WHAT IF Check report

This file was created 2011-12-29 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1j6y.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 HIS   (   1-)  A    Zero
   2 MET   (   2-)  A    Zero
   3 ALA   (   3-)  A    Zero
   4 SER   (   4-)  A    Zero
   5 ARG   (   5-)  A    Zero
   6 ASP   (   6-)  A    Zero
   7 GLN   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 LYS   (   9-)  A    Zero
  10 ALA   (  10-)  A    Zero
  11 SER   (  11-)  A    Zero
  12 HIS   (  12-)  A    Zero
  13 ILE   (  13-)  A    Zero
  14 LEU   (  14-)  A    Zero
  15 ILE   (  15-)  A    Zero
  16 LYS   (  16-)  A    Zero
  17 HIS   (  17-)  A    Zero
  18 GLN   (  18-)  A    Zero
  19 GLY   (  19-)  A    Zero
  20 SER   (  20-)  A    Zero
  21 ARG   (  21-)  A    Zero
  22 ARG   (  22-)  A    Zero
  23 LYS   (  23-)  A    Zero
  24 ALA   (  24-)  A    Zero
  25 SER   (  25-)  A    Zero
And so on for a total of 2400 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 : 0.992
Model 2 : 0.988
Model 3 : 0.986
Model 4 : 0.991
Model 5 : 0.983
Model 6 : 0.987
Model 7 : 0.985
Model 8 : 0.989
Model 9 : 0.988
Model 10 : 0.988
Model 11 : 0.984
Model 12 : 0.986
Model 13 : 0.984
Model 14 : 0.990
Model 15 : 0.994
Model 16 : 0.986
Model 17 : 0.985
Model 18 : 0.992
Model 19 : 0.984
Model 20 : 0.986

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.

   1 HIS   (   1-)  A      CA   CB   CG  109.53   -4.3
  12 HIS   (  12-)  A      CA   CB   CG  109.68   -4.1
  58 ALA   (  58-)  A      N    CA   CB  104.16   -4.2
  64 ALA   (  64-)  A      N    CA   CB  104.29   -4.1
  87 MET   (  87-)  A      N    CA   CB  103.59   -4.1
  91 PHE   (  91-)  A      CA   CB   CG  108.28   -5.5
 121 HIS   (   1-)  A      CA   CB   CG  109.46   -4.3
 178 ALA   (  58-)  A      N    CA   CB  104.14   -4.2
 180 PHE   (  60-)  A      CA   CB   CG  109.41   -4.4
 211 PHE   (  91-)  A      CA   CB   CG  109.09   -4.7
 241 HIS   (   1-)  A      CA   CB   CG  109.45   -4.3
 252 HIS   (  12-)  A      CA   CB   CG  109.32   -4.5
 298 ALA   (  58-)  A      N    CA   CB  103.96   -4.3
 300 PHE   (  60-)  A      CA   CB   CG  109.75   -4.1
 322 PHE   (  82-)  A      CA   CB   CG  109.68   -4.1
 327 MET   (  87-)  A      N    CA   CB  103.57   -4.1
 331 PHE   (  91-)  A      CA   CB   CG  109.05   -4.7
 361 HIS   (   1-)  A      CA   CB   CG  109.49   -4.3
 401 ALA   (  41-)  A      N    CA   CB  104.31   -4.1
 411 GLU   (  51-)  A      N    CA   CB  103.34   -4.2
 417 LYS   (  57-)  A      N    CA   CB  102.00   -5.0
 418 ALA   (  58-)  A      N    CA   CB  104.02   -4.3
 420 PHE   (  60-)  A      CA   CB   CG  109.42   -4.4
 428 SER   (  68-)  A      N    CA   CB  103.61   -4.1
 442 PHE   (  82-)  A      CA   CB   CG  109.49   -4.3
And so on for a total of 142 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.385
Model 2 : 1.390
Model 3 : 1.399
Model 4 : 1.402
Model 5 : 1.401
Model 6 : 1.403
Model 7 : 1.398
Model 8 : 1.403
Model 9 : 1.399
Model 10 : 1.386
Model 11 : 1.395
Model 12 : 1.394
Model 13 : 1.402
Model 14 : 1.401
Model 15 : 1.401
Model 16 : 1.395
Model 17 : 1.399
Model 18 : 1.396
Model 19 : 1.393
Model 20 : 1.396

Note: Per-model averages for chirality check

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

Model 1 : 1.460
Model 2 : 1.459
Model 3 : 1.438
Model 4 : 1.448
Model 5 : 1.471
Model 6 : 1.453
Model 7 : 1.450
Model 8 : 1.463
Model 9 : 1.453
Model 10 : 1.443
Model 11 : 1.463
Model 12 : 1.463
Model 13 : 1.465
Model 14 : 1.449
Model 15 : 1.461
Model 16 : 1.455
Model 17 : 1.453
Model 18 : 1.464
Model 19 : 1.455
Model 20 : 1.461

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.

1805 ARG   (   5-)  A 1   8.61
 245 ARG   (   5-)  A    8.61
 485 ARG   (   5-)  A    8.60
 965 ARG   (   5-)  A    8.51
1730 ARG   (  50-)  A 1   8.50
1506 ARG   (  66-)  A 1   8.50
 382 ARG   (  22-)  A    8.48
1026 ARG   (  66-)  A    8.48
1386 ARG   (  66-)  A 1   8.44
2398 ARG   ( 118-)  A 2   8.42
1130 ARG   (  50-)  A 1   8.39
 381 ARG   (  21-)  A    8.37
2165 ARG   (   5-)  A 1   8.36
1438 ARG   ( 118-)  A 1   8.34
1685 ARG   (   5-)  A 1   8.28
 519 ARG   (  39-)  A    8.23
 324 ARG   (  84-)  A    8.21
1325 ARG   (   5-)  A 1   8.20
1959 ARG   (  39-)  A 1   8.16
1341 ARG   (  21-)  A 1   8.12
1035 ARG   (  75-)  A    8.09
   5 ARG   (   5-)  A    8.09
 684 ARG   (  84-)  A    8.05
1746 ARG   (  66-)  A 1   8.03
1198 ARG   ( 118-)  A 1   8.03
And so on for a total of 151 lines.

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 : -8.196

Note: Per-model averages for Ramachandran check

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

Model 1 : -7.421
Model 2 : -8.482
Model 3 : -7.197
Model 4 : -7.704
Model 5 : -7.973
Model 6 : -7.847
Model 7 : -8.384
Model 8 : -8.552
Model 9 : -8.425
Model 10 : -8.275
Model 11 : -7.922
Model 12 : -8.260
Model 13 : -8.729
Model 14 : -7.998
Model 15 : -8.753
Model 16 : -8.756
Model 17 : -7.843
Model 18 : -8.110
Model 19 : -8.603
Model 20 : -8.687

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.

1836 THR   (  36-)  A 1   -3.7
 479 THR   ( 119-)  A    -3.7
1079 THR   ( 119-)  A    -3.6
 469 THR   ( 109-)  A    -3.5
 349 THR   ( 109-)  A    -3.5
 109 THR   ( 109-)  A    -3.4
1069 THR   ( 109-)  A    -3.4
1559 THR   ( 119-)  A 1   -3.4
  36 THR   (  36-)  A    -3.3
1117 THR   (  37-)  A 1   -3.3
1429 THR   ( 109-)  A 1   -3.3
1309 THR   ( 109-)  A 1   -3.2
1937 HIS   (  17-)  A 1   -3.2
1217 HIS   (  17-)  A 1   -3.2
1716 THR   (  36-)  A 1   -3.2
 737 HIS   (  17-)  A    -3.2
2316 THR   (  36-)  A 2   -3.2
 617 HIS   (  17-)  A    -3.2
2297 HIS   (  17-)  A 2   -3.2
1817 HIS   (  17-)  A 1   -3.1
 377 HIS   (  17-)  A    -3.1
1189 THR   ( 109-)  A 1   -3.1
 497 HIS   (  17-)  A    -3.1
1457 HIS   (  17-)  A 1   -3.1
1097 HIS   (  17-)  A 1   -3.1
And so on for a total of 631 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 MET   (   2-)  A  Poor phi/psi
   4 SER   (   4-)  A  Poor phi/psi
   6 ASP   (   6-)  A  Poor phi/psi
  10 ALA   (  10-)  A  Poor phi/psi
  12 HIS   (  12-)  A  Poor phi/psi
  21 ARG   (  21-)  A  Poor phi/psi
  22 ARG   (  22-)  A  Poor phi/psi
  24 ALA   (  24-)  A  Poor phi/psi
  31 GLY   (  31-)  A  Poor phi/psi
  36 THR   (  36-)  A  Poor phi/psi
  39 ARG   (  39-)  A  Poor phi/psi
  57 LYS   (  57-)  A  Poor phi/psi
  58 ALA   (  58-)  A  Poor phi/psi
  59 ASN   (  59-)  A  Poor phi/psi
  61 GLU   (  61-)  A  Poor phi/psi
  67 VAL   (  67-)  A  Poor phi/psi
  86 GLN   (  86-)  A  Poor phi/psi
  87 MET   (  87-)  A  Poor phi/psi
  88 GLN   (  88-)  A  Poor phi/psi
  90 PRO   (  90-)  A  Poor phi/psi
 100 VAL   ( 100-)  A  Poor phi/psi
 103 ILE   ( 103-)  A  Poor phi/psi
 104 SER   ( 104-)  A  Poor phi/psi
 106 ILE   ( 106-)  A  Poor phi/psi
 109 THR   ( 109-)  A  Poor phi/psi
And so on for a total of 550 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 : -7.749

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 : -8.036
Model 2 : -7.416
Model 3 : -7.422
Model 4 : -7.809
Model 5 : -7.965
Model 6 : -7.694
Model 7 : -7.725
Model 8 : -7.895
Model 9 : -7.916
Model 10 : -8.023
Model 11 : -8.218
Model 12 : -7.960
Model 13 : -7.585
Model 14 : -7.912
Model 15 : -7.860
Model 16 : -7.221
Model 17 : -7.227
Model 18 : -7.962
Model 19 : -7.725
Model 20 : -7.410

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.

1631 SER   (  71-)  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 ALA   (   3-)  A      0
   5 ARG   (   5-)  A      0
   6 ASP   (   6-)  A      0
   7 GLN   (   7-)  A      0
  11 SER   (  11-)  A      0
  12 HIS   (  12-)  A      0
  16 LYS   (  16-)  A      0
  17 HIS   (  17-)  A      0
  18 GLN   (  18-)  A      0
  20 SER   (  20-)  A      0
  21 ARG   (  21-)  A      0
  22 ARG   (  22-)  A      0
  23 LYS   (  23-)  A      0
  24 ALA   (  24-)  A      0
  25 SER   (  25-)  A      0
  26 TRP   (  26-)  A      0
  27 LYS   (  27-)  A      0
  30 GLU   (  30-)  A      0
  32 LYS   (  32-)  A      0
  35 LEU   (  35-)  A      0
  36 THR   (  36-)  A      0
  37 THR   (  37-)  A      0
  39 ARG   (  39-)  A      0
  54 VAL   (  54-)  A      0
  55 SER   (  55-)  A      0
And so on for a total of 1434 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 : -2.254

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 : 0.770

Note: Per-model averages for omega angle check

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

Model 1 : 0.800
Model 2 : 0.733
Model 3 : 0.704
Model 4 : 0.759
Model 5 : 0.844
Model 6 : 0.729
Model 7 : 0.809
Model 8 : 0.736
Model 9 : 0.724
Model 10 : 0.703
Model 11 : 0.620
Model 12 : 0.721
Model 13 : 0.652
Model 14 : 0.817
Model 15 : 0.865
Model 16 : 0.675
Model 17 : 0.705
Model 18 : 0.694
Model 19 : 0.746
Model 20 : 0.763

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!

 739 GLY   (  19-)  A   2.76   11
1831 GLY   (  31-)  A 1  2.73   15
1880 GLY   (  80-)  A 1  2.33   18
 200 GLY   (  80-)  A   2.30   20
1520 GLY   (  80-)  A 1  2.29   16
 920 GLY   (  80-)  A   2.28   20
1760 GLY   (  80-)  A 1  2.27   20
 320 GLY   (  80-)  A   2.27   13
2000 GLY   (  80-)  A 1  2.24   12
1280 GLY   (  80-)  A 1  2.23   15
1160 GLY   (  80-)  A 1  2.22   15
2059 GLY   (  19-)  A 1  2.22   14
  80 GLY   (  80-)  A   2.20   20
 800 GLY   (  80-)  A   2.20   19
2240 GLY   (  80-)  A 1  2.19   15
 680 GLY   (  80-)  A   2.15   13
2120 GLY   (  80-)  A 1  2.14   18
2360 GLY   (  80-)  A 2  2.13   13
1400 GLY   (  80-)  A 1  2.08   12
2191 GLY   (  31-)  A 1  1.98   20
 859 GLY   (  19-)  A   1.94   11
1219 GLY   (  19-)  A 1  1.92   10
1699 GLY   (  19-)  A 1  1.75   17
1819 GLY   (  19-)  A 1  1.75   12
2311 GLY   (  31-)  A 2  1.70   44
2141 GLY   ( 101-)  A 1  1.56   14

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.

1889 LYS   (  89-)  A 1    N   <-> 1890 PRO   (  90-)  A 1    CD     0.45    2.55
1169 LYS   (  89-)  A 1    N   <-> 1170 PRO   (  90-)  A 1    CD     0.45    2.55
 734 LEU   (  14-)  A      CD1 <->  834 HIS   ( 114-)  A      NE2    0.45    2.65
1409 LYS   (  89-)  A 1    N   <-> 1410 PRO   (  90-)  A 1    CD     0.44    2.56
1759 LEU   (  79-)  A 1    CD2 <-> 1767 MET   (  87-)  A 1    SD     0.44    2.96
 929 LYS   (  89-)  A      N   <->  930 PRO   (  90-)  A      CD     0.44    2.56
1402 PHE   (  82-)  A 1    CE2 <-> 1407 MET   (  87-)  A 1    SD     0.44    2.96
 374 LEU   (  14-)  A      CD1 <->  474 HIS   ( 114-)  A      NE2    0.43    2.67
 734 LEU   (  14-)  A      CD2 <->  789 ASP   (  69-)  A      CB     0.43    2.77
1049 LYS   (  89-)  A      N   <-> 1050 PRO   (  90-)  A      CD     0.43    2.57
 211 PHE   (  91-)  A      CE2 <->  236 ILE   ( 116-)  A      CD1    0.43    2.77
 809 LYS   (  89-)  A      N   <->  810 PRO   (  90-)  A      CD     0.43    2.57
  11 SER   (  11-)  A      CB  <->   78 ASP   (  78-)  A      CB     0.42    2.78
1767 MET   (  87-)  A 1    SD  <-> 1771 PHE   (  91-)  A 1    CE1    0.42    2.98
1282 PHE   (  82-)  A 1    CE2 <-> 1287 MET   (  87-)  A 1    SD     0.42    2.98
2051 SER   (  11-)  A 1    CB  <-> 2118 ASP   (  78-)  A 1    CB     0.41    2.79
 689 LYS   (  89-)  A      N   <->  690 PRO   (  90-)  A      CD     0.41    2.59
1811 SER   (  11-)  A 1    CB  <-> 1878 ASP   (  78-)  A 1    CB     0.41    2.79
 130 ALA   (  10-)  A      CB  <->  215 THR   (  95-)  A      CG2    0.41    2.79
2174 LEU   (  14-)  A 1    CD1 <-> 2274 HIS   ( 114-)  A 1    CE1    0.41    2.79
1694 LEU   (  14-)  A 1    CD1 <-> 1794 HIS   ( 114-)  A 1    CE1    0.41    2.79
2129 LYS   (  89-)  A 1    N   <-> 2130 PRO   (  90-)  A 1    CD     0.41    2.59
 734 LEU   (  14-)  A      CD1 <->  834 HIS   ( 114-)  A      CE1    0.41    2.79
2362 PHE   (  82-)  A 2    CE2 <-> 2367 MET   (  87-)  A 2    SD     0.41    2.99
 851 SER   (  11-)  A      CB  <->  918 ASP   (  78-)  A      CB     0.41    2.79
And so on for a total of 2533 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

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


Warning: Abnormal packing Z-score for sequential 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