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 pdb1zbj.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 VAL   (   1-)  A    Zero
   2 THR   (   2-)  A    Zero
   3 LEU   (   3-)  A    Zero
   4 PHE   (   4-)  A    Zero
   5 VAL   (   5-)  A    Zero
   6 ALA   (   6-)  A    Zero
   7 LEU   (   7-)  A    Zero
   8 TYR   (   8-)  A    Zero
   9 ASP   (   9-)  A    Zero
  10 TYR   (  10-)  A    Zero
  11 GLU   (  11-)  A    Zero
  12 ALA   (  12-)  A    Zero
  13 ARG   (  13-)  A    Zero
  14 THR   (  14-)  A    Zero
  15 GLU   (  15-)  A    Zero
  16 ASP   (  16-)  A    Zero
  17 ASP   (  17-)  A    Zero
  18 LEU   (  18-)  A    Zero
  19 SER   (  19-)  A    Zero
  20 PHE   (  20-)  A    Zero
  21 HIS   (  21-)  A    Zero
  22 LYS   (  22-)  A    Zero
  23 GLY   (  23-)  A    Zero
  24 GLU   (  24-)  A    Zero
  25 LYS   (  25-)  A    Zero
And so on for a total of 1180 lines.

Nomenclature related problems

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  17 ASP   (  17-)  A
  35 ASP   (  35-)  A
  59 ASP   (  59-)  A
  76 ASP   (  17-)  A
 153 ASP   (  35-)  A
 194 ASP   (  17-)  A
 212 ASP   (  35-)  A
 236 ASP   (  59-)  A
 245 ASP   (   9-)  A
 253 ASP   (  17-)  A
 304 ASP   (   9-)  A
 311 ASP   (  16-)  A
 330 ASP   (  35-)  A
 354 ASP   (  59-)  A
 389 ASP   (  35-)  A
 413 ASP   (  59-)  A
 429 ASP   (  16-)  A
 430 ASP   (  17-)  A
 488 ASP   (  16-)  A
 489 ASP   (  17-)  A
 531 ASP   (  59-)  A
 540 ASP   (   9-)  A 1
 566 ASP   (  35-)  A 1
 590 ASP   (  59-)  A 1
 599 ASP   (   9-)  A 1
 649 ASP   (  59-)  A 1
 658 ASP   (   9-)  A 1
 666 ASP   (  17-)  A 1
 743 ASP   (  35-)  A 1
 767 ASP   (  59-)  A 1
 826 ASP   (  59-)  A 1
 835 ASP   (   9-)  A 1
 861 ASP   (  35-)  A 1
 885 ASP   (  59-)  A 1
 901 ASP   (  16-)  A 1
1012 ASP   (   9-)  A 1
1038 ASP   (  35-)  A 1
1062 ASP   (  59-)  A 1
1071 ASP   (   9-)  A 1
1121 ASP   (  59-)  A 1
1138 ASP   (  17-)  A 2

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  11 GLU   (  11-)  A
  24 GLU   (  24-)  A
  74 GLU   (  15-)  A
  83 GLU   (  24-)  A
 129 GLU   (  11-)  A
 156 GLU   (  38-)  A
 164 GLU   (  46-)  A
 210 GLU   (  33-)  A
 260 GLU   (  24-)  A
 269 GLU   (  33-)  A
 306 GLU   (  11-)  A
 310 GLU   (  15-)  A
 328 GLU   (  33-)  A
 387 GLU   (  33-)  A
 392 GLU   (  38-)  A
 400 GLU   (  46-)  A
 424 GLU   (  11-)  A
 428 GLU   (  15-)  A
 451 GLU   (  38-)  A
 483 GLU   (  11-)  A
 487 GLU   (  15-)  A
 510 GLU   (  38-)  A
 542 GLU   (  11-)  A 1
 577 GLU   (  46-)  A 1
 605 GLU   (  15-)  A 1
 614 GLU   (  24-)  A 1
 636 GLU   (  46-)  A 1
 695 GLU   (  46-)  A 1
 741 GLU   (  33-)  A 1
 754 GLU   (  46-)  A 1
 791 GLU   (  24-)  A 1
 837 GLU   (  11-)  A 1
 864 GLU   (  38-)  A 1
 900 GLU   (  15-)  A 1
 923 GLU   (  38-)  A 1
 955 GLU   (  11-)  A 1
1027 GLU   (  24-)  A 1
1036 GLU   (  33-)  A 1
1041 GLU   (  38-)  A 1
1049 GLU   (  46-)  A 1
1073 GLU   (  11-)  A 1
1132 GLU   (  11-)  A 2
1154 GLU   (  33-)  A 2
1159 GLU   (  38-)  A 2

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.637
Model 2 : 0.637
Model 3 : 0.638
Model 4 : 0.637
Model 5 : 0.636
Model 6 : 0.637
Model 7 : 0.637
Model 8 : 0.636
Model 9 : 0.637
Model 10 : 0.635
Model 11 : 0.636
Model 12 : 0.636
Model 13 : 0.638
Model 14 : 0.635
Model 15 : 0.637
Model 16 : 0.635
Model 17 : 0.632
Model 18 : 0.638
Model 19 : 0.636
Model 20 : 0.634

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.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.983
Model 2 : 0.982
Model 3 : 0.985
Model 4 : 0.985
Model 5 : 0.984
Model 6 : 0.984
Model 7 : 0.984
Model 8 : 0.984
Model 9 : 0.985
Model 10 : 0.983
Model 11 : 0.983
Model 12 : 0.982
Model 13 : 0.984
Model 14 : 0.983
Model 15 : 0.985
Model 16 : 0.983
Model 17 : 0.982
Model 18 : 0.983
Model 19 : 0.983
Model 20 : 0.982

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  11 GLU   (  11-)  A
  17 ASP   (  17-)  A
  24 GLU   (  24-)  A
  35 ASP   (  35-)  A
  59 ASP   (  59-)  A
  74 GLU   (  15-)  A
  76 ASP   (  17-)  A
  83 GLU   (  24-)  A
 129 GLU   (  11-)  A
 153 ASP   (  35-)  A
 156 GLU   (  38-)  A
 164 GLU   (  46-)  A
 194 ASP   (  17-)  A
 210 GLU   (  33-)  A
 212 ASP   (  35-)  A
 236 ASP   (  59-)  A
 245 ASP   (   9-)  A
 253 ASP   (  17-)  A
 260 GLU   (  24-)  A
 269 GLU   (  33-)  A
 304 ASP   (   9-)  A
 306 GLU   (  11-)  A
 310 GLU   (  15-)  A
 311 ASP   (  16-)  A
 328 GLU   (  33-)  A
And so on for a total of 85 lines.

Note: Per-model averages for chirality check

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

Model 1 : 0.756
Model 2 : 0.747
Model 3 : 0.751
Model 4 : 0.761
Model 5 : 0.770
Model 6 : 0.733
Model 7 : 0.763
Model 8 : 0.807
Model 9 : 0.725
Model 10 : 0.735
Model 11 : 0.734
Model 12 : 0.764
Model 13 : 0.770
Model 14 : 0.756
Model 15 : 0.765
Model 16 : 0.753
Model 17 : 0.738
Model 18 : 0.755
Model 19 : 0.754
Model 20 : 0.735

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 : -5.667

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.844
Model 2 : -6.470
Model 3 : -6.107
Model 4 : -6.171
Model 5 : -5.477
Model 6 : -6.320
Model 7 : -5.616
Model 8 : -5.798
Model 9 : -6.240
Model 10 : -4.992
Model 11 : -5.679
Model 12 : -5.687
Model 13 : -5.746
Model 14 : -5.054
Model 15 : -5.991
Model 16 : -5.056
Model 17 : -5.437
Model 18 : -5.876
Model 19 : -6.112
Model 20 : -4.678

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.

   8 TYR   (   8-)  A    -3.2
 470 PRO   (  57-)  A    -3.0
 234 PRO   (  57-)  A    -2.9
  50 ILE   (  50-)  A    -2.9
  51 PRO   (  51-)  A    -2.9
 190 ARG   (  13-)  A    -2.8
 147 LEU   (  29-)  A    -2.8
 522 ILE   (  50-)  A    -2.8
 883 PRO   (  57-)  A 1   -2.8
 131 ARG   (  13-)  A    -2.8
 206 LEU   (  29-)  A    -2.8
 324 LEU   (  29-)  A    -2.8
1032 LEU   (  29-)  A 1   -2.8
 560 LEU   (  29-)  A 1   -2.8
 592 THR   (   2-)  A 1   -2.7
 302 LEU   (   7-)  A    -2.7
 456 THR   (  43-)  A    -2.7
 993 TYR   (  49-)  A 1   -2.7
1106 THR   (  44-)  A 1   -2.7
 220 THR   (  43-)  A    -2.7
1150 LEU   (  29-)  A 2   -2.7
 935 ILE   (  50-)  A 1   -2.7
  14 THR   (  14-)  A    -2.7
1139 LEU   (  18-)  A 2   -2.6
 286 ILE   (  50-)  A    -2.6
And so on for a total of 314 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.

  35 ASP   (  35-)  A  Poor phi/psi
  43 THR   (  43-)  A  Poor phi/psi
  88 LEU   (  29-)  A  Poor phi/psi
  91 SER   (  32-)  A  Poor phi/psi
  92 GLU   (  33-)  A  Poor phi/psi
  94 ASP   (  35-)  A  Poor phi/psi
 102 THR   (  43-)  A  Poor phi/psi
 138 PHE   (  20-)  A  Poor phi/psi
 147 LEU   (  29-)  A  Poor phi/psi
 151 GLU   (  33-)  A  Poor phi/psi
 158 ARG   (  40-)  A  Poor phi/psi
 179 THR   (   2-)  A  Poor phi/psi
 189 ALA   (  12-)  A  Poor phi/psi
 190 ARG   (  13-)  A  Poor phi/psi
 195 LEU   (  18-)  A  Poor phi/psi
 201 GLU   (  24-)  A  Poor phi/psi
 210 GLU   (  33-)  A  Poor phi/psi
 268 SER   (  32-)  A  Poor phi/psi
 269 GLU   (  33-)  A  Poor phi/psi
 271 ASP   (  35-)  A  Poor phi/psi
 294 VAL   (  58-)  A  Poor phi/psi
 299 PHE   (   4-)  A  Poor phi/psi
 313 LEU   (  18-)  A  Poor phi/psi
 319 GLU   (  24-)  A  Poor phi/psi
 327 SER   (  32-)  A  Poor phi/psi
And so on for a total of 81 lines.

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

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

chi-1/chi-2 correlation Z-score : -7.668

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

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

Model 1 : -7.807
Model 2 : -8.032
Model 3 : -7.893
Model 4 : -7.648
Model 5 : -7.463
Model 6 : -8.099
Model 7 : -8.067
Model 8 : -7.192
Model 9 : -8.449
Model 10 : -7.468
Model 11 : -7.287
Model 12 : -8.208
Model 13 : -7.787
Model 14 : -6.301
Model 15 : -7.604
Model 16 : -7.657
Model 17 : -7.339
Model 18 : -8.065
Model 19 : -7.924
Model 20 : -7.060

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!

   8 TYR   (   8-)  A      0
   9 ASP   (   9-)  A      0
  17 ASP   (  17-)  A      0
  22 LYS   (  22-)  A      0
  24 GLU   (  24-)  A      0
  28 ILE   (  28-)  A      0
  29 LEU   (  29-)  A      0
  30 ASN   (  30-)  A      0
  31 SER   (  31-)  A      0
  32 SER   (  32-)  A      0
  33 GLU   (  33-)  A      0
  35 ASP   (  35-)  A      0
  36 TRP   (  36-)  A      0
  42 LEU   (  42-)  A      0
  43 THR   (  43-)  A      0
  44 THR   (  44-)  A      0
  49 TYR   (  49-)  A      0
  50 ILE   (  50-)  A      0
  52 SER   (  52-)  A      0
  53 ASN   (  53-)  A      0
  55 VAL   (  55-)  A      0
  58 VAL   (  58-)  A      0
  59 ASP   (  59-)  A      0
  60 VAL   (   1-)  A      0
  61 THR   (   2-)  A      0
And so on for a total of 731 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.000

Note: Per-model averages for omega angle check

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

Model 1 : 0.000
Model 2 : 0.000
Model 3 : 0.056
Model 4 : 0.031
Model 5 : 0.000
Model 6 : 0.110
Model 7 : 0.096
Model 8 : 0.097
Model 9 : 0.000
Model 10 : 0.069
Model 11 : 0.083
Model 12 : 0.000
Model 13 : 0.091
Model 14 : 0.000
Model 15 : 0.000
Model 16 : 0.081
Model 17 : 0.039
Model 18 : 0.048
Model 19 : 0.077
Model 20 : 0.000

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!

 211 GLY   (  34-)  A   2.47   26
1026 GLY   (  23-)  A 1  1.79   80
 672 GLY   (  23-)  A 1  1.77   11
1166 GLY   (  45-)  A 2  1.57   21
 200 GLY   (  23-)  A   1.54   15

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]

  51 PRO   (  51-)  A    0.18 LOW
  57 PRO   (  57-)  A    0.18 LOW
 110 PRO   (  51-)  A    0.18 LOW
 116 PRO   (  57-)  A    0.18 LOW
 169 PRO   (  51-)  A    0.18 LOW
 175 PRO   (  57-)  A    0.18 LOW
 228 PRO   (  51-)  A    0.18 LOW
 234 PRO   (  57-)  A    0.18 LOW
 287 PRO   (  51-)  A    0.18 LOW
 293 PRO   (  57-)  A    0.18 LOW
 346 PRO   (  51-)  A    0.18 LOW
 352 PRO   (  57-)  A    0.18 LOW
 405 PRO   (  51-)  A    0.18 LOW
 411 PRO   (  57-)  A    0.18 LOW
 464 PRO   (  51-)  A    0.18 LOW
 470 PRO   (  57-)  A    0.18 LOW
 523 PRO   (  51-)  A    0.18 LOW
 529 PRO   (  57-)  A    0.18 LOW
 582 PRO   (  51-)  A 1   0.18 LOW
 588 PRO   (  57-)  A 1   0.18 LOW
 641 PRO   (  51-)  A 1   0.18 LOW
 647 PRO   (  57-)  A 1   0.18 LOW
 700 PRO   (  51-)  A 1   0.18 LOW
 706 PRO   (  57-)  A 1   0.18 LOW
 759 PRO   (  51-)  A 1   0.18 LOW
 765 PRO   (  57-)  A 1   0.18 LOW
 818 PRO   (  51-)  A 1   0.18 LOW
 824 PRO   (  57-)  A 1   0.18 LOW
 877 PRO   (  51-)  A 1   0.18 LOW
 883 PRO   (  57-)  A 1   0.18 LOW
 936 PRO   (  51-)  A 1   0.18 LOW
 942 PRO   (  57-)  A 1   0.18 LOW
 995 PRO   (  51-)  A 1   0.18 LOW
1001 PRO   (  57-)  A 1   0.18 LOW
1054 PRO   (  51-)  A 1   0.18 LOW
1060 PRO   (  57-)  A 1   0.18 LOW
1113 PRO   (  51-)  A 1   0.18 LOW
1119 PRO   (  57-)  A 1   0.18 LOW
1172 PRO   (  51-)  A 2   0.18 LOW
1178 PRO   (  57-)  A 2   0.18 LOW

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.

 389 ASP   (  35-)  A      CB  <->  390 TRP   (  36-)  A      N      0.09    2.61        B3
  35 ASP   (  35-)  A      CB  <->   36 TRP   (  36-)  A      N      0.08    2.62        B3
1036 GLU   (  33-)  A 1    CB  <-> 1037 GLY   (  34-)  A 1    N      0.05    2.65        B3
 268 SER   (  32-)  A      CB  <->  269 GLU   (  33-)  A      N      0.05    2.65        B3
 856 ASN   (  30-)  A 1    O   <->  863 TRP   (  37-)  A 1    NE1    0.05    2.65
 681 SER   (  32-)  A 1    CB  <->  682 GLU   (  33-)  A 1    N      0.05    2.65        B3
 363 ASP   (   9-)  A      OD1 <->  376 LYS   (  22-)  A      NZ     0.04    2.66
 661 ALA   (  12-)  A 1    N   <->  668 SER   (  19-)  A 1    OG     0.03    2.67
 271 ASP   (  35-)  A      CB  <->  272 TRP   (  36-)  A      N      0.03    2.67        B3
 407 ASN   (  53-)  A      N   <->  408 TYR   (  54-)  A      N      0.02    2.58        B3
1115 ASN   (  53-)  A 1    N   <-> 1116 TYR   (  54-)  A 1    N      0.02    2.58        B3
 348 ASN   (  53-)  A      N   <->  349 TYR   (  54-)  A      N      0.02    2.58        B3
 938 ASN   (  53-)  A 1    N   <->  939 TYR   (  54-)  A 1    N      0.02    2.58        B3
1156 ASP   (  35-)  A 2    N   <-> 1157 TRP   (  36-)  A 2    N      0.02    2.58        B3
1163 LEU   (  42-)  A 2    N   <-> 1164 THR   (  43-)  A 2    N      0.02    2.58        B3
 986 LEU   (  42-)  A 1    N   <->  987 THR   (  43-)  A 1    N      0.02    2.58        B3
1174 ASN   (  53-)  A 2    N   <-> 1175 TYR   (  54-)  A 2    N      0.02    2.58        B3
 178 VAL   (   1-)  A      N   <->  235 VAL   (  58-)  A      O      0.02    2.68
 466 ASN   (  53-)  A      N   <->  467 TYR   (  54-)  A      N      0.02    2.58        B3
 178 VAL   (   1-)  A      N   <->  179 THR   (   2-)  A      N      0.02    2.58        B3
1056 ASN   (  53-)  A 1    N   <-> 1057 TYR   (  54-)  A 1    N      0.02    2.58        B3
 809 LEU   (  42-)  A 1    N   <->  810 THR   (  43-)  A 1    N      0.02    2.58        B3
 702 ASN   (  53-)  A 1    N   <->  703 TYR   (  54-)  A 1    N      0.02    2.58        B3
 709 VAL   (   1-)  A 1    N   <->  710 THR   (   2-)  A 1    N      0.02    2.58        B3
 219 LEU   (  42-)  A      N   <->  220 THR   (  43-)  A      N      0.02    2.58        B3
 997 ASN   (  53-)  A 1    N   <->  998 TYR   (  54-)  A 1    N      0.02    2.58        B3
 289 ASN   (  53-)  A      N   <->  290 TYR   (  54-)  A      N      0.02    2.58        B3
1104 LEU   (  42-)  A 1    N   <-> 1105 THR   (  43-)  A 1    N      0.02    2.58        B3
 101 LEU   (  42-)  A      N   <->  102 THR   (  43-)  A      N      0.02    2.58        B3
 927 LEU   (  42-)  A 1    N   <->  928 THR   (  43-)  A 1    N      0.02    2.58        B3
 820 ASN   (  53-)  A 1    N   <->  821 TYR   (  54-)  A 1    N      0.02    2.58        B3
 861 ASP   (  35-)  A 1    CB  <->  862 TRP   (  36-)  A 1    N      0.02    2.68        B3
 455 LEU   (  42-)  A      N   <->  456 THR   (  43-)  A      N      0.02    2.58        B3
 573 LEU   (  42-)  A 1    N   <->  574 THR   (  43-)  A 1    N      0.02    2.58        B3
  53 ASN   (  53-)  A      N   <->   54 TYR   (  54-)  A      N      0.02    2.58        B3
 396 LEU   (  42-)  A      N   <->  397 THR   (  43-)  A      N      0.02    2.58        B3
 160 LEU   (  42-)  A      N   <->  161 THR   (  43-)  A      N      0.01    2.59        B3
 184 LEU   (   7-)  A      N   <->  185 TYR   (   8-)  A      N      0.01    2.59        B3
 514 LEU   (  42-)  A      N   <->  515 THR   (  43-)  A      N      0.01    2.59        B3
 337 LEU   (  42-)  A      N   <->  338 THR   (  43-)  A      N      0.01    2.59        B3
  66 LEU   (   7-)  A      N   <->   67 TYR   (   8-)  A      N      0.01    2.59        B3
 525 ASN   (  53-)  A      N   <->  526 TYR   (  54-)  A      N      0.01    2.59        B3
 663 THR   (  14-)  A 1    CG2 <->  664 GLU   (  15-)  A 1    N      0.01    2.99
 643 ASN   (  53-)  A 1    N   <->  644 TYR   (  54-)  A 1    N      0.01    2.59        B3
 774 LEU   (   7-)  A 1    N   <->  775 TYR   (   8-)  A 1    N      0.01    2.59        B3
 230 ASN   (  53-)  A      N   <->  231 TYR   (  54-)  A      N      0.01    2.59        B3
1045 LEU   (  42-)  A 1    N   <-> 1046 THR   (  43-)  A 1    N      0.01    2.59        B3
 691 LEU   (  42-)  A 1    N   <->  692 THR   (  43-)  A 1    N      0.01    2.59        B3
 879 ASN   (  53-)  A 1    N   <->  880 TYR   (  54-)  A 1    N      0.01    2.59        B3

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.166

Note: Per-model averages for inside/outside residue distributi ...heck




















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

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