WHAT IF Check report

This file was created 2011-12-28 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 pdb1ffj.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 LEU   (   1-)  A    Zero
   2 LYS   (   2-)  A    Zero
   3 CYS   (   3-)  A    Zero
   4 LYS   (   4-)  A    Zero
   5 LYS   (   5-)  A    Zero
   6 LEU   (   6-)  A    Zero
   7 VAL   (   7-)  A    Zero
   8 PRO   (   8-)  A    Zero
   9 LEU   (   9-)  A    Zero
  10 PHE   (  10-)  A    Zero
  11 SER   (  11-)  A    Zero
  12 LYS   (  12-)  A    Zero
  13 THR   (  13-)  A    Zero
  14 CYS   (  14-)  A    Zero
  15 PRO   (  15-)  A    Zero
  16 ALA   (  16-)  A    Zero
  17 GLY   (  17-)  A    Zero
  18 LYS   (  18-)  A    Zero
  19 ASN   (  19-)  A    Zero
  20 LEU   (  20-)  A    Zero
  21 CYS   (  21-)  A    Zero
  22 TYR   (  22-)  A    Zero
  23 LYS   (  23-)  A    Zero
  24 MET   (  24-)  A    Zero
  25 PHE   (  25-)  A    Zero
And so on for a total of 1200 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.

 100 ASP   (  40-)  A
 340 ASP   (  40-)  A
 400 ASP   (  40-)  A
 640 ASP   (  40-)  A 1
 700 ASP   (  40-)  A 1
 880 ASP   (  40-)  A 1
 940 ASP   (  40-)  A 1
1000 ASP   (  40-)  A 1
1180 ASP   (  40-)  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 : 0.477
Model 2 : 0.483
Model 3 : 0.483
Model 4 : 0.485
Model 5 : 0.496
Model 6 : 0.481
Model 7 : 0.504
Model 8 : 0.514
Model 9 : 0.480
Model 10 : 0.477
Model 11 : 0.507
Model 12 : 0.533
Model 13 : 0.497
Model 14 : 0.493
Model 15 : 0.497
Model 16 : 0.494
Model 17 : 0.479
Model 18 : 0.515
Model 19 : 0.488
Model 20 : 0.487

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 : 0.864
Model 2 : 0.864
Model 3 : 0.863
Model 4 : 0.864
Model 5 : 0.865
Model 6 : 0.863
Model 7 : 0.865
Model 8 : 0.863
Model 9 : 0.865
Model 10 : 0.864
Model 11 : 0.865
Model 12 : 0.864
Model 13 : 0.865
Model 14 : 0.864
Model 15 : 0.864
Model 16 : 0.863
Model 17 : 0.864
Model 18 : 0.863
Model 19 : 0.864
Model 20 : 0.864

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.

 100 ASP   (  40-)  A
 340 ASP   (  40-)  A
 400 ASP   (  40-)  A
 640 ASP   (  40-)  A 1
 700 ASP   (  40-)  A 1
 880 ASP   (  40-)  A 1
 940 ASP   (  40-)  A 1
1000 ASP   (  40-)  A 1
1180 ASP   (  40-)  A 2

Note: Per-model averages for chirality check

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

Model 1 : 0.749
Model 2 : 0.749
Model 3 : 0.750
Model 4 : 0.749
Model 5 : 0.750
Model 6 : 0.751
Model 7 : 0.751
Model 8 : 0.749
Model 9 : 0.751
Model 10 : 0.749
Model 11 : 0.747
Model 12 : 0.750
Model 13 : 0.750
Model 14 : 0.750
Model 15 : 0.750
Model 16 : 0.749
Model 17 : 0.748
Model 18 : 0.749
Model 19 : 0.751
Model 20 : 0.750

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.602

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.803
Model 2 : -3.853
Model 3 : -3.444
Model 4 : -3.247
Model 5 : -3.940
Model 6 : -3.315
Model 7 : -4.967
Model 8 : -3.610
Model 9 : -3.458
Model 10 : -2.532
Model 11 : -2.850
Model 12 : -4.003
Model 13 : -4.314
Model 14 : -3.741
Model 15 : -3.782
Model 16 : -3.556
Model 17 : -3.419
Model 18 : -3.563
Model 19 : -3.274
Model 20 : -3.366

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.

1119 ILE   (  39-)  A 1   -3.0
 699 ILE   (  39-)  A 1   -3.0
 759 ILE   (  39-)  A 1   -3.0
 519 ILE   (  39-)  A    -3.0
  99 ILE   (  39-)  A    -3.0
 459 ILE   (  39-)  A    -3.0
 579 ILE   (  39-)  A 1   -3.0
 879 ILE   (  39-)  A 1   -3.0
 399 ILE   (  39-)  A    -3.0
 219 ILE   (  39-)  A    -3.0
 999 ILE   (  39-)  A 1   -3.0
 639 ILE   (  39-)  A 1   -3.0
  39 ILE   (  39-)  A    -2.9
 819 ILE   (  39-)  A 1   -2.9
1179 ILE   (  39-)  A 2   -2.9
 159 ILE   (  39-)  A    -2.9
 339 ILE   (  39-)  A    -2.9
 939 ILE   (  39-)  A 1   -2.9
 279 ILE   (  39-)  A    -2.8
 178 LYS   (  58-)  A    -2.8
 275 LYS   (  35-)  A    -2.7
 691 HIS   (  31-)  A 1   -2.7
 238 LYS   (  58-)  A    -2.7
 718 LYS   (  58-)  A 1   -2.7
 658 LYS   (  58-)  A 1   -2.7
And so on for a total of 141 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

   8 PRO   (   8-)  A  Poor phi/psi
  68 PRO   (   8-)  A  Poor phi/psi
 118 LYS   (  58-)  A  Poor phi/psi
 128 PRO   (   8-)  A  Poor phi/psi
 178 LYS   (  58-)  A  Poor phi/psi
 188 PRO   (   8-)  A  Poor phi/psi
 238 LYS   (  58-)  A  Poor phi/psi
 248 PRO   (   8-)  A  Poor phi/psi
 294 CYS   (  54-)  A  Poor phi/psi
 298 LYS   (  58-)  A  Poor phi/psi
 308 PRO   (   8-)  A  Poor phi/psi
 358 LYS   (  58-)  A  Poor phi/psi
 368 PRO   (   8-)  A  Poor phi/psi
 418 LYS   (  58-)  A  Poor phi/psi
 428 PRO   (   8-)  A  Poor phi/psi
 478 LYS   (  58-)  A  Poor phi/psi
 488 PRO   (   8-)  A  Poor phi/psi
 548 PRO   (   8-)  A 1 Poor phi/psi
 598 LYS   (  58-)  A 1 Poor phi/psi
 608 PRO   (   8-)  A 1 Poor phi/psi
 668 PRO   (   8-)  A 1 Poor phi/psi
 718 LYS   (  58-)  A 1 Poor phi/psi
 728 PRO   (   8-)  A 1 Poor phi/psi
 778 LYS   (  58-)  A 1 Poor phi/psi
 788 PRO   (   8-)  A 1 Poor phi/psi
 815 LYS   (  35-)  A 1 Poor phi/psi
 838 LYS   (  58-)  A 1 Poor phi/psi
 848 PRO   (   8-)  A 1 Poor phi/psi
 898 LYS   (  58-)  A 1 Poor phi/psi
 908 PRO   (   8-)  A 1 Poor phi/psi
 968 PRO   (   8-)  A 1 Poor phi/psi
1028 PRO   (   8-)  A 1 Poor phi/psi
1088 PRO   (   8-)  A 1 Poor phi/psi
1138 LYS   (  58-)  A 1 Poor phi/psi
1148 PRO   (   8-)  A 2 Poor phi/psi
1198 LYS   (  58-)  A 2 Poor phi/psi
 chi-1/chi-2 correlation Z-score : -6.800

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 : -6.800

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 : -7.024
Model 2 : -6.524
Model 3 : -6.756
Model 4 : -6.620
Model 5 : -7.460
Model 6 : -6.407
Model 7 : -7.048
Model 8 : -6.445
Model 9 : -6.034
Model 10 : -6.696
Model 11 : -7.068
Model 12 : -7.176
Model 13 : -6.051
Model 14 : -7.369
Model 15 : -7.319
Model 16 : -6.557
Model 17 : -6.780
Model 18 : -6.504
Model 19 : -7.004
Model 20 : -7.154

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.

 132 LYS   (  12-)  A    0.33

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!

   6 LEU   (   6-)  A      0
   7 VAL   (   7-)  A      0
   8 PRO   (   8-)  A      0
   9 LEU   (   9-)  A      0
  10 PHE   (  10-)  A      0
  16 ALA   (  16-)  A      0
  18 LYS   (  18-)  A      0
  26 MET   (  26-)  A      0
  27 VAL   (  27-)  A      0
  28 ALA   (  28-)  A      0
  29 ALA   (  29-)  A      0
  31 HIS   (  31-)  A      0
  36 ARG   (  36-)  A      0
  38 CYS   (  38-)  A      0
  56 THR   (  56-)  A      0
  58 LYS   (  58-)  A      0
  59 CYS   (  59-)  A      0
  60 ASN   (  60-)  A      0
  61 LEU   (   1-)  A      0
  62 LYS   (   2-)  A      0
  63 CYS   (   3-)  A      0
  64 LYS   (   4-)  A      0
  65 LYS   (   5-)  A      0
  66 LEU   (   6-)  A      0
  67 VAL   (   7-)  A      0
And so on for a total of 752 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 : 0.124
Model 3 : 0.000
Model 4 : 0.117
Model 5 : 0.059
Model 6 : 0.000
Model 7 : 0.000
Model 8 : 0.000
Model 9 : 0.000
Model 10 : 0.000
Model 11 : 0.000
Model 12 : 0.103
Model 13 : 0.046
Model 14 : 0.079
Model 15 : 0.000
Model 16 : 0.000
Model 17 : 0.000
Model 18 : 0.000
Model 19 : 0.000
Model 20 : 0.000

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]

   8 PRO   (   8-)  A    0.18 LOW
  15 PRO   (  15-)  A    0.18 LOW
  30 PRO   (  30-)  A    0.18 LOW
  33 PRO   (  33-)  A    0.18 LOW
  43 PRO   (  43-)  A    0.18 LOW
  68 PRO   (   8-)  A    0.18 LOW
  75 PRO   (  15-)  A    0.18 LOW
  90 PRO   (  30-)  A    0.18 LOW
  93 PRO   (  33-)  A    0.18 LOW
 103 PRO   (  43-)  A    0.18 LOW
 128 PRO   (   8-)  A    0.18 LOW
 135 PRO   (  15-)  A    0.18 LOW
 150 PRO   (  30-)  A    0.18 LOW
 153 PRO   (  33-)  A    0.18 LOW
 163 PRO   (  43-)  A    0.18 LOW
 188 PRO   (   8-)  A    0.18 LOW
 195 PRO   (  15-)  A    0.18 LOW
 210 PRO   (  30-)  A    0.18 LOW
 213 PRO   (  33-)  A    0.18 LOW
 223 PRO   (  43-)  A    0.18 LOW
 248 PRO   (   8-)  A    0.18 LOW
 255 PRO   (  15-)  A    0.18 LOW
 270 PRO   (  30-)  A    0.18 LOW
 273 PRO   (  33-)  A    0.18 LOW
 283 PRO   (  43-)  A    0.18 LOW
And so on for a total of 100 lines.

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.

 986 MET   (  26-)  A 1    N   <-> 1217 HOH   (  61 )  A 1    O      0.53    2.17
1166 MET   (  26-)  A 2    N   <-> 1220 HOH   (  61 )  A 2    O      0.53    2.17
1106 MET   (  26-)  A 1    N   <-> 1219 HOH   (  61 )  A 1    O      0.50    2.20
 802 TYR   (  22-)  A 1    CE2 <->  817 GLY   (  37-)  A 1    C      0.49    2.71
 742 TYR   (  22-)  A 1    CE2 <->  757 GLY   (  37-)  A 1    C      0.49    2.71
 926 MET   (  26-)  A 1    N   <-> 1216 HOH   (  61 )  A 1    O      0.49    2.21
 142 TYR   (  22-)  A      CE2 <->  157 GLY   (  37-)  A      C      0.48    2.72
  86 MET   (  26-)  A      N   <-> 1202 HOH   (  61 )  A      O      0.48    2.22
 806 MET   (  26-)  A 1    N   <-> 1214 HOH   (  61 )  A 1    O      0.47    2.23
 202 TYR   (  22-)  A      CE2 <->  217 GLY   (  37-)  A      C      0.45    2.75
 682 TYR   (  22-)  A 1    CE2 <->  697 GLY   (  37-)  A 1    C      0.44    2.76
 382 TYR   (  22-)  A      CE1 <->  397 GLY   (  37-)  A      C      0.42    2.78
 742 TYR   (  22-)  A 1    CE2 <->  757 GLY   (  37-)  A 1    CA     0.41    2.79
 206 MET   (  26-)  A      N   <-> 1204 HOH   (  61 )  A      O      0.41    2.29
 862 TYR   (  22-)  A 1    CE2 <->  877 GLY   (  37-)  A 1    C      0.40    2.80
 566 MET   (  26-)  A 1    N   <-> 1210 HOH   (  61 )  A 1    O      0.39    2.31
1042 TYR   (  22-)  A 1    CE2 <-> 1057 GLY   (  37-)  A 1    C      0.39    2.81
 386 MET   (  26-)  A      N   <-> 1207 HOH   (  61 )  A      O      0.38    2.32
 686 MET   (  26-)  A 1    O   <-> 1212 HOH   (  61 )  A 1    O      0.38    2.02
 202 TYR   (  22-)  A      CE2 <->  217 GLY   (  37-)  A      CA     0.38    2.82
 142 TYR   (  22-)  A      CD2 <->  157 GLY   (  37-)  A      C      0.38    2.82
 682 TYR   (  22-)  A 1    CD2 <->  697 GLY   (  37-)  A 1    C      0.37    2.83
 622 TYR   (  22-)  A 1    CE2 <->  637 GLY   (  37-)  A 1    C      0.36    2.84
 326 MET   (  26-)  A      N   <-> 1206 HOH   (  61 )  A      O      0.36    2.34
 626 MET   (  26-)  A 1    N   <-> 1211 HOH   (  61 )  A 1    O      0.36    2.34
And so on for a total of 450 lines.

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 : 1.259

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: Structural average packing environment a bit worrysome

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Warning: Low packing Z-score for some residues


Note: Per-model averages for NQA




















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds


Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure