WHAT IF Check report

This file was created 2011-12-28 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 pdb1fjd.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

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

Warning: B-factors outside the range 0.0 - 100.0

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

   1 GLY   (  28-)  A    Zero
   2 SER   (  29-)  A    Zero
   3 GLY   (  30-)  A    Zero
   4 PRO   (  31-)  A    Zero
   5 LYS   (  32-)  A    Zero
   6 GLY   (  33-)  A    Zero
   7 GLY   (  34-)  A    Zero
   8 GLY   (  35-)  A    Zero
   9 ASN   (  36-)  A    Zero
  10 ALA   (  37-)  A    Zero
  11 VAL   (  38-)  A    Zero
  12 LYS   (  39-)  A    Zero
  13 VAL   (  40-)  A    Zero
  14 ARG   (  41-)  A    Zero
  15 HIS   (  42-)  A    Zero
  16 ILE   (  43-)  A    Zero
  17 LEU   (  44-)  A    Zero
  18 CYS   (  45-)  A    Zero
  19 GLU   (  46-)  A    Zero
  20 LYS   (  47-)  A    Zero
  21 HIS   (  48-)  A    Zero
  22 GLY   (  49-)  A    Zero
  23 LYS   (  50-)  A    Zero
  24 ILE   (  51-)  A    Zero
  25 MET   (  52-)  A    Zero
And so on for a total of 1976 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 : 0.975
Model 2 : 0.978
Model 3 : 0.981
Model 4 : 0.974
Model 5 : 0.965
Model 6 : 0.984
Model 7 : 0.993
Model 8 : 0.978
Model 9 : 0.977
Model 10 : 0.988
Model 11 : 0.984
Model 12 : 0.990
Model 13 : 0.983
Model 14 : 0.988
Model 15 : 0.988
Model 16 : 0.989
Model 17 : 0.983
Model 18 : 0.985
Model 19 : 0.986
Model 20 : 0.989

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.

  21 HIS   (  48-)  A      CA   CB   CG  109.32   -4.5
  67 PHE   (  94-)  A      CA   CB   CG  109.48   -4.3
  72 PHE   (  99-)  A      CA   CB   CG  109.35   -4.4
  79 MET   ( 106-)  A      N    CA   CB  103.48   -4.1
  84 PHE   ( 111-)  A      CA   CB   CG  109.55   -4.3
  93 PHE   ( 120-)  A      CA   CB   CG  109.42   -4.4
  99 MET   ( 126-)  A      N    CA   CB  103.55   -4.1
 125 HIS   (  48-)  A      CA   CB   CG  109.44   -4.4
 141 PHE   (  64-)  A      CA   CB   CG  109.26   -4.5
 171 PHE   (  94-)  A      CA   CB   CG  109.51   -4.3
 176 PHE   (  99-)  A      CA   CB   CG  109.63   -4.2
 188 PHE   ( 111-)  A      CA   CB   CG  109.27   -4.5
 197 PHE   ( 120-)  A      CA   CB   CG  109.58   -4.2
 225 LEU   (  44-)  A      N    CA   CB  103.10   -4.4
 229 HIS   (  48-)  A      CA   CB   CG  108.78   -5.0
 245 PHE   (  64-)  A      CA   CB   CG  109.52   -4.3
 275 PHE   (  94-)  A      CA   CB   CG  109.39   -4.4
 280 PHE   (  99-)  A      CA   CB   CG  109.40   -4.4
 292 PHE   ( 111-)  A      CA   CB   CG  109.30   -4.5
 301 PHE   ( 120-)  A      CA   CB   CG  109.44   -4.4
 329 LEU   (  44-)  A      N    CA   CB  103.34   -4.2
 333 HIS   (  48-)  A      CA   CB   CG  108.76   -5.0
 349 PHE   (  64-)  A      CA   CB   CG  109.42   -4.4
 379 PHE   (  94-)  A      CA   CB   CG  109.39   -4.4
 384 PHE   (  99-)  A      CA   CB   CG  109.22   -4.6
And so on for a total of 152 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.407
Model 2 : 1.394
Model 3 : 1.412
Model 4 : 1.403
Model 5 : 1.403
Model 6 : 1.401
Model 7 : 1.395
Model 8 : 1.422
Model 9 : 1.410
Model 10 : 1.421
Model 11 : 1.397
Model 12 : 1.406
Model 13 : 1.416
Model 14 : 1.414
Model 15 : 1.399
Model 16 : 1.412
Model 17 : 1.420
Model 18 : 1.414
Model 19 : 1.417
Model 20 : 1.415

Note: Per-model averages for chirality check

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

Model 1 : 1.378
Model 2 : 1.372
Model 3 : 1.379
Model 4 : 1.403
Model 5 : 1.370
Model 6 : 1.386
Model 7 : 1.359
Model 8 : 1.384
Model 9 : 1.384
Model 10 : 1.411
Model 11 : 1.378
Model 12 : 1.394
Model 13 : 1.397
Model 14 : 1.384
Model 15 : 1.398
Model 16 : 1.400
Model 17 : 1.401
Model 18 : 1.364
Model 19 : 1.390
Model 20 : 1.361

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.

1586 GLU   (  53-)  A 1   4.47
 130 GLU   (  53-)  A    4.39
 546 GLU   (  53-)  A    4.34
1898 GLU   (  53-)  A 1   4.27
 338 GLU   (  53-)  A    4.19
1274 GLU   (  53-)  A 1   4.09

Error: Side chain planarity problems

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

 452 ARG   (  63-)  A    8.64
 996 ARG   (  87-)  A 1   8.63
 935 ARG   ( 130-)  A    8.63
1204 ARG   (  87-)  A 1   8.62
 580 ARG   (  87-)  A    8.60
1908 ARG   (  63-)  A 1   8.58
1143 ARG   ( 130-)  A 1   8.58
1678 ARG   (  41-)  A 1   8.56
 430 ARG   (  41-)  A    8.53
1828 ARG   (  87-)  A 1   8.52
1402 ARG   (  77-)  A 1   8.45
1922 ARG   (  77-)  A 1   8.41
1076 ARG   (  63-)  A 1   8.33
 519 ARG   ( 130-)  A    8.27
1516 ARG   (  87-)  A 1   8.27
 882 ARG   (  77-)  A    8.23
1351 ARG   ( 130-)  A 1   8.17
1262 ARG   (  41-)  A 1   8.16
 684 ARG   (  87-)  A    8.16
 476 ARG   (  87-)  A    8.15
1975 ARG   ( 130-)  A 1   8.07
1663 ARG   ( 130-)  A 1   8.06
 415 ARG   ( 130-)  A    8.04
 972 ARG   (  63-)  A 1   7.96
1700 ARG   (  63-)  A 1   7.95
And so on for a total of 85 lines.

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 : -7.085

Note: Per-model averages for Ramachandran check

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

Model 1 : -7.146
Model 2 : -7.161
Model 3 : -7.147
Model 4 : -6.806
Model 5 : -6.749
Model 6 : -7.437
Model 7 : -7.212
Model 8 : -6.870
Model 9 : -7.474
Model 10 : -6.522
Model 11 : -6.621
Model 12 : -7.753
Model 13 : -7.415
Model 14 : -7.383
Model 15 : -6.921
Model 16 : -6.626
Model 17 : -7.270
Model 18 : -7.013
Model 19 : -7.059
Model 20 : -7.120

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.

1237 PHE   ( 120-)  A 1   -3.7
1755 THR   ( 118-)  A 1   -3.6
 195 THR   ( 118-)  A    -3.6
1651 THR   ( 118-)  A 1   -3.5
 717 PHE   ( 120-)  A    -3.4
1547 THR   ( 118-)  A 1   -3.3
 587 PHE   (  94-)  A    -3.3
 957 HIS   (  48-)  A 1   -3.1
 611 THR   ( 118-)  A    -3.0
1090 ARG   (  77-)  A 1   -3.0
  93 PHE   ( 120-)  A    -2.9
1757 PHE   ( 120-)  A 1   -2.9
 299 THR   ( 118-)  A    -2.9
1320 PHE   (  99-)  A 1   -2.9
 986 ARG   (  77-)  A 1   -2.9
1685 HIS   (  48-)  A 1   -2.8
1964 LYS   ( 119-)  A 1   -2.8
1236 LYS   ( 119-)  A 1   -2.8
 705 LYS   ( 108-)  A    -2.8
 570 ARG   (  77-)  A    -2.8
2026 ARG   (  77-)  A 2   -2.8
 820 LYS   ( 119-)  A    -2.8
1949 SER   ( 104-)  A 1   -2.8
 389 SER   ( 104-)  A    -2.8
1429 SER   ( 104-)  A 1   -2.8
And so on for a total of 450 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.

  21 HIS   (  48-)  A  Poor phi/psi
  35 MET   (  62-)  A  Poor phi/psi
  46 GLU   (  73-)  A  Poor phi/psi
  47 ASP   (  74-)  A  Poor phi/psi
  48 LYS   (  75-)  A  Poor phi/psi
  49 ALA   (  76-)  A  Poor phi/psi
  51 GLN   (  78-)  A  Poor phi/psi
  55 LEU   (  82-)  A  Poor phi/psi
  64 VAL   (  91-)  A  Poor phi/psi
  70 ALA   (  97-)  A  Poor phi/psi
  77 SER   ( 104-)  A  Poor phi/psi
  79 MET   ( 106-)  A  Poor phi/psi
  82 PRO   ( 109-)  A  Poor phi/psi
  83 VAL   ( 110-)  A  Poor phi/psi
  85 THR   ( 112-)  A  Poor phi/psi
  92 LYS   ( 119-)  A  Poor phi/psi
 125 HIS   (  48-)  A  Poor phi/psi
 127 LYS   (  50-)  A  Poor phi/psi
 136 LYS   (  59-)  A  Poor phi/psi
 138 GLY   (  61-)  A  Poor phi/psi
 139 MET   (  62-)  A  Poor phi/psi
 150 GLU   (  73-)  A  Poor phi/psi
 151 ASP   (  74-)  A  Poor phi/psi
 153 ALA   (  76-)  A  Poor phi/psi
 165 GLY   (  88-)  A  Poor phi/psi
And so on for a total of 387 lines.

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

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

chi-1/chi-2 correlation Z-score : -7.696

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -7.426
Model 2 : -7.347
Model 3 : -7.892
Model 4 : -8.017
Model 5 : -7.947
Model 6 : -7.718
Model 7 : -7.568
Model 8 : -8.037
Model 9 : -6.421
Model 10 : -8.332
Model 11 : -8.018
Model 12 : -7.601
Model 13 : -7.976
Model 14 : -7.781
Model 15 : -8.429
Model 16 : -7.677
Model 17 : -7.651
Model 18 : -7.492
Model 19 : -7.300
Model 20 : -7.295

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!

   4 PRO   (  31-)  A      0
   5 LYS   (  32-)  A      0
   9 ASN   (  36-)  A      0
  15 HIS   (  42-)  A      0
  21 HIS   (  48-)  A      0
  33 SER   (  60-)  A      0
  35 MET   (  62-)  A      0
  36 ARG   (  63-)  A      0
  37 PHE   (  64-)  A      0
  43 GLN   (  70-)  A      0
  46 GLU   (  73-)  A      0
  47 ASP   (  74-)  A      0
  48 LYS   (  75-)  A      0
  49 ALA   (  76-)  A      0
  51 GLN   (  78-)  A      0
  54 ASP   (  81-)  A      0
  55 LEU   (  82-)  A      0
  57 TRP   (  84-)  A      0
  60 ARG   (  87-)  A      0
  63 MET   (  90-)  A      0
  64 VAL   (  91-)  A      0
  76 VAL   ( 103-)  A      0
  77 SER   ( 104-)  A      0
  79 MET   ( 106-)  A      0
  81 LYS   ( 108-)  A      0
And so on for a total of 1075 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.004

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 : 1.061

Note: Per-model averages for omega angle check

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

Model 1 : 0.860
Model 2 : 0.886
Model 3 : 0.806
Model 4 : 1.028
Model 5 : 0.940
Model 6 : 0.944
Model 7 : 1.062
Model 8 : 0.962
Model 9 : 1.108
Model 10 : 1.117
Model 11 : 1.051
Model 12 : 1.206
Model 13 : 1.198
Model 14 : 1.009
Model 15 : 1.160
Model 16 : 1.142
Model 17 : 1.091
Model 18 : 1.033
Model 19 : 0.978
Model 20 : 0.953

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!

1255 GLY   (  34-)  A 1  3.36   30
1254 GLY   (  33-)  A 1  3.24   26
1046 GLY   (  33-)  A 1  3.19   10
1105 GLY   (  92-)  A 1  2.11   11
 320 GLY   (  35-)  A   2.07   25
1001 GLY   (  92-)  A 1  1.99   12
1870 GLY   ( 129-)  A 1  1.79   12
 734 GLY   (  33-)  A   1.72   80
1729 GLY   (  92-)  A 1  1.68   14
 422 GLY   (  33-)  A   1.61   14
 943 GLY   (  34-)  A 1  1.60   14
1625 GLY   (  92-)  A 1  1.60   17
1672 GLY   (  35-)  A 1  1.53   18
1209 GLY   (  92-)  A 1  1.51   20

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]

   4 PRO   (  31-)  A    0.00 LOW
  66 PRO   (  93-)  A    0.01 LOW
  75 PRO   ( 102-)  A    0.03 LOW
  82 PRO   ( 109-)  A    0.07 LOW
  87 PRO   ( 114-)  A    0.03 LOW
  88 PRO   ( 115-)  A    0.07 LOW
 108 PRO   (  31-)  A    0.00 LOW
 170 PRO   (  93-)  A    0.00 LOW
 179 PRO   ( 102-)  A    0.04 LOW
 186 PRO   ( 109-)  A    0.10 LOW
 191 PRO   ( 114-)  A    0.02 LOW
 192 PRO   ( 115-)  A    0.05 LOW
 212 PRO   (  31-)  A    0.01 LOW
 274 PRO   (  93-)  A    0.01 LOW
 283 PRO   ( 102-)  A    0.03 LOW
 290 PRO   ( 109-)  A    0.04 LOW
 295 PRO   ( 114-)  A    0.01 LOW
 296 PRO   ( 115-)  A    0.03 LOW
 316 PRO   (  31-)  A    0.00 LOW
 378 PRO   (  93-)  A    0.02 LOW
 387 PRO   ( 102-)  A    0.02 LOW
 394 PRO   ( 109-)  A    0.07 LOW
 399 PRO   ( 114-)  A    0.03 LOW
 400 PRO   ( 115-)  A    0.07 LOW
 420 PRO   (  31-)  A    0.01 LOW
And so on for a total of 120 lines.

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

 745 LEU   (  44-)  A      CD1 <->  746 CYS   (  45-)  A      N      0.50    2.50
1474 CYS   (  45-)  A 1    SG  <-> 1480 ILE   (  51-)  A 1    N      0.49    2.81
1786 CYS   (  45-)  A 1    SG  <-> 1789 HIS   (  48-)  A 1    ND1    0.49    2.81
1991 HIS   (  42-)  A 2    C   <-> 2026 ARG   (  77-)  A 2    CG     0.48    2.72
 641 LEU   (  44-)  A      CD2 <->  720 HIS   ( 123-)  A      CB     0.48    2.72
1685 HIS   (  48-)  A 1    NE2 <-> 1759 TYR   ( 122-)  A 1    CB     0.48    2.62
1162 CYS   (  45-)  A 1    SG  <-> 1168 ILE   (  51-)  A 1    N      0.48    2.82
 746 CYS   (  45-)  A      SG  <->  752 ILE   (  51-)  A      N      0.47    2.83
 713 VAL   ( 116-)  A      CG2 <->  720 HIS   ( 123-)  A      NE2    0.47    2.63
 225 LEU   (  44-)  A      CD1 <->  226 CYS   (  45-)  A      N      0.47    2.53
 434 CYS   (  45-)  A      SG  <->  437 HIS   (  48-)  A      ND1    0.46    2.84
 850 CYS   (  45-)  A      SG  <->  856 ILE   (  51-)  A      N      0.46    2.84
1119 MET   ( 106-)  A 1    N   <-> 1139 MET   ( 126-)  A 1    SD     0.46    2.84
 957 HIS   (  48-)  A 1    CE1 <-> 1031 TYR   ( 122-)  A 1    CB     0.46    2.74
 954 CYS   (  45-)  A 1    SG  <->  960 ILE   (  51-)  A 1    N      0.46    2.84
  36 ARG   (  63-)  A      NE  <->   39 GLU   (  66-)  A      CD     0.46    2.64
1269 HIS   (  48-)  A 1    NE2 <-> 1343 TYR   ( 122-)  A 1    CD1    0.45    2.65
  50 ARG   (  77-)  A      NH2 <->   97 ILE   ( 124-)  A      CG2    0.45    2.65
 974 ASN   (  65-)  A 1    CB  <->  987 GLN   (  78-)  A 1    N      0.45    2.65
2026 ARG   (  77-)  A 2    O   <-> 2030 ASP   (  81-)  A 2    N      0.45    2.25
1813 SER   (  72-)  A 1    CB  <-> 1817 ALA   (  76-)  A 1    N      0.45    2.65
1382 LYS   (  57-)  A 1    C   <-> 1387 MET   (  62-)  A 1    SD     0.44    2.96
1233 VAL   ( 116-)  A 1    CG2 <-> 1240 HIS   ( 123-)  A 1    NE2    0.44    2.66
1362 ALA   (  37-)  A 1    O   <-> 1456 LYS   ( 131-)  A 1    N      0.44    2.26
 957 HIS   (  48-)  A 1    NE2 <-> 1024 PRO   ( 115-)  A 1    CB     0.44    2.66
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


Error: Abnormal average packing environment

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Note: 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