WHAT IF Check report

This file was created 2012-01-30 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 pdb2o2o.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

Note: Ramachandran plot

Chain identifier: A; Model number 21

Note: Ramachandran plot

Chain identifier: A; Model number 22

Note: Ramachandran plot

Chain identifier: A; Model number 23

Note: Ramachandran plot

Chain identifier: A; Model number 24

Note: Ramachandran plot

Chain identifier: A; Model number 25

Note: Ramachandran plot

Chain identifier: A; Model number 26

Note: Ramachandran plot

Chain identifier: A; Model number 27

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  36 VAL   ( 127-)  A      N    CA    1.37   -4.8
  91 PHE   ( 107-)  A      CE1  CZ    1.51    4.1
  91 PHE   ( 107-)  A      CE2  CZ    1.26   -4.0
 111 VAL   ( 127-)  A      N    CA    1.37   -4.4
 186 VAL   ( 127-)  A      N    CA    1.37   -4.6
 261 VAL   ( 127-)  A      N    CA    1.37   -4.5
 336 VAL   ( 127-)  A      N    CA    1.37   -4.6
 411 VAL   ( 127-)  A      N    CA    1.37   -4.7
 486 VAL   ( 127-)  A      N    CA    1.38   -4.2
 561 VAL   ( 127-)  A      N    CA    1.37   -4.5
 636 VAL   ( 127-)  A      N    CA    1.37   -4.5
 711 VAL   ( 127-)  A 1    N    CA    1.37   -4.5
 766 PHE   ( 107-)  A 1    CE1  CZ    1.50    4.0
 786 VAL   ( 127-)  A 1    N    CA    1.38   -4.3
 861 VAL   ( 127-)  A 1    N    CA    1.38   -4.4
 936 VAL   ( 127-)  A 1    N    CA    1.36   -5.2
1011 VAL   ( 127-)  A 1    N    CA    1.37   -4.6
1086 VAL   ( 127-)  A 1    N    CA    1.37   -4.5
1161 VAL   ( 127-)  A 1    N    CA    1.38   -4.4
1236 VAL   ( 127-)  A 1    N    CA    1.37   -4.7
1311 VAL   ( 127-)  A 1    N    CA    1.37   -4.8
1386 VAL   ( 127-)  A 1    N    CA    1.38   -4.3
1461 VAL   ( 127-)  A 2    N    CA    1.37   -4.8
1536 VAL   ( 127-)  A 2    N    CA    1.37   -4.7
1611 VAL   ( 127-)  A 2    N    CA    1.37   -4.4
1686 VAL   ( 127-)  A 2    N    CA    1.37   -4.4
1761 VAL   ( 127-)  A 2    N    CA    1.37   -4.8
1836 VAL   ( 127-)  A 2    N    CA    1.37   -4.6
1911 VAL   ( 127-)  A 2    N    CA    1.37   -4.5
1986 VAL   ( 127-)  A 2    N    CA    1.37   -4.5

Note: Per-model averages for bond-length check

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

Model 1 : 0.876
Model 2 : 0.911
Model 3 : 0.913
Model 4 : 0.903
Model 5 : 0.876
Model 6 : 0.877
Model 7 : 0.899
Model 8 : 0.888
Model 9 : 0.913
Model 10 : 0.928
Model 11 : 0.911
Model 12 : 0.920
Model 13 : 0.911
Model 14 : 0.895
Model 15 : 0.907
Model 16 : 0.899
Model 17 : 0.905
Model 18 : 0.941
Model 19 : 0.895
Model 20 : 0.877
Model 21 : 0.880
Model 22 : 0.900
Model 23 : 0.881
Model 24 : 0.873
Model 25 : 0.862
Model 26 : 0.853
Model 27 : 0.916

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.

  16 PHE   ( 107-)  A      N    CA   CB  102.15   -4.9
  36 VAL   ( 127-)  A      N    CA   CB  102.74   -4.6
  91 PHE   ( 107-)  A      N    CA   CB  102.43   -4.7
 111 VAL   ( 127-)  A      N    CA   CB  102.85   -4.5
 166 PHE   ( 107-)  A      N    CA   CB  102.49   -4.7
 186 VAL   ( 127-)  A      N    CA   CB  102.71   -4.6
 241 PHE   ( 107-)  A      N    CA   CB  102.49   -4.7
 261 VAL   ( 127-)  A      N    CA   CB  102.48   -4.7
 283 SER   ( 149-)  A      N    CA   CB  103.51   -4.1
 316 PHE   ( 107-)  A      N    CA   CB  102.37   -4.8
 336 VAL   ( 127-)  A      N    CA   CB  103.08   -4.4
 391 PHE   ( 107-)  A      N    CA   CB  102.79   -4.5
 411 VAL   ( 127-)  A      N    CA   CB  103.12   -4.3
 466 PHE   ( 107-)  A      N    CA   CB  102.19   -4.9
 541 PHE   ( 107-)  A      N    CA   CB  102.26   -4.8
 561 VAL   ( 127-)  A      N    CA   CB  103.65   -4.0
 616 PHE   ( 107-)  A      N    CA   CB  102.84   -4.5
 636 VAL   ( 127-)  A      N    CA   CB  102.14   -4.9
 691 PHE   ( 107-)  A 1    N    CA   CB  102.29   -4.8
 711 VAL   ( 127-)  A 1    N    CA   CB  103.10   -4.4
 766 PHE   ( 107-)  A 1    N    CA   CB  102.62   -4.6
 786 VAL   ( 127-)  A 1    N    CA   CB  102.87   -4.5
 841 PHE   ( 107-)  A 1    N    CA   CB  102.29   -4.8
 861 VAL   ( 127-)  A 1    N    CA   CB  103.03   -4.4
 916 PHE   ( 107-)  A 1    N    CA   CB  102.42   -4.8
And so on for a total of 59 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.905
Model 2 : 0.928
Model 3 : 0.900
Model 4 : 0.929
Model 5 : 0.890
Model 6 : 0.928
Model 7 : 0.926
Model 8 : 0.928
Model 9 : 0.914
Model 10 : 0.954
Model 11 : 0.901
Model 12 : 0.923
Model 13 : 0.983
Model 14 : 0.922
Model 15 : 0.936
Model 16 : 0.967
Model 17 : 0.977
Model 18 : 0.966
Model 19 : 0.955
Model 20 : 0.915
Model 21 : 0.934
Model 22 : 0.931
Model 23 : 0.949
Model 24 : 0.956
Model 25 : 0.945
Model 26 : 0.919
Model 27 : 0.997

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.

  36 VAL   ( 127-)  A      C      6.5     9.01     0.15
 111 VAL   ( 127-)  A      C      6.1     8.55     0.15
 261 VAL   ( 127-)  A      CA     6.1    42.01    33.23
 636 VAL   ( 127-)  A      C      6.9     9.60     0.15
 786 VAL   ( 127-)  A 1    C      6.1     8.49     0.15
1236 VAL   ( 127-)  A 1    C      7.2    10.04     0.15
1311 VAL   ( 127-)  A 1    C      6.4     8.86     0.15
1461 VAL   ( 127-)  A 2    C      6.1     8.45     0.15
1761 VAL   ( 127-)  A 2    CA     6.1    42.01    33.23
1761 VAL   ( 127-)  A 2    C      6.1     8.50     0.15
1911 VAL   ( 127-)  A 2    C      6.0     8.43     0.15
1986 VAL   ( 127-)  A 2    C      6.0     8.37     0.15
The average deviation= 1.197

Note: Per-model averages for chirality check

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

Model 1 : 1.148
Model 2 : 1.156
Model 3 : 1.130
Model 4 : 1.172
Model 5 : 1.127
Model 6 : 1.169
Model 7 : 1.141
Model 8 : 1.154
Model 9 : 1.161
Model 10 : 1.119
Model 11 : 1.149
Model 12 : 1.124
Model 13 : 1.172
Model 14 : 1.119
Model 15 : 1.165
Model 16 : 1.200
Model 17 : 1.193
Model 18 : 1.189
Model 19 : 1.178
Model 20 : 1.200
Model 21 : 1.188
Model 22 : 1.152
Model 23 : 1.143
Model 24 : 1.193
Model 25 : 1.131
Model 26 : 1.145
Model 27 : 1.184

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.

1521 GLN   ( 112-)  A 2   4.38
1666 PHE   ( 107-)  A 2   4.30

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 : -5.513

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.101
Model 2 : -5.109
Model 3 : -5.894
Model 4 : -5.488
Model 5 : -5.556
Model 6 : -5.314
Model 7 : -6.030
Model 8 : -5.255
Model 9 : -5.269
Model 10 : -5.866
Model 11 : -5.624
Model 12 : -5.141
Model 13 : -5.349
Model 14 : -5.393
Model 15 : -4.953
Model 16 : -6.036
Model 17 : -5.453
Model 18 : -5.479
Model 19 : -5.329
Model 20 : -5.865
Model 21 : -5.695
Model 22 : -5.462
Model 23 : -5.313
Model 24 : -5.716
Model 25 : -5.768
Model 26 : -6.151
Model 27 : -5.246

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.

 983 ARG   (  99-)  A 1   -2.9
 821 LEU   ( 162-)  A 1   -2.8
 138 GLU   ( 154-)  A    -2.7
 533 ARG   (  99-)  A    -2.7
 888 GLU   ( 154-)  A 1   -2.6
1863 GLU   ( 154-)  A 2   -2.6
 439 LEU   ( 155-)  A    -2.6
 892 GLU   ( 158-)  A 1   -2.6
1038 GLU   ( 154-)  A 1   -2.6
 442 GLU   ( 158-)  A    -2.6
1638 GLU   ( 154-)  A 2   -2.6
 738 GLU   ( 154-)  A 1   -2.6
1565 SER   ( 156-)  A 2   -2.6
1713 GLU   ( 154-)  A 2   -2.6
 663 GLU   ( 154-)  A    -2.6
 963 GLU   ( 154-)  A 1   -2.6
 813 GLU   ( 154-)  A 1   -2.6
 213 GLU   ( 154-)  A    -2.6
1263 GLU   ( 154-)  A 1   -2.6
1338 GLU   ( 154-)  A 1   -2.6
1189 LEU   ( 155-)  A 1   -2.6
 152 ASN   (  93-)  A    -2.6
 683 ARG   (  99-)  A 1   -2.6
 588 GLU   ( 154-)  A    -2.5
1938 GLU   ( 154-)  A 2   -2.5
And so on for a total of 361 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.

   7 ARG   (  98-)  A  Poor phi/psi
   8 ARG   (  99-)  A  Poor phi/psi
  15 ALA   ( 106-)  A  omega poor
  19 LEU   ( 110-)  A  PRO omega poor
  24 ASP   ( 115-)  A  Poor phi/psi
  28 LEU   ( 119-)  A  omega poor
  30 VAL   ( 121-)  A  Poor phi/psi, omega poor
  35 GLU   ( 126-)  A  omega poor
  36 VAL   ( 127-)  A  Poor phi/psi
  42 GLU   ( 133-)  A  Poor phi/psi
  58 SER   ( 149-)  A  omega poor
  63 GLU   ( 154-)  A  Poor phi/psi, omega poor
  64 LEU   ( 155-)  A  omega poor
  65 SER   ( 156-)  A  Poor phi/psi
  67 GLU   ( 158-)  A  Poor phi/psi
  68 SER   ( 159-)  A  Poor phi/psi
  71 LEU   ( 162-)  A  Poor phi/psi
  82 ARG   (  98-)  A  Poor phi/psi
  83 ARG   (  99-)  A  Poor phi/psi
  90 ALA   ( 106-)  A  omega poor
  94 LEU   ( 110-)  A  PRO omega poor
  95 PRO   ( 111-)  A  omega poor
  99 ASP   ( 115-)  A  Poor phi/psi
 103 LEU   ( 119-)  A  omega poor
 105 VAL   ( 121-)  A  Poor phi/psi, omega poor
And so on for a total of 487 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 : -6.025

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 : -6.019
Model 2 : -6.143
Model 3 : -6.317
Model 4 : -6.441
Model 5 : -5.238
Model 6 : -6.613
Model 7 : -6.235
Model 8 : -4.860
Model 9 : -6.799
Model 10 : -6.527
Model 11 : -6.267
Model 12 : -5.843
Model 13 : -5.790
Model 14 : -5.586
Model 15 : -5.005
Model 16 : -4.756
Model 17 : -6.700
Model 18 : -6.730
Model 19 : -6.821
Model 20 : -5.311
Model 21 : -5.684
Model 22 : -6.477
Model 23 : -6.160
Model 24 : -6.301
Model 25 : -6.285
Model 26 : -5.820
Model 27 : -5.936

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 LYS   (  94-)  A      0
   6 GLU   (  97-)  A      0
   7 ARG   (  98-)  A      0
   8 ARG   (  99-)  A      0
   9 ARG   ( 100-)  A      0
  15 ALA   ( 106-)  A      0
  16 PHE   ( 107-)  A      0
  19 LEU   ( 110-)  A      0
  20 PRO   ( 111-)  A      0
  21 GLN   ( 112-)  A      0
  22 ASN   ( 113-)  A      0
  23 ASP   ( 114-)  A      0
  24 ASP   ( 115-)  A      0
  29 LYS   ( 120-)  A      0
  30 VAL   ( 121-)  A      0
  36 VAL   ( 127-)  A      0
  37 VAL   ( 128-)  A      0
  39 GLU   ( 130-)  A      0
  40 VAL   ( 131-)  A      0
  42 GLU   ( 133-)  A      0
  45 TRP   ( 136-)  A      0
  46 GLU   ( 137-)  A      0
  49 LEU   ( 140-)  A      0
  53 THR   ( 144-)  A      0
  55 MET   ( 146-)  A      0
And so on for a total of 1450 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 : -2.030

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 : 11.574

Note: Per-model averages for omega angle check

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

Model 1 : 10.591
Model 2 : 10.909
Model 3 : 10.872
Model 4 : 10.837
Model 5 : 11.387
Model 6 : 11.147
Model 7 : 11.028
Model 8 : 10.658
Model 9 : 10.746
Model 10 : 10.996
Model 11 : 10.788
Model 12 : 10.524
Model 13 : 11.268
Model 14 : 11.264
Model 15 : 11.450
Model 16 : 11.376
Model 17 : 12.038
Model 18 : 11.795
Model 19 : 11.989
Model 20 : 10.813
Model 21 : 11.587
Model 22 : 12.306
Model 23 : 14.218
Model 24 : 12.326
Model 25 : 13.797
Model 26 : 13.741
Model 27 : 12.161

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].

  20 PRO   ( 111-)  A    22.8 half-chair N/C-delta (18 degrees)
 170 PRO   ( 111-)  A    20.6 half-chair N/C-delta (18 degrees)
 320 PRO   ( 111-)  A    26.7 half-chair N/C-delta (18 degrees)
 395 PRO   ( 111-)  A    27.6 envelop C-delta (36 degrees)
 470 PRO   ( 111-)  A    24.5 half-chair N/C-delta (18 degrees)
 620 PRO   ( 111-)  A    25.5 half-chair N/C-delta (18 degrees)
 695 PRO   ( 111-)  A 1   29.6 envelop C-delta (36 degrees)
 845 PRO   ( 111-)  A 1   22.9 half-chair N/C-delta (18 degrees)
 995 PRO   ( 111-)  A 1   27.2 envelop C-delta (36 degrees)
1070 PRO   ( 111-)  A 1   30.2 envelop C-delta (36 degrees)
1220 PRO   ( 111-)  A 1  -63.6 envelop C-beta (-72 degrees)
1295 PRO   ( 111-)  A 1   28.7 envelop C-delta (36 degrees)
1370 PRO   ( 111-)  A 1  -64.1 envelop C-beta (-72 degrees)
1445 PRO   ( 111-)  A 2   25.1 half-chair N/C-delta (18 degrees)
1520 PRO   ( 111-)  A 2   26.4 half-chair N/C-delta (18 degrees)
1595 PRO   ( 111-)  A 2  -62.4 half-chair C-beta/C-alpha (-54 degrees)
1670 PRO   ( 111-)  A 2   27.0 envelop C-delta (36 degrees)
1745 PRO   ( 111-)  A 2  -65.5 envelop C-beta (-72 degrees)
1970 PRO   ( 111-)  A 2   29.0 envelop C-delta (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.

 843 TYR   ( 109-)  A 1    CE2 <->  845 PRO   ( 111-)  A 1    CG     0.42    2.78
1218 TYR   ( 109-)  A 1    CE2 <-> 1220 PRO   ( 111-)  A 1    CG     0.42    2.78
 168 TYR   ( 109-)  A      CE2 <->  170 PRO   ( 111-)  A      CG     0.42    2.78
 318 TYR   ( 109-)  A      CE2 <->  320 PRO   ( 111-)  A      CG     0.42    2.78
 468 TYR   ( 109-)  A      CE2 <->  470 PRO   ( 111-)  A      CG     0.42    2.78
1668 TYR   ( 109-)  A 2    CE2 <-> 1670 PRO   ( 111-)  A 2    CG     0.42    2.78
1593 TYR   ( 109-)  A 2    CE2 <-> 1595 PRO   ( 111-)  A 2    CG     0.42    2.78
1293 TYR   ( 109-)  A 1    CE2 <-> 1295 PRO   ( 111-)  A 1    CG     0.42    2.78
 243 TYR   ( 109-)  A      CE2 <->  245 PRO   ( 111-)  A      CG     0.42    2.78
  93 TYR   ( 109-)  A      CE2 <->   95 PRO   ( 111-)  A      CG     0.41    2.79
  18 TYR   ( 109-)  A      CE2 <->   20 PRO   ( 111-)  A      CG     0.41    2.79
 768 TYR   ( 109-)  A 1    CE2 <->  770 PRO   ( 111-)  A 1    CG     0.41    2.79
 393 TYR   ( 109-)  A      CE2 <->  395 PRO   ( 111-)  A      CG     0.41    2.79
1968 TYR   ( 109-)  A 2    CE2 <-> 1970 PRO   ( 111-)  A 2    CG     0.41    2.79
 618 TYR   ( 109-)  A      CE2 <->  620 PRO   ( 111-)  A      CG     0.41    2.79
1068 TYR   ( 109-)  A 1    CE2 <-> 1070 PRO   ( 111-)  A 1    CG     0.41    2.79
1518 TYR   ( 109-)  A 2    CE2 <-> 1520 PRO   ( 111-)  A 2    CG     0.41    2.79
 693 TYR   ( 109-)  A 1    CE2 <->  695 PRO   ( 111-)  A 1    CG     0.41    2.79
1143 TYR   ( 109-)  A 1    CE2 <-> 1145 PRO   ( 111-)  A 1    CG     0.40    2.80
 993 TYR   ( 109-)  A 1    CE2 <->  995 PRO   ( 111-)  A 1    CG     0.40    2.80
1443 TYR   ( 109-)  A 2    CE2 <-> 1445 PRO   ( 111-)  A 2    CG     0.40    2.80
1368 TYR   ( 109-)  A 1    CE2 <-> 1370 PRO   ( 111-)  A 1    CG     0.40    2.80
 918 TYR   ( 109-)  A 1    CE2 <->  920 PRO   ( 111-)  A 1    CG     0.40    2.80
 543 TYR   ( 109-)  A      CE2 <->  545 PRO   ( 111-)  A      CG     0.40    2.80
1893 TYR   ( 109-)  A 2    CE2 <-> 1895 PRO   ( 111-)  A 2    CG     0.39    2.81
And so on for a total of 2184 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 21

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 22

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 23

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 24

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 25

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 26

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 27

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

Note: Quality value plot

Chain identifier: A; Model number 21

Note: Quality value plot

Chain identifier: A; Model number 22

Note: Quality value plot

Chain identifier: A; Model number 23

Note: Quality value plot

Chain identifier: A; Model number 24

Note: Quality value plot

Chain identifier: A; Model number 25

Note: Quality value plot

Chain identifier: A; Model number 26

Note: Quality value plot

Chain identifier: A; Model number 27

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

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 21

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 22

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 23

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 24

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 25

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 26

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 27

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