi/psi
2582 LYS   (  77-)  A 1 Poor phi/psi
2917 ASP   (  78-)  A 1 Poor phi/psi
2918 THR   (  79-)  A 1 Poor phi/psi
3000 GLU   ( 213-)  B 1 Poor phi/psi
3045 LEU   (  39-)  A 1 Poor phi/psi
3084 ASP   (  78-)  A 1 Poor phi/psi
3085 THR   (  79-)  A 1 Poor phi/psi
3167 GLU   ( 213-)  B 1 Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.661

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 : 1.165
Model 2 : 0.822
Model 3 : 1.033
Model 4 : 0.415
Model 5 : 0.677
Model 6 : 0.426
Model 7 : 0.416
Model 8 : 0.529
Model 9 : 0.825
Model 10 : 0.940
Model 11 : 0.974
Model 12 : 0.619
Model 13 : 0.772
Model 14 : 0.339
Model 15 : 0.290
Model 16 : 1.434
Model 17 : -0.609
Model 18 : 0.595
Model 19 : 1.185
Model 20 : 0.376

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.

 441 HIS   ( 107-)  A    0.33
 675 GLU   (   7-)  A    0.33
1827 SER   ( 209-)  B 1   0.33
2345 GLU   (   7-)  A 1   0.33
1159 SER   ( 209-)  B    0.36
1493 SER   ( 209-)  B    0.36
1660 SER   ( 209-)  B 1   0.36
3330 SER   ( 209-)  B 2   0.36

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!

  21 LYS   (  21-)  A      0
  22 ASP   (  22-)  A      0
  24 ASP   (  24-)  A      0
  39 LEU   (  39-)  A      0
  41 GLN   (  41-)  A      0
  57 ALA   (  57-)  A      0
  60 ASN   (  60-)  A      0
  94 LYS   (  94-)  A      0
  97 ASN   (  97-)  A      0
  99 TYR   (  99-)  A      0
 112 LEU   ( 112-)  A      0
 115 LYS   ( 115-)  A      0
 130 ILE   ( 130-)  A      0
 146 THR   ( 146-)  A      0
 147 ALA   ( 147-)  A      0
 148 LYS   ( 148-)  A      0
 149 MET   ( 201-)  B      0
 150 ASP   ( 202-)  B      0
 161 GLU   ( 213-)  B      0
 166 ALA   ( 218-)  B      0
 167 ALA   ( 219-)  B      0
 168 ALA   (   1-)  A      0
 169 ASP   (   2-)  A      0
 170 GLN   (   3-)  A      0
 188 LYS   (  21-)  A      0
And so on for a total of 879 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 : 0.990

Note: Per-model averages for omega angle check

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

Model 1 : 0.949
Model 2 : 0.935
Model 3 : 0.958
Model 4 : 1.007
Model 5 : 0.960
Model 6 : 0.831
Model 7 : 0.921
Model 8 : 0.939
Model 9 : 0.910
Model 10 : 0.926
Model 11 : 0.906
Model 12 : 0.906
Model 13 : 1.012
Model 14 : 0.957
Model 15 : 0.962
Model 16 : 1.001
Model 17 : 0.937
Model 18 : 0.878
Model 19 : 0.956
Model 20 : 0.978

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].

1068 PRO   (  66-)  A  -112.6 envelop C-gamma (-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.

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.

2360 ASP   (  22-)  A 1    CB   <->  3442  CA   ( 300-)  A 1   CA    0.61    2.59
 739 MET   (  71-)  A      SD   <->   822 LYS   ( 206-)  B      NZ   0.54    2.76
1147 MET   ( 145-)  A      SD   <->  1160 LYS   ( 210-)  B      NZ   0.54    2.76
2222 MET   (  51-)  A 1    SD   <->  2321 ASP   ( 202-)  B 1    N    0.53    2.77
 537 MET   (  36-)  A      SD   <->   650 MET   ( 201-)  B      N    0.52    2.78
2708 MET   (  36-)  A 1    SD   <->  2821 MET   ( 201-)  B 1    N    0.48    2.82
1372 MET   (  36-)  A      SD   <->  3398 ACE   ( 200-)  B      C    0.46    2.94
2040 MET   (  36-)  A 1    SD   <->  3426 ACE   ( 200-)  B 1    C    0.45    2.95
3192 PHE   (  19-)  A 2    CE2  <->  3326 MET   ( 205-)  B 2    SD   0.45    2.95
2708 MET   (  36-)  A 1    SD   <->  3454 ACE   ( 200-)  B 1    C    0.44    2.96
2795 GLU   ( 123-)  A 1    CD   <->  2798 ARG   ( 126-)  A 1    NH2  0.44    2.66
2723 MET   (  51-)  A 1    CE   <->  2821 MET   ( 201-)  B 1    SD   0.44    2.96
3192 PHE   (  19-)  A 2    CZ   <->  3326 MET   ( 205-)  B 2    SD   0.43    2.97
 208 GLN   (  41-)  A      NE2  <->   316 MET   ( 201-)  B      SD   0.43    2.87
3214 GLN   (  41-)  A 2    NE2  <->  3475 ACE   ( 200-)  B 2    C    0.42    2.68
 412 ASP   (  78-)  A      CG   <->   492 LYS   ( 210-)  B      NZ   0.42    2.68
 208 GLN   (  41-)  A      NE2  <->   316 MET   ( 201-)  B      CG   0.42    2.68
1721 MET   (  51-)  A 1    SD   <->  1820 ASP   ( 202-)  B 1    N    0.42    2.88
1205 MET   (  36-)  A      SD   <->  1318 MET   ( 201-)  B      SD   0.42    3.03
1711 GLN   (  41-)  A 1    NE2  <->  1819 MET   ( 201-)  B 1    SD   0.42    2.88
 537 MET   (  36-)  A      SD   <->   650 MET   ( 201-)  B      SD   0.42    3.03
2379 GLN   (  41-)  A 1    NE2  <->  2487 MET   ( 201-)  B 1    CG   0.41    2.69
1151 MET   ( 201-)  B      SD   <->  1152 ASP   ( 202-)  B      N    0.41    2.79
3042 MET   (  36-)  A 1    SD   <->  3156 ASP   ( 202-)  B 1    CB   0.40    3.00
1372 MET   (  36-)  A      SD   <->  1485 MET   ( 201-)  B      N    0.39    2.91
And so on for a total of 1579 lines.

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck




















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 20

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: B; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: B; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: B; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: B; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: B; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: B; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: B; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: B; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: B; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: B; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: B; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: B; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: B; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: B; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: B; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: B; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: B; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: B; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: B; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Note: Quality value plot

Chain identifier: B; Model number 20

Warning: Low packing Z-score for some residues


Warning: Abnormal packing Z-score for sequential residues


Note: Per-model averages for NQA




















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 20

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Unusual ion packing


Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure