WHAT IF Check report

This file was created 2012-01-25 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 pdb2fek.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 MET   (   1-)  A    Zero
   2 PHE   (   2-)  A    Zero
   3 ASN   (   3-)  A    Zero
   4 ASN   (   4-)  A    Zero
   5 ILE   (   5-)  A    Zero
   6 LEU   (   6-)  A    Zero
   7 VAL   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 CYS   (   9-)  A    Zero
  10 VAL   (  10-)  A    Zero
  11 GLY   (  11-)  A    Zero
  12 ASN   (  12-)  A    Zero
  13 ILE   (  13-)  A    Zero
  14 CYS   (  14-)  A    Zero
  15 ARG   (  15-)  A    Zero
  16 SER   (  16-)  A    Zero
  17 PRO   (  17-)  A    Zero
  18 THR   (  18-)  A    Zero
  19 ALA   (  19-)  A    Zero
  20 GLU   (  20-)  A    Zero
  21 ARG   (  21-)  A    Zero
  22 LEU   (  22-)  A    Zero
  23 LEU   (  23-)  A    Zero
  24 GLN   (  24-)  A    Zero
  25 ARG   (  25-)  A    Zero
And so on for a total of 2940 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 : 0.521
Model 2 : 0.525
Model 3 : 0.525
Model 4 : 0.534
Model 5 : 0.531
Model 6 : 0.529
Model 7 : 0.531
Model 8 : 0.529
Model 9 : 0.524
Model 10 : 0.525
Model 11 : 0.522
Model 12 : 0.532
Model 13 : 0.528
Model 14 : 0.526
Model 15 : 0.527
Model 16 : 0.530
Model 17 : 0.522
Model 18 : 0.526
Model 19 : 0.526
Model 20 : 0.529

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.

  12 ASN   (  12-)  A      CB   CG   ND2 122.55    4.1
 162 ARG   (  15-)  A      CB   CG   CD  104.62   -4.7
 233 HIS   (  86-)  A      CB   CG   ND1 127.78    4.1
 306 ASN   (  12-)  A      CA   CB   CG  119.74    7.1
 380 HIS   (  86-)  A      CA   CB   CG  118.31    4.5
 380 HIS   (  86-)  A      CB   CG   ND1 128.12    4.3
 453 ASN   (  12-)  A      CA   CB   CG  119.31    6.7
 453 ASN   (  12-)  A      CB   CG   ND2 123.16    4.5
 453 ASN   (  12-)  A      ND2  CG   OD1 118.57   -4.0
 527 HIS   (  86-)  A      CB   CG   ND1 128.35    4.5
 600 ASN   (  12-)  A      CA   CB   CG  118.65    6.1
 600 ASN   (  12-)  A      CB   CG   ND2 122.76    4.2
 615 HIS   (  27-)  A      CB   CG   ND1 127.62    4.0
 674 HIS   (  86-)  A      CB   CG   ND1 128.12    4.3
 733 GLU   ( 145-)  A     -C    N    CA  130.63    5.0
 738 ASN   (   3-)  A     -C    N    CA  129.14    4.1
 747 ASN   (  12-)  A      CA   CB   CG  118.23    5.6
 781 ASP   (  46-)  A      CA   CB   CG  108.49   -4.1
 816 THR   (  81-)  A      C    CA   CB  118.10    4.2
 821 HIS   (  86-)  A      CB   CG   ND1 128.17    4.4
 880 GLU   ( 145-)  A     -C    N    CA  129.36    4.3
 885 ASN   (   3-)  A     -C    N    CA  129.44    4.3
 894 ASN   (  12-)  A      CA   CB   CG  117.02    4.4
 894 ASN   (  12-)  A      CB   CG   ND2 122.43    4.0
 894 ASN   (  12-)  A      ND2  CG   OD1 118.50   -4.1
And so on for a total of 64 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.016
Model 2 : 1.022
Model 3 : 1.017
Model 4 : 1.042
Model 5 : 1.043
Model 6 : 1.017
Model 7 : 1.029
Model 8 : 1.042
Model 9 : 1.016
Model 10 : 0.996
Model 11 : 1.004
Model 12 : 1.022
Model 13 : 1.014
Model 14 : 1.025
Model 15 : 1.014
Model 16 : 1.047
Model 17 : 1.014
Model 18 : 1.021
Model 19 : 1.029
Model 20 : 1.028

Note: Per-model averages for chirality check

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

Model 1 : 0.867
Model 2 : 0.838
Model 3 : 0.812
Model 4 : 0.819
Model 5 : 0.841
Model 6 : 0.880
Model 7 : 0.820
Model 8 : 0.875
Model 9 : 0.823
Model 10 : 0.804
Model 11 : 0.809
Model 12 : 0.826
Model 13 : 0.818
Model 14 : 0.839
Model 15 : 0.848
Model 16 : 0.934
Model 17 : 0.859
Model 18 : 0.804
Model 19 : 0.850
Model 20 : 0.898

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.

1431 ASP   ( 108-)  A 1   5.28
2313 ASP   ( 108-)  A 1   5.25
2166 ASP   ( 108-)  A 1   4.96
 843 ASP   ( 108-)  A    4.91
1137 ASP   ( 108-)  A    4.83
2754 ASP   ( 108-)  A 1   4.74
2460 ASP   ( 108-)  A 1   4.67
2019 ASP   ( 108-)  A 1   4.62
1872 ASP   ( 108-)  A 1   4.57
 402 ASP   ( 108-)  A    4.00

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.

 504 HIS   (  63-)  A      CB   4.28
2196 TRP   ( 138-)  A 1    CB   4.14
1827 HIS   (  63-)  A 1    CB   4.02
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.094

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -1.179
Model 2 : -1.511
Model 3 : -0.482
Model 4 : -0.630
Model 5 : -1.490
Model 6 : -1.285
Model 7 : -1.069
Model 8 : -0.963
Model 9 : -0.959
Model 10 : -1.203
Model 11 : -0.120
Model 12 : -0.626
Model 13 : -0.800
Model 14 : -1.321
Model 15 : -1.502
Model 16 : -1.822
Model 17 : -1.221
Model 18 : -0.890
Model 19 : -1.202
Model 20 : -1.598

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.

2874 THR   (  81-)  A 2   -3.0
  81 THR   (  81-)  A    -2.9
 228 THR   (  81-)  A    -2.8
1350 HIS   (  27-)  A 1   -2.7
2469 TYR   ( 117-)  A 1   -2.6
1881 TYR   ( 117-)  A 1   -2.6
2673 HIS   (  27-)  A 1   -2.6
2820 HIS   (  27-)  A 2   -2.6
 265 ARG   ( 118-)  A    -2.6
2028 TYR   ( 117-)  A 1   -2.5
1439 PRO   ( 116-)  A 1   -2.5
 705 TYR   ( 117-)  A    -2.5
 117 TYR   ( 117-)  A    -2.5
 354 LEU   (  60-)  A    -2.5
2175 TYR   ( 117-)  A 1   -2.5
2321 PRO   ( 116-)  A 1   -2.5
 999 TYR   ( 117-)  A    -2.5
1205 GLU   (  29-)  A    -2.4
2350 GLU   ( 145-)  A 1   -2.4
1257 THR   (  81-)  A    -2.4
2232 HIS   (  27-)  A 1   -2.4
2315 GLU   ( 110-)  A 1   -2.3
  27 HIS   (  27-)  A    -2.3
 174 HIS   (  27-)  A    -2.3
 852 TYR   ( 117-)  A    -2.3
And so on for a total of 98 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 PHE   (   2-)  A  Poor phi/psi
  12 ASN   (  12-)  A  Poor phi/psi
  14 CYS   (  14-)  A  Poor phi/psi
 117 TYR   ( 117-)  A  Poor phi/psi
 144 ALA   ( 144-)  A  Poor phi/psi
 149 PHE   (   2-)  A  Poor phi/psi
 159 ASN   (  12-)  A  Poor phi/psi
 161 CYS   (  14-)  A  Poor phi/psi
 246 GLY   (  99-)  A  Poor phi/psi
 265 ARG   ( 118-)  A  Poor phi/psi
 296 PHE   (   2-)  A  Poor phi/psi
 399 GLY   ( 105-)  A  Poor phi/psi
 412 ARG   ( 118-)  A  Poor phi/psi
 453 ASN   (  12-)  A  Poor phi/psi
 546 GLY   ( 105-)  A  Poor phi/psi
 559 ARG   ( 118-)  A  Poor phi/psi
 590 PHE   (   2-)  A  Poor phi/psi
 600 ASN   (  12-)  A  Poor phi/psi
 602 CYS   (  14-)  A  Poor phi/psi
 645 GLN   (  57-)  A  Poor phi/psi
 693 GLY   ( 105-)  A  Poor phi/psi
 705 TYR   ( 117-)  A  Poor phi/psi
 738 ASN   (   3-)  A  Poor phi/psi
 747 ASN   (  12-)  A  Poor phi/psi
 852 TYR   ( 117-)  A  Poor phi/psi
And so on for a total of 79 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 : -3.152
Model 2 : -2.919
Model 3 : -2.681
Model 4 : -3.048
Model 5 : -2.643
Model 6 : -2.587
Model 7 : -2.240
Model 8 : -2.036
Model 9 : -3.174
Model 10 : -2.152
Model 11 : -2.532
Model 12 : -2.465
Model 13 : -1.908
Model 14 : -2.705
Model 15 : -2.141
Model 16 : -2.597
Model 17 : -1.528
Model 18 : -2.186
Model 19 : -2.639
Model 20 : -2.357

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.

2844 SER   (  51-)  A 2   0.34
2780 SER   ( 134-)  A 1   0.35
 722 SER   ( 134-)  A    0.35
  51 SER   (  51-)  A    0.35
2109 SER   (  51-)  A 1   0.35
 198 SER   (  51-)  A    0.36
1080 SER   (  51-)  A    0.36
1298 GLU   ( 122-)  A    0.36
1521 SER   (  51-)  A 1   0.36
1592 GLU   ( 122-)  A 1   0.36
1898 SER   ( 134-)  A 1   0.36
2045 SER   ( 134-)  A 1   0.36
2633 SER   ( 134-)  A 1   0.36
2878 ARG   (  85-)  A 2   0.36
2927 SER   ( 134-)  A 2   0.36
 869 SER   ( 134-)  A    0.37
2403 SER   (  51-)  A 1   0.37
1457 SER   ( 134-)  A 1   0.37
1604 SER   ( 134-)  A 1   0.37
2339 SER   ( 134-)  A 1   0.38

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 ASN   (   3-)  A      0
   4 ASN   (   4-)  A      0
  10 VAL   (  10-)  A      0
  12 ASN   (  12-)  A      0
  13 ILE   (  13-)  A      0
  14 CYS   (  14-)  A      0
  15 ARG   (  15-)  A      0
  26 TYR   (  26-)  A      0
  33 GLU   (  33-)  A      0
  34 SER   (  34-)  A      0
  37 LEU   (  37-)  A      0
  39 ALA   (  39-)  A      0
  40 LEU   (  40-)  A      0
  41 VAL   (  41-)  A      0
  45 ALA   (  45-)  A      0
  60 LEU   (  60-)  A      0
  61 GLU   (  61-)  A      0
  63 HIS   (  63-)  A      0
  65 ALA   (  65-)  A      0
  77 ASP   (  77-)  A      0
  82 MET   (  82-)  A      0
  83 GLU   (  83-)  A      0
  93 MET   (  93-)  A      0
 108 ASP   ( 108-)  A      0
 109 ASN   ( 109-)  A      0
And so on for a total of 1083 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 5.879
Model 2 : 5.536
Model 3 : 5.395
Model 4 : 5.632
Model 5 : 5.545
Model 6 : 6.097
Model 7 : 5.885
Model 8 : 5.977
Model 9 : 5.729
Model 10 : 6.185
Model 11 : 5.807
Model 12 : 5.912
Model 13 : 5.348
Model 14 : 6.135
Model 15 : 5.845
Model 16 : 5.927
Model 17 : 6.045
Model 18 : 5.666
Model 19 : 5.871
Model 20 : 5.779

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!

1532 GLY   (  62-)  A 1  1.71   15

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.

1103 ARG   (  74-)  A      NH2 <-> 1126 MET   (  97-)  A      SD     0.16    3.14
2220 ARG   (  15-)  A 1    NH2 <-> 2291 HIS   (  86-)  A 1    NE2    0.14    2.86
1626 CYS   (   9-)  A 1    SG  <-> 1632 ARG   (  15-)  A 1    NE     0.13    3.17
1038 CYS   (   9-)  A      SG  <-> 1039 VAL   (  10-)  A      N      0.11    3.09
2073 ARG   (  15-)  A 1    NH2 <-> 2144 HIS   (  86-)  A 1    NE2    0.11    2.89
1479 CYS   (   9-)  A 1    SG  <-> 1552 MET   (  82-)  A 1    CG     0.11    3.29
 450 CYS   (   9-)  A      SG  <->  451 VAL   (  10-)  A      N      0.10    3.10
1626 CYS   (   9-)  A 1    SG  <-> 1627 VAL   (  10-)  A 1    N      0.10    3.10
 162 ARG   (  15-)  A      NH1 <->  233 HIS   (  86-)  A      NE2    0.09    2.91
 254 TRP   ( 107-)  A      NE1 <->  285 TRP   ( 138-)  A      CD1    0.09    3.01
 156 CYS   (   9-)  A      SG  <->  162 ARG   (  15-)  A      CB     0.09    3.31
1577 TRP   ( 107-)  A 1    NE1 <-> 1608 TRP   ( 138-)  A 1    CD1    0.09    3.01
1038 CYS   (   9-)  A      SG  <-> 1044 ARG   (  15-)  A      NE     0.08    3.22
2437 ARG   (  85-)  A 1    NH2 <-> 2438 HIS   (  86-)  A 1    NE2    0.06    2.94
2018 TRP   ( 107-)  A 1    NE1 <-> 2049 TRP   ( 138-)  A 1    CD1    0.05    3.05
 946 CYS   (  64-)  A      SG  <->  948 ARG   (  66-)  A      NH2    0.05    3.25
2508 CYS   (   9-)  A 1    SG  <-> 2581 MET   (  82-)  A 1    SD     0.05    3.40
 228 THR   (  81-)  A      C   <->  229 MET   (  82-)  A      SD     0.05    3.25
 883 MET   (   1-)  A      SD  <-> 1028 GLN   ( 146-)  A      NE2    0.05    3.25
 603 ARG   (  15-)  A      NH2 <->  674 HIS   (  86-)  A      NE2    0.05    2.95
1041 ASN   (  12-)  A      ND2 <-> 1092 HIS   (  63-)  A      NE2    0.04    2.96
1776 ASN   (  12-)  A 1    ND2 <-> 1827 HIS   (  63-)  A 1    NE2    0.04    2.96
1283 TRP   ( 107-)  A      NE1 <-> 1314 TRP   ( 138-)  A      CD1    0.04    3.06
2307 MET   ( 102-)  A 1    CE  <-> 2343 TRP   ( 138-)  A 1    CH2    0.03    3.17
 747 ASN   (  12-)  A      ND2 <->  798 HIS   (  63-)  A      NE2    0.03    2.97
 107 TRP   ( 107-)  A      NE1 <->  138 TRP   ( 138-)  A      CD1    0.03    3.07
 155 VAL   (   8-)  A      C   <->  156 CYS   (   9-)  A      SG     0.03    3.27
2658 ASN   (  12-)  A 1    ND2 <-> 2709 HIS   (  63-)  A 1    NE2    0.03    2.97
1044 ARG   (  15-)  A      NH2 <-> 1115 HIS   (  86-)  A      NE2    0.03    2.97
  14 CYS   (  14-)  A      SG  <->   15 ARG   (  15-)  A      N      0.03    3.17
1773 CYS   (   9-)  A 1    SG  <-> 1779 ARG   (  15-)  A 1    CB     0.02    3.38
 401 TRP   ( 107-)  A      NE1 <->  432 TRP   ( 138-)  A      CD1    0.02    3.08
1871 TRP   ( 107-)  A 1    NE1 <-> 1902 TRP   ( 138-)  A 1    CD1    0.02    3.08
 306 ASN   (  12-)  A      ND2 <->  357 HIS   (  63-)  A      NE2    0.01    2.99
 450 CYS   (   9-)  A      SG  <->  456 ARG   (  15-)  A      NE     0.01    3.29
2807 CYS   (  14-)  A 2    SG  <-> 2808 ARG   (  15-)  A 2    N      0.01    3.19
2366 CYS   (  14-)  A 1    SG  <-> 2367 ARG   (  15-)  A 1    N      0.01    3.19
 148 MET   (   1-)  A      SD  <->  149 PHE   (   2-)  A      N      0.01    3.19

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


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