WHAT IF Check report

This file was created 2011-12-29 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 pdb1jns.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

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.

  12 LYS   (  12-)  A
 772 LYS   (  36-)  A
 890 ASP   (  62-)  A 1
 939 ASP   (  19-)  A 1
1074 ASP   (  62-)  A 1
1258 ASP   (  62-)  A 1
1441 PHE   (  61-)  A 1
1621 MET   (  57-)  A 1

Warning: B-factors outside the range 0.0 - 100.0

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

   1 ALA   (   1-)  A    Zero
   2 LYS   (   2-)  A    Zero
   3 THR   (   3-)  A    Zero
   4 ALA   (   4-)  A    Zero
   5 ALA   (   5-)  A    Zero
   6 ALA   (   6-)  A    Zero
   7 LEU   (   7-)  A    Zero
   8 HIS   (   8-)  A    Zero
   9 ILE   (   9-)  A    Zero
  10 LEU   (  10-)  A    Zero
  11 VAL   (  11-)  A    Zero
  12 LYS   (  12-)  A    Zero
  13 GLU   (  13-)  A    Zero
  14 GLU   (  14-)  A    Zero
  15 LYS   (  15-)  A    Zero
  16 LEU   (  16-)  A    Zero
  17 ALA   (  17-)  A    Zero
  18 LEU   (  18-)  A    Zero
  19 ASP   (  19-)  A    Zero
  20 LEU   (  20-)  A    Zero
  21 LEU   (  21-)  A    Zero
  22 GLU   (  22-)  A    Zero
  23 GLN   (  23-)  A    Zero
  24 ILE   (  24-)  A    Zero
  25 LYS   (  25-)  A    Zero
And so on for a total of 1656 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 : 0.958
Model 2 : 0.963
Model 3 : 0.968
Model 4 : 0.963
Model 5 : 0.971
Model 6 : 0.960
Model 7 : 0.972
Model 8 : 0.964
Model 9 : 0.967
Model 10 : 0.958
Model 11 : 0.965
Model 12 : 0.960
Model 13 : 0.964
Model 14 : 0.961
Model 15 : 0.969
Model 16 : 0.972
Model 17 : 0.965
Model 18 : 0.964

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.

   8 HIS   (   8-)  A      CA   CB   CG  109.66   -4.1
  30 PHE   (  30-)  A      CA   CB   CG  109.54   -4.3
  37 HIS   (  37-)  A      CA   CB   CG  109.36   -4.4
  52 PHE   (  52-)  A      CA   CB   CG  109.59   -4.2
  61 PHE   (  61-)  A      CA   CB   CG  108.74   -5.1
  66 PHE   (  66-)  A      CA   CB   CG  109.18   -4.6
  78 HIS   (  78-)  A      CA   CB   CG  108.84   -5.0
  81 PHE   (  81-)  A      CA   CB   CG  109.26   -4.5
 100 HIS   (   8-)  A      CA   CB   CG  109.58   -4.2
 112 LEU   (  20-)  A      N    CA   CB  103.53   -4.1
 122 PHE   (  30-)  A      CA   CB   CG  109.73   -4.1
 129 HIS   (  37-)  A      CA   CB   CG  109.67   -4.1
 153 PHE   (  61-)  A      CA   CB   CG  109.49   -4.3
 158 PHE   (  66-)  A      CA   CB   CG  109.33   -4.5
 170 HIS   (  78-)  A      CA   CB   CG  109.17   -4.6
 173 PHE   (  81-)  A      CA   CB   CG  109.50   -4.3
 192 HIS   (   8-)  A      CA   CB   CG  109.65   -4.1
 221 HIS   (  37-)  A      CA   CB   CG  109.55   -4.2
 241 MET   (  57-)  A      N    CA   CB  103.46   -4.1
 245 PHE   (  61-)  A      CA   CB   CG  109.29   -4.5
 250 PHE   (  66-)  A      CA   CB   CG  109.50   -4.3
 262 HIS   (  78-)  A      CA   CB   CG  109.60   -4.2
 265 PHE   (  81-)  A      CA   CB   CG  109.54   -4.3
 284 HIS   (   8-)  A      CA   CB   CG  109.77   -4.0
 296 LEU   (  20-)  A      N    CA   CB  103.62   -4.0
And so on for a total of 135 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.378
Model 2 : 1.379
Model 3 : 1.353
Model 4 : 1.359
Model 5 : 1.370
Model 6 : 1.370
Model 7 : 1.364
Model 8 : 1.366
Model 9 : 1.367
Model 10 : 1.374
Model 11 : 1.373
Model 12 : 1.372
Model 13 : 1.374
Model 14 : 1.370
Model 15 : 1.369
Model 16 : 1.364
Model 17 : 1.368
Model 18 : 1.382

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 147 GLY   (  55-)  A      C     -6.1    -7.93     0.06
 438 VAL   (  70-)  A      C     -7.1    -9.51     0.15
1160 GLN   (  56-)  A 1    C     -6.7   -10.33     0.15
1436 GLN   (  56-)  A 1    C     -7.3   -11.19     0.15
1528 GLN   (  56-)  A 1    C     -6.9   -10.58     0.15
1620 GLN   (  56-)  A 1    C     -6.2    -9.47     0.15
The average deviation= 2.310

Note: Per-model averages for chirality check

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

Model 1 : 1.770
Model 2 : 1.866
Model 3 : 1.780
Model 4 : 1.796
Model 5 : 1.838
Model 6 : 1.831
Model 7 : 1.792
Model 8 : 1.812
Model 9 : 1.829
Model 10 : 1.776
Model 11 : 1.857
Model 12 : 1.784
Model 13 : 1.790
Model 14 : 1.803
Model 15 : 1.812
Model 16 : 1.805
Model 17 : 1.807
Model 18 : 1.866

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -0.817
Model 2 : -0.913
Model 3 : -2.125
Model 4 : -0.272
Model 5 : -1.096
Model 6 : -1.720
Model 7 : -0.587
Model 8 : -0.982
Model 9 : -1.734
Model 10 : -1.399
Model 11 : -2.090
Model 12 : -1.053
Model 13 : -0.691
Model 14 : -0.300
Model 15 : -1.038
Model 16 : -1.628
Model 17 : -1.053
Model 18 : -1.146

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.

 696 PHE   (  52-)  A    -3.0
1524 PHE   (  52-)  A 1   -3.0
 328 PHE   (  52-)  A    -3.0
 274 TYR   (  90-)  A    -2.9
 683 ILE   (  39-)  A    -2.9
 439 LEU   (  71-)  A    -2.8
1359 LEU   (  71-)  A 1   -2.8
 434 PHE   (  66-)  A    -2.8
1163 PRO   (  59-)  A 1   -2.8
1567 THR   (   3-)  A 1   -2.7
 991 LEU   (  71-)  A 1   -2.7
 928 HIS   (   8-)  A 1   -2.7
1064 PHE   (  52-)  A 1   -2.7
1358 VAL   (  70-)  A 1   -2.6
 438 VAL   (  70-)  A    -2.6
1199 THR   (   3-)  A 1   -2.6
 162 VAL   (  70-)  A    -2.6
 367 ARG   (  91-)  A    -2.6
1634 VAL   (  70-)  A 1   -2.6
 884 GLN   (  56-)  A 1   -2.6
1195 ARG   (  91-)  A 1   -2.5
 990 VAL   (  70-)  A 1   -2.5
 551 ARG   (  91-)  A    -2.5
1170 PHE   (  66-)  A 1   -2.5
 887 PRO   (  59-)  A 1   -2.5
And so on for a total of 96 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.

  28 ALA   (  28-)  A  Poor phi/psi
  29 ASP   (  29-)  A  Poor phi/psi
  57 MET   (  57-)  A  Poor phi/psi
  71 LEU   (  71-)  A  Poor phi/psi
  75 GLY   (  75-)  A  PRO omega poor
  90 TYR   (  90-)  A  Poor phi/psi
  91 ARG   (  91-)  A  Poor phi/psi
 120 ALA   (  28-)  A  Poor phi/psi
 121 ASP   (  29-)  A  Poor phi/psi
 145 ARG   (  53-)  A  Poor phi/psi
 162 VAL   (  70-)  A  Poor phi/psi
 167 GLY   (  75-)  A  PRO omega poor
 182 TYR   (  90-)  A  Poor phi/psi
 183 ARG   (  91-)  A  Poor phi/psi
 196 LYS   (  12-)  A  Poor phi/psi
 212 ALA   (  28-)  A  Poor phi/psi
 213 ASP   (  29-)  A  Poor phi/psi
 238 GLN   (  54-)  A  Poor phi/psi
 240 GLN   (  56-)  A  Poor phi/psi
 241 MET   (  57-)  A  Poor phi/psi
 255 LEU   (  71-)  A  Poor phi/psi
 259 GLY   (  75-)  A  PRO omega poor
 274 TYR   (  90-)  A  Poor phi/psi
 275 ARG   (  91-)  A  Poor phi/psi
 304 ALA   (  28-)  A  Poor phi/psi
And so on for a total of 156 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 : -1.652
Model 2 : -1.165
Model 3 : -1.578
Model 4 : -1.612
Model 5 : -0.823
Model 6 : -2.593
Model 7 : -1.466
Model 8 : -1.814
Model 9 : -1.720
Model 10 : -1.227
Model 11 : -2.093
Model 12 : -1.342
Model 13 : -0.266
Model 14 : -0.992
Model 15 : -0.875
Model 16 : -1.443
Model 17 : -2.541
Model 18 : -2.094

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 THR   (   3-)  A      0
  28 ALA   (  28-)  A      0
  29 ASP   (  29-)  A      0
  39 ILE   (  39-)  A      0
  40 CYS   (  40-)  A      0
  42 SER   (  42-)  A      0
  44 LYS   (  44-)  A      0
  48 ASP   (  48-)  A      0
  49 LEU   (  49-)  A      0
  51 GLU   (  51-)  A      0
  56 GLN   (  56-)  A      0
  57 MET   (  57-)  A      0
  58 VAL   (  58-)  A      0
  67 SER   (  67-)  A      0
  68 CYS   (  68-)  A      0
  74 THR   (  74-)  A      0
  76 PRO   (  76-)  A      0
  77 LEU   (  77-)  A      0
  81 PHE   (  81-)  A      0
  83 TYR   (  83-)  A      0
  89 LEU   (  89-)  A      0
  90 TYR   (  90-)  A      0
  91 ARG   (  91-)  A      0
  92 ASN   (  92-)  A      0
  93 ALA   (   1-)  A      0
And so on for a total of 701 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 4.515
Model 2 : 4.912
Model 3 : 4.641
Model 4 : 4.706
Model 5 : 4.949
Model 6 : 4.910
Model 7 : 4.762
Model 8 : 4.803
Model 9 : 4.823
Model 10 : 4.512
Model 11 : 4.933
Model 12 : 4.584
Model 13 : 4.685
Model 14 : 4.686
Model 15 : 4.666
Model 16 : 4.747
Model 17 : 4.630
Model 18 : 5.106

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!

 975 GLY   (  55-)  A 1  3.09   14
 239 GLY   (  55-)  A   2.19   37
1619 GLY   (  55-)  A 1  1.83   11
1527 GLY   (  55-)  A 1  1.78   11
  55 GLY   (  55-)  A   1.76   37
1159 GLY   (  55-)  A 1  1.68   11
1646 GLY   (  82-)  A 1  1.63   10
 887 PRO   (  59-)  A 1  1.58   14
1278 GLY   (  82-)  A 1  1.57   10
 967 GLY   (  47-)  A 1  1.50   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 345 PRO   (  69-)  A    0.14 LOW
1265 PRO   (  69-)  A 1   0.18 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].

  59 PRO   (  59-)  A  -114.4 envelop C-gamma (-108 degrees)
 133 PRO   (  41-)  A  -124.5 half-chair C-delta/C-gamma (-126 degrees)
 161 PRO   (  69-)  A   -55.4 half-chair C-beta/C-alpha (-54 degrees)
 243 PRO   (  59-)  A  -129.6 half-chair C-delta/C-gamma (-126 degrees)
 257 PRO   (  73-)  A   106.4 envelop C-beta (108 degrees)
 335 PRO   (  59-)  A  -130.5 half-chair C-delta/C-gamma (-126 degrees)
 409 PRO   (  41-)  A  -123.2 half-chair C-delta/C-gamma (-126 degrees)
 437 PRO   (  69-)  A   -63.1 envelop C-beta (-72 degrees)
 441 PRO   (  73-)  A   101.0 envelop C-beta (108 degrees)
 519 PRO   (  59-)  A  -169.8 half-chair N/C-delta (-162 degrees)
 533 PRO   (  73-)  A  -130.1 half-chair C-delta/C-gamma (-126 degrees)
 611 PRO   (  59-)  A  -123.9 half-chair C-delta/C-gamma (-126 degrees)
 685 PRO   (  41-)  A  -126.1 half-chair C-delta/C-gamma (-126 degrees)
 717 PRO   (  73-)  A   102.1 envelop C-beta (108 degrees)
 777 PRO   (  41-)  A  -121.7 half-chair C-delta/C-gamma (-126 degrees)
 887 PRO   (  59-)  A 1  141.5 envelop C-alpha (144 degrees)
 961 PRO   (  41-)  A 1  108.0 envelop C-beta (108 degrees)
1053 PRO   (  41-)  A 1  100.2 envelop C-beta (108 degrees)
1071 PRO   (  59-)  A 1 -144.2 envelop C-delta (-144 degrees)
1088 PRO   (  76-)  A 1  -37.9 envelop C-alpha (-36 degrees)
1145 PRO   (  41-)  A 1 -131.8 half-chair C-delta/C-gamma (-126 degrees)
1163 PRO   (  59-)  A 1 -171.5 envelop N (180 degrees)
1237 PRO   (  41-)  A 1 -131.5 half-chair C-delta/C-gamma (-126 degrees)
1269 PRO   (  73-)  A 1  107.9 envelop C-beta (108 degrees)
1272 PRO   (  76-)  A 1  -60.6 half-chair C-beta/C-alpha (-54 degrees)
1361 PRO   (  73-)  A 1  108.4 envelop C-beta (108 degrees)
1421 PRO   (  41-)  A 1 -134.7 half-chair C-delta/C-gamma (-126 degrees)
1439 PRO   (  59-)  A 1 -114.7 envelop C-gamma (-108 degrees)
1531 PRO   (  59-)  A 1 -124.2 half-chair C-delta/C-gamma (-126 degrees)
1545 PRO   (  73-)  A 1  105.0 envelop C-beta (108 degrees)
1623 PRO   (  59-)  A 1 -118.8 half-chair C-delta/C-gamma (-126 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.

1311 GLN   (  23-)  A 1    NE2 <-> 1325 HIS   (  37-)  A 1    NE2    0.47    2.53
 776 CYS   (  40-)  A      SG  <->  779 GLY   (  43-)  A      N      0.47    2.83
 316 CYS   (  40-)  A      SG  <->  319 GLY   (  43-)  A      N      0.46    2.84
 500 CYS   (  40-)  A      SG  <->  503 GLY   (  43-)  A      N      0.46    2.84
 132 CYS   (  40-)  A      SG  <->  135 GLY   (  43-)  A      N      0.46    2.84
 408 CYS   (  40-)  A      SG  <->  411 GLY   (  43-)  A      N      0.46    2.84
 592 CYS   (  40-)  A      SG  <->  595 GLY   (  43-)  A      N      0.44    2.86
1236 CYS   (  40-)  A 1    SG  <-> 1239 GLY   (  43-)  A 1    N      0.44    2.86
 190 ALA   (   6-)  A      CB  <->  192 HIS   (   8-)  A      NE2    0.44    2.66
 834 ALA   (   6-)  A 1    CB  <->  836 HIS   (   8-)  A 1    NE2    0.44    2.66
 328 PHE   (  52-)  A      CD1 <->  332 GLN   (  56-)  A      NE2    0.43    2.67
1202 ALA   (   6-)  A 1    CB  <-> 1204 HIS   (   8-)  A 1    NE2    0.43    2.67
   8 HIS   (   8-)  A      NE2 <->   61 PHE   (  61-)  A      CE1    0.43    2.67
 374 ALA   (   6-)  A      CB  <->  376 HIS   (   8-)  A      NE2    0.42    2.68
 851 GLN   (  23-)  A 1    NE2 <->  861 LEU   (  33-)  A 1    CD2    0.42    2.68
1432 PHE   (  52-)  A 1    CB  <-> 1436 GLN   (  56-)  A 1    CD     0.40    2.80
 652 HIS   (   8-)  A      CD2 <->  693 LEU   (  49-)  A      CD1    0.39    2.81
 153 PHE   (  61-)  A      CZ  <->  157 VAL   (  65-)  A      CG2    0.39    2.81
1110 ALA   (   6-)  A 1    CB  <-> 1112 HIS   (   8-)  A 1    NE2    0.37    2.73
1496 ILE   (  24-)  A 1    CG1 <-> 1505 LEU   (  33-)  A 1    CD1    0.37    2.83
 389 LEU   (  21-)  A      CD1 <->  390 GLU   (  22-)  A      N      0.37    2.63
1296 HIS   (   8-)  A 1    NE2 <-> 1349 PHE   (  61-)  A 1    CE1    0.37    2.73
 921 ALA   (   1-)  A 1    CB  <-> 1012 ASN   (  92-)  A 1    CB     0.37    2.83
 392 ILE   (  24-)  A      CG1 <->  401 LEU   (  33-)  A      CD1    0.36    2.84
 205 LEU   (  21-)  A      CD1 <->  206 GLU   (  22-)  A      N      0.36    2.64
And so on for a total of 1169 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

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: 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

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