WHAT IF Check report

This file was created 2012-01-19 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 pdb2dcr.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   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 GLY   (   4-)  A    Zero
   5 SER   (   5-)  A    Zero
   6 SER   (   6-)  A    Zero
   7 GLY   (   7-)  A    Zero
   8 GLU   (   8-)  A    Zero
   9 VAL   (   9-)  A    Zero
  10 GLN   (  10-)  A    Zero
  11 LYS   (  11-)  A    Zero
  12 PRO   (  12-)  A    Zero
  13 LEU   (  13-)  A    Zero
  14 HIS   (  14-)  A    Zero
  15 GLU   (  15-)  A    Zero
  16 GLN   (  16-)  A    Zero
  17 LEU   (  17-)  A    Zero
  18 TRP   (  18-)  A    Zero
  19 TYR   (  19-)  A    Zero
  20 HIS   (  20-)  A    Zero
  21 GLY   (  21-)  A    Zero
  22 ALA   (  22-)  A    Zero
  23 ILE   (  23-)  A    Zero
  24 PRO   (  24-)  A    Zero
  25 ARG   (  25-)  A    Zero
And so on for a total of 2280 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 : 0.536
Model 2 : 0.523
Model 3 : 0.529
Model 4 : 0.532
Model 5 : 0.534
Model 6 : 0.529
Model 7 : 0.522
Model 8 : 0.524
Model 9 : 0.530
Model 10 : 0.526
Model 11 : 0.523
Model 12 : 0.541
Model 13 : 0.525
Model 14 : 0.527
Model 15 : 0.526
Model 16 : 0.517
Model 17 : 0.527
Model 18 : 0.534
Model 19 : 0.531
Model 20 : 0.530

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.

  65 GLN   (  65-)  A     -C    N    CA  129.67    4.4
 218 HIS   ( 104-)  A      CB   CG   ND1 127.67    4.0
 332 HIS   ( 104-)  A      CA   CB   CG  118.38    4.6
 364 ALA   (  22-)  A     -C    N    CA  129.12    4.1
 524 ASP   (  68-)  A      CA   CB   CG  108.44   -4.2
 543 HIS   (  87-)  A      CA   CB   CG  118.41    4.6
 543 HIS   (  87-)  A      CB   CG   ND1 128.24    4.4
 560 HIS   ( 104-)  A      CA   CB   CG  121.51    7.7
 611 ARG   (  41-)  A      CD   NE   CZ  129.02    4.1
 674 HIS   ( 104-)  A      CA   CB   CG  118.27    4.5
 788 HIS   ( 104-)  A      CA   CB   CG  119.02    5.2
 788 HIS   ( 104-)  A      CB   CG   ND1 129.47    5.2
 788 HIS   ( 104-)  A      CB   CG   CD2 122.87   -4.8
 902 HIS   ( 104-)  A      CA   CB   CG  118.47    4.7
 902 HIS   ( 104-)  A      CB   CG   ND1 128.08    4.3
 927 GLU   (  15-)  A      N    CA   CB  103.53   -4.1
1016 HIS   ( 104-)  A      CA   CB   CG  119.03    5.2
1016 HIS   ( 104-)  A      CB   CG   ND1 128.97    4.9
1067 ARG   (  41-)  A 1    CD   NE   CZ  129.14    4.1
1069 SER   (  43-)  A 1   -C    N    CA  129.32    4.2
1155 GLU   (  15-)  A 1    C    CA   CB  118.25    4.3
1215 GLY   (  75-)  A 1   -C    N    CA  128.15    4.4
1227 HIS   (  87-)  A 1    CB   CG   ND1 129.23    5.1
1227 HIS   (  87-)  A 1    CB   CG   CD2 123.78   -4.1
1359 ARG   ( 105-)  A 1    CD   NE   CZ  128.92    4.0
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 : 1.129
Model 2 : 1.133
Model 3 : 1.131
Model 4 : 1.137
Model 5 : 1.177
Model 6 : 1.137
Model 7 : 1.173
Model 8 : 1.161
Model 9 : 1.191
Model 10 : 1.138
Model 11 : 1.160
Model 12 : 1.187
Model 13 : 1.172
Model 14 : 1.180
Model 15 : 1.188
Model 16 : 1.161
Model 17 : 1.185
Model 18 : 1.180
Model 19 : 1.168
Model 20 : 1.212

Note: Per-model averages for chirality check

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

Model 1 : 1.157
Model 2 : 1.121
Model 3 : 1.139
Model 4 : 1.080
Model 5 : 1.196
Model 6 : 1.178
Model 7 : 1.122
Model 8 : 1.219
Model 9 : 1.094
Model 10 : 1.064
Model 11 : 1.078
Model 12 : 1.313
Model 13 : 1.064
Model 14 : 1.109
Model 15 : 1.060
Model 16 : 1.081
Model 17 : 1.209
Model 18 : 1.156
Model 19 : 1.130
Model 20 : 1.167

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.

1272 TRP   (  18-)  A 1   6.19
1509 GLU   (  27-)  A 1   5.55
1167 GLU   (  27-)  A 1   5.43
1524 GLU   (  42-)  A 1   5.27
 644 GLU   (  74-)  A    5.21
1737 GLU   (  27-)  A 1   5.10
 464 GLU   (   8-)  A    5.03
2128 GLU   (  76-)  A 1   5.03
 262 HIS   (  34-)  A    5.02
  55 TRP   (  55-)  A    4.98
1657 HIS   (  61-)  A 1   4.69
 483 GLU   (  27-)  A    4.68
1851 GLU   (  27-)  A 1   4.47
 600 GLU   (  30-)  A    4.45
 543 HIS   (  87-)  A    4.39
 530 GLU   (  74-)  A    4.33
2079 GLU   (  27-)  A 1   4.33
1771 HIS   (  61-)  A 1   4.28
 891 GLN   (  93-)  A    4.26
 973 HIS   (  61-)  A    4.12
1682 ASP   (  86-)  A 1   4.09
1291 ASP   (  37-)  A 1   4.05

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 832 HIS   (  34-)  A      CB   7.29
 560 HIS   ( 104-)  A      CB   6.44
 859 HIS   (  61-)  A      CB   5.25
 674 HIS   ( 104-)  A      CB   4.47
1201 HIS   (  61-)  A 1    CB   4.32
 885 HIS   (  87-)  A      CB   4.30
 299 TYR   (  71-)  A      OH   4.24
  71 TYR   (  71-)  A      CB   4.12
1615 TYR   (  19-)  A 1    OH   4.12
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.408

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 : -4.408

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.158
Model 2 : -4.840
Model 3 : -3.620
Model 4 : -4.351
Model 5 : -5.461
Model 6 : -4.727
Model 7 : -4.531
Model 8 : -4.840
Model 9 : -4.601
Model 10 : -3.989
Model 11 : -4.102
Model 12 : -4.531
Model 13 : -4.505
Model 14 : -4.443
Model 15 : -3.821
Model 16 : -4.859
Model 17 : -3.463
Model 18 : -4.495
Model 19 : -4.412
Model 20 : -4.419

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.

 906 PRO   ( 108-)  A    -2.7
 381 LEU   (  39-)  A    -2.7
 523 LEU   (  67-)  A    -2.7
 609 LEU   (  39-)  A    -2.7
1236 THR   (  96-)  A 1   -2.7
1065 LEU   (  39-)  A 1   -2.7
1407 LEU   (  39-)  A 1   -2.7
2205 LEU   (  39-)  A 2   -2.7
1521 LEU   (  39-)  A 1   -2.6
 837 LEU   (  39-)  A    -2.6
1863 LEU   (  39-)  A 1   -2.6
 267 LEU   (  39-)  A    -2.6
1350 THR   (  96-)  A 1   -2.6
 751 LEU   (  67-)  A    -2.6
1179 LEU   (  39-)  A 1   -2.6
2262 THR   (  96-)  A 2   -2.6
1321 LEU   (  67-)  A 1   -2.6
 865 LEU   (  67-)  A    -2.6
  39 LEU   (  39-)  A    -2.6
 409 LEU   (  67-)  A    -2.6
 153 LEU   (  39-)  A    -2.6
1920 THR   (  96-)  A 1   -2.6
 666 THR   (  96-)  A    -2.6
2119 LEU   (  67-)  A 1   -2.6
1093 LEU   (  67-)  A 1   -2.6
And so on for a total of 175 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.

   8 GLU   (   8-)  A  Poor phi/psi
  33 VAL   (  33-)  A  Poor phi/psi
  44 GLN   (  44-)  A  Poor phi/psi
  47 GLN   (  47-)  A  Poor phi/psi, omega poor
  52 SER   (  52-)  A  omega poor
  66 SER   (  66-)  A  Poor phi/psi
  67 LEU   (  67-)  A  omega poor
  68 ASP   (  68-)  A  Poor phi/psi
  87 HIS   (  87-)  A  omega poor
  92 GLN   (  92-)  A  Poor phi/psi
  99 SER   (  99-)  A  Poor phi/psi
 147 VAL   (  33-)  A  Poor phi/psi
 159 GLY   (  45-)  A  Poor phi/psi
 170 ASP   (  56-)  A  Poor phi/psi
 180 SER   (  66-)  A  Poor phi/psi
 183 ASN   (  69-)  A  omega poor
 197 LEU   (  83-)  A  omega poor
 201 HIS   (  87-)  A  omega poor
 204 SER   (  90-)  A  omega poor
 206 GLN   (  92-)  A  Poor phi/psi
 213 SER   (  99-)  A  omega poor
 214 GLY   ( 100-)  A  omega poor
 223 SER   ( 109-)  A  omega poor
 230 SER   (   2-)  A  Poor phi/psi
 234 SER   (   6-)  A  Poor phi/psi
And so on for a total of 231 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 : -6.032

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 : -6.432
Model 2 : -5.966
Model 3 : -6.399
Model 4 : -6.440
Model 5 : -6.652
Model 6 : -6.207
Model 7 : -5.803
Model 8 : -5.794
Model 9 : -6.624
Model 10 : -5.949
Model 11 : -5.660
Model 12 : -5.120
Model 13 : -5.664
Model 14 : -5.360
Model 15 : -6.292
Model 16 : -5.726
Model 17 : -5.988
Model 18 : -6.414
Model 19 : -6.336
Model 20 : -5.820

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.

 962 VAL   (  50-)  A    0.39

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 SER   (   3-)  A      0
   6 SER   (   6-)  A      0
   8 GLU   (   8-)  A      0
  10 GLN   (  10-)  A      0
  18 TRP   (  18-)  A      0
  22 ALA   (  22-)  A      0
  31 LEU   (  31-)  A      0
  32 LEU   (  32-)  A      0
  35 SER   (  35-)  A      0
  37 ASP   (  37-)  A      0
  43 SER   (  43-)  A      0
  44 GLN   (  44-)  A      0
  47 GLN   (  47-)  A      0
  55 TRP   (  55-)  A      0
  65 GLN   (  65-)  A      0
  67 LEU   (  67-)  A      0
  68 ASP   (  68-)  A      0
  69 ASN   (  69-)  A      0
  72 ARG   (  72-)  A      0
  73 LEU   (  73-)  A      0
  74 GLU   (  74-)  A      0
  76 GLU   (  76-)  A      0
  92 GLN   (  92-)  A      0
  95 LEU   (  95-)  A      0
  96 THR   (  96-)  A      0
And so on for a total of 1190 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.880

Note: Per-model averages for omega angle check

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

Model 1 : 7.425
Model 2 : 8.206
Model 3 : 7.736
Model 4 : 7.307
Model 5 : 8.571
Model 6 : 7.944
Model 7 : 8.707
Model 8 : 8.115
Model 9 : 7.254
Model 10 : 8.227
Model 11 : 7.262
Model 12 : 7.929
Model 13 : 6.820
Model 14 : 7.491
Model 15 : 7.172
Model 16 : 8.130
Model 17 : 8.273
Model 18 : 8.867
Model 19 : 8.720
Model 20 : 7.391

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!

1755 GLY   (  45-)  A 1  2.31   24
 843 GLY   (  45-)  A   1.94   18
 957 GLY   (  45-)  A   1.75   47
1486 GLY   (   4-)  A 1  1.59   12
 311 LEU   (  83-)  A   1.55   17
1600 GLY   (   4-)  A 1  1.51   38

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].

 222 PRO   ( 108-)  A   -43.7 envelop C-alpha (-36 degrees)
 336 PRO   ( 108-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 424 PRO   (  82-)  A  -112.9 envelop C-gamma (-108 degrees)
 450 PRO   ( 108-)  A   -49.2 half-chair C-beta/C-alpha (-54 degrees)
 564 PRO   ( 108-)  A   -59.7 half-chair C-beta/C-alpha (-54 degrees)
 567 PRO   ( 111-)  A   -64.1 envelop C-beta (-72 degrees)
 906 PRO   ( 108-)  A   -56.7 half-chair C-beta/C-alpha (-54 degrees)
1020 PRO   ( 108-)  A   -53.4 half-chair C-beta/C-alpha (-54 degrees)
1248 PRO   ( 108-)  A 1  -45.8 half-chair C-beta/C-alpha (-54 degrees)
1362 PRO   ( 108-)  A 1  -61.1 half-chair C-beta/C-alpha (-54 degrees)
1590 PRO   ( 108-)  A 1  -61.2 half-chair C-beta/C-alpha (-54 degrees)
1704 PRO   ( 108-)  A 1  -64.0 envelop C-beta (-72 degrees)
1818 PRO   ( 108-)  A 1  -45.1 half-chair C-beta/C-alpha (-54 degrees)
1932 PRO   ( 108-)  A 1  -54.1 half-chair C-beta/C-alpha (-54 degrees)
2046 PRO   ( 108-)  A 1  -54.7 half-chair C-beta/C-alpha (-54 degrees)
2274 PRO   ( 108-)  A 2  -39.6 envelop C-alpha (-36 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.

1346 GLN   (  92-)  A 1    C   <-> 1356 VAL   ( 102-)  A 1    CG1    0.15    3.05
 434 GLN   (  92-)  A      C   <->  444 VAL   ( 102-)  A      CG1    0.15    3.05
 537 ILE   (  81-)  A      N   <->  538 PRO   (  82-)  A      CD     0.11    2.89
 762 PHE   (  78-)  A      CZ  <->  771 HIS   (  87-)  A      CD2    0.10    3.10
2019 ILE   (  81-)  A 1    N   <-> 2020 PRO   (  82-)  A 1    CD     0.09    2.91
1905 ILE   (  81-)  A 1    N   <-> 1906 PRO   (  82-)  A 1    CD     0.09    2.91
 651 ILE   (  81-)  A      N   <->  652 PRO   (  82-)  A      CD     0.09    2.91
1107 ILE   (  81-)  A 1    N   <-> 1108 PRO   (  82-)  A 1    CD     0.09    2.91
2247 ILE   (  81-)  A 2    N   <-> 2248 PRO   (  82-)  A 2    CD     0.09    2.91
 423 ILE   (  81-)  A      N   <->  424 PRO   (  82-)  A      CD     0.09    2.91
1091 GLN   (  65-)  A 1    NE2 <-> 1110 LEU   (  84-)  A 1    CD1    0.09    3.01
  81 ILE   (  81-)  A      N   <->   82 PRO   (  82-)  A      CD     0.09    2.91
 765 ILE   (  81-)  A      N   <->  766 PRO   (  82-)  A      CD     0.09    2.91
1563 ILE   (  81-)  A 1    N   <-> 1564 PRO   (  82-)  A 1    CD     0.09    2.91
 309 ILE   (  81-)  A      N   <->  310 PRO   (  82-)  A      CD     0.08    2.92
 195 ILE   (  81-)  A      N   <->  196 PRO   (  82-)  A      CD     0.08    2.92
2133 ILE   (  81-)  A 1    N   <-> 2134 PRO   (  82-)  A 1    CD     0.08    2.92
1992 LEU   (  54-)  A 1    CD1 <-> 1995 GLY   (  57-)  A 1    N      0.08    3.02
1335 ILE   (  81-)  A 1    N   <-> 1336 PRO   (  82-)  A 1    CD     0.08    2.92
1449 ILE   (  81-)  A 1    N   <-> 1450 PRO   (  82-)  A 1    CD     0.07    2.93
 879 ILE   (  81-)  A      N   <->  880 PRO   (  82-)  A      CD     0.07    2.93
1791 ILE   (  81-)  A 1    N   <-> 1792 PRO   (  82-)  A 1    CD     0.07    2.93
1677 ILE   (  81-)  A 1    N   <-> 1678 PRO   (  82-)  A 1    CD     0.07    2.93
 993 ILE   (  81-)  A      N   <->  994 PRO   (  82-)  A      CD     0.06    2.94
1874 VAL   (  50-)  A 1    CG2 <-> 1887 ILE   (  63-)  A 1    CD1    0.06    3.14
1221 ILE   (  81-)  A 1    N   <-> 1222 PRO   (  82-)  A 1    CD     0.06    2.94
1428 ARG   (  60-)  A 1    CB  <-> 1430 PHE   (  62-)  A 1    CE2    0.04    3.16
1074 GLU   (  48-)  A 1    CD  <-> 1089 ILE   (  63-)  A 1    CD1    0.02    3.18
 593 ILE   (  23-)  A      O   <->  611 ARG   (  41-)  A      NE     0.02    2.68
 944 LEU   (  32-)  A      CD1 <->  966 LEU   (  54-)  A      N      0.01    3.09
 997 ILE   (  85-)  A      O   <-> 1001 LEU   (  89-)  A      N      0.01    2.69
1460 GLN   (  92-)  A 1    C   <-> 1470 VAL   ( 102-)  A 1    CG1    0.01    3.19
 634 ILE   (  64-)  A      CG2 <->  635 GLN   (  65-)  A      N      0.01    2.99
2075 ILE   (  23-)  A 1    CD1 <-> 2083 LEU   (  31-)  A 1    CD1    0.01    3.19
 269 ARG   (  41-)  A      O   <->  278 VAL   (  50-)  A      N      0.01    2.69

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


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