WHAT IF Check report

This file was created 2011-12-16 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 pdb2ko7.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2341 JZF   ( 130-)  A  2
2342 JZF   ( 130-)  A  3
2343 JZF   ( 130-)  A  4
2344 JZF   ( 130-)  A  5
2345 JZF   ( 130-)  A  6
2346 JZF   ( 130-)  A  7
2347 JZF   ( 130-)  A  8
2348 JZF   ( 130-)  A  9
2349 JZF   ( 130-)  A 10
2350 JZF   ( 130-)  A 11
2351 JZF   ( 130-)  A 12
2352 JZF   ( 130-)  A 13
2353 JZF   ( 130-)  A 14
2354 JZF   ( 130-)  A 15
2355 JZF   ( 130-)  A 16
2356 JZF   ( 130-)  A 17
2357 JZF   ( 130-)  A 18
2358 JZF   ( 130-)  A 19
2359 JZF   ( 130-)  A 20
2360 JZF   ( 130-)  A  1

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 GLY   (   1-)  A    Zero
   2 PRO   (   2-)  A    Zero
   3 GLY   (   3-)  A    Zero
   4 SER   (   4-)  A    Zero
   5 MET   (   5-)  A    Zero
   6 THR   (   6-)  A    Zero
   7 VAL   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 THR   (   9-)  A    Zero
  10 THR   (  10-)  A    Zero
  11 GLU   (  11-)  A    Zero
  12 SER   (  12-)  A    Zero
  13 GLY   (  13-)  A    Zero
  14 LEU   (  14-)  A    Zero
  15 LYS   (  15-)  A    Zero
  16 TYR   (  16-)  A    Zero
  17 GLU   (  17-)  A    Zero
  18 ASP   (  18-)  A    Zero
  19 LEU   (  19-)  A    Zero
  20 THR   (  20-)  A    Zero
  21 GLU   (  21-)  A    Zero
  22 GLY   (  22-)  A    Zero
  23 SER   (  23-)  A    Zero
  24 GLY   (  24-)  A    Zero
  25 ALA   (  25-)  A    Zero
And so on for a total of 2340 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 : 0.116
Model 2 : 0.118
Model 3 : 0.117
Model 4 : 0.117
Model 5 : 0.118
Model 6 : 0.117
Model 7 : 0.116
Model 8 : 0.117
Model 9 : 0.117
Model 10 : 0.119
Model 11 : 0.118
Model 12 : 0.116
Model 13 : 0.116
Model 14 : 0.116
Model 15 : 0.117
Model 16 : 0.117
Model 17 : 0.118
Model 18 : 0.119
Model 19 : 0.115
Model 20 : 0.117

Note: Per-model averages for bond-angle check

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

Model 1 : 0.252
Model 2 : 0.250
Model 3 : 0.249
Model 4 : 0.250
Model 5 : 0.251
Model 6 : 0.251
Model 7 : 0.250
Model 8 : 0.250
Model 9 : 0.250
Model 10 : 0.250
Model 11 : 0.251
Model 12 : 0.250
Model 13 : 0.250
Model 14 : 0.250
Model 15 : 0.249
Model 16 : 0.249
Model 17 : 0.250
Model 18 : 0.250
Model 19 : 0.250
Model 20 : 0.249

Note: Per-model averages for chirality check

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

Model 1 : 0.296
Model 2 : 0.298
Model 3 : 0.297
Model 4 : 0.298
Model 5 : 0.297
Model 6 : 0.296
Model 7 : 0.295
Model 8 : 0.298
Model 9 : 0.295
Model 10 : 0.296
Model 11 : 0.296
Model 12 : 0.297
Model 13 : 0.297
Model 14 : 0.297
Model 15 : 0.296
Model 16 : 0.296
Model 17 : 0.296
Model 18 : 0.297
Model 19 : 0.297
Model 20 : 0.297

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 : -3.821

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.855
Model 2 : -4.005
Model 3 : -3.583
Model 4 : -3.904
Model 5 : -3.610
Model 6 : -3.769
Model 7 : -3.772
Model 8 : -3.672
Model 9 : -3.670
Model 10 : -4.294
Model 11 : -3.818
Model 12 : -4.079
Model 13 : -3.631
Model 14 : -4.086
Model 15 : -3.627
Model 16 : -3.961
Model 17 : -3.941
Model 18 : -3.742
Model 19 : -3.565
Model 20 : -3.835

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.

1775 THR   (  20-)  A 1   -2.9
 176 PHE   (  59-)  A    -2.9
1073 THR   (  20-)  A 1   -2.9
2009 THR   (  20-)  A 1   -2.8
1190 THR   (  20-)  A 1   -2.8
 488 THR   (  20-)  A    -2.8
2048 PHE   (  59-)  A 1   -2.8
1814 PHE   (  59-)  A 1   -2.7
1229 PHE   (  59-)  A 1   -2.7
1644 THR   (   6-)  A 1   -2.7
 444 TYR   (  93-)  A    -2.6
 605 THR   (  20-)  A    -2.6
   6 THR   (   6-)  A    -2.6
 374 SER   (  23-)  A    -2.6
1848 TYR   (  93-)  A 1   -2.6
 839 THR   (  20-)  A    -2.6
 140 SER   (  23-)  A    -2.6
 959 SER   (  23-)  A    -2.6
1293 THR   (   6-)  A 1   -2.6
 878 PHE   (  59-)  A    -2.5
1310 SER   (  23-)  A 1   -2.5
1544 SER   (  23-)  A 1   -2.5
 254 THR   (  20-)  A    -2.5
2325 ILE   ( 102-)  A 2   -2.5
2165 PHE   (  59-)  A 1   -2.5
And so on for a total of 285 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.

  23 SER   (  23-)  A  Poor phi/psi
  54 ASN   (  54-)  A  Poor phi/psi
  55 ASP   (  55-)  A  Poor phi/psi
  76 GLY   (  76-)  A  Poor phi/psi
 139 GLY   (  22-)  A  Poor phi/psi
 140 SER   (  23-)  A  Poor phi/psi
 165 ASP   (  48-)  A  Poor phi/psi
 181 GLY   (  64-)  A  Poor phi/psi
 193 GLY   (  76-)  A  Poor phi/psi
 282 ASP   (  48-)  A  Poor phi/psi
 288 ASN   (  54-)  A  Poor phi/psi
 310 GLY   (  76-)  A  Poor phi/psi
 374 SER   (  23-)  A  Poor phi/psi
 399 ASP   (  48-)  A  Poor phi/psi
 405 ASN   (  54-)  A  Poor phi/psi
 427 GLY   (  76-)  A  Poor phi/psi
 522 ASN   (  54-)  A  Poor phi/psi
 523 ASP   (  55-)  A  Poor phi/psi
 544 GLY   (  76-)  A  Poor phi/psi
 590 MET   (   5-)  A  Poor phi/psi
 639 ASN   (  54-)  A  Poor phi/psi
 649 GLY   (  64-)  A  Poor phi/psi
 661 GLY   (  76-)  A  Poor phi/psi
 706 SER   (   4-)  A  Poor phi/psi
 724 GLY   (  22-)  A  Poor phi/psi
And so on for a total of 84 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 : -6.374

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 : -6.217
Model 2 : -6.455
Model 3 : -6.375
Model 4 : -6.067
Model 5 : -5.998
Model 6 : -6.568
Model 7 : -5.850
Model 8 : -6.827
Model 9 : -5.937
Model 10 : -6.231
Model 11 : -6.214
Model 12 : -6.928
Model 13 : -6.764
Model 14 : -5.854
Model 15 : -6.723
Model 16 : -6.603
Model 17 : -6.578
Model 18 : -6.256
Model 19 : -6.521
Model 20 : -6.517

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!

   4 SER   (   4-)  A      0
  12 SER   (  12-)  A      0
  20 THR   (  20-)  A      0
  21 GLU   (  21-)  A      0
  23 SER   (  23-)  A      0
  29 ALA   (  29-)  A      0
  46 LYS   (  46-)  A      0
  47 PHE   (  47-)  A      0
  48 ASP   (  48-)  A      0
  53 ARG   (  53-)  A      0
  54 ASN   (  54-)  A      0
  55 ASP   (  55-)  A      0
  58 ALA   (  58-)  A      0
  59 PHE   (  59-)  A      0
  61 LEU   (  61-)  A      0
  65 MET   (  65-)  A      0
  66 VAL   (  66-)  A      0
  67 ILE   (  67-)  A      0
  77 MET   (  77-)  A      0
  79 VAL   (  79-)  A      0
  93 TYR   (  93-)  A      0
  95 ALA   (  95-)  A      0
  96 ARG   (  96-)  A      0
  98 ALA   (  98-)  A      0
 103 PRO   ( 103-)  A      0
And so on for a total of 963 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 : 0.245

Note: Per-model averages for omega angle check

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

Model 1 : 0.065
Model 2 : 0.000
Model 3 : 0.000
Model 4 : 0.000
Model 5 : 0.055
Model 6 : 0.092
Model 7 : 0.064
Model 8 : 0.091
Model 9 : 0.141
Model 10 : 0.132
Model 11 : 0.172
Model 12 : 0.086
Model 13 : 0.115
Model 14 : 0.000
Model 15 : 0.000
Model 16 : 0.047
Model 17 : 0.145
Model 18 : 0.000
Model 19 : 0.083
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!

1311 GLY   (  24-)  A 1  2.61   10
  24 GLY   (  24-)  A   2.45   16
1194 GLY   (  24-)  A 1  2.42   17
1428 GLY   (  24-)  A 1  2.33   15
 609 GLY   (  24-)  A   2.22   18
 843 GLY   (  24-)  A   2.04   15
1117 GLY   (  64-)  A 1  2.03   14
1662 GLY   (  24-)  A 1  2.02   17
1702 GLY   (  64-)  A 1  1.99   16
 298 GLY   (  64-)  A   1.96   12
 492 GLY   (  24-)  A   1.92   18
1936 GLY   (  64-)  A 1  1.86   18
1779 GLY   (  24-)  A 1  1.81   18
  64 GLY   (  64-)  A   1.78   22
  81 GLY   (  81-)  A   1.72   15
1819 GLY   (  64-)  A 1  1.72   12
1351 GLY   (  64-)  A 1  1.70   23
1017 GLY   (  81-)  A   1.69   11
 451 GLY   ( 100-)  A   1.68   14
 192 GLN   (  75-)  A   1.65   10
1234 GLY   (  64-)  A 1  1.64   20
1387 GLY   ( 100-)  A 1  1.62   15
 100 GLY   ( 100-)  A   1.61   10
1504 GLY   ( 100-)  A 1  1.61   10
1485 GLY   (  81-)  A 1  1.61   16
1738 GLY   ( 100-)  A 1  1.61   15
 783 GLY   (  81-)  A   1.61   13
1300 GLY   (  13-)  A 1  1.57   80
1011 GLN   (  75-)  A   1.57   10
 426 GLN   (  75-)  A   1.56   10
1153 GLY   ( 100-)  A 1  1.56   16
 532 GLY   (  64-)  A   1.55   13
 949 GLY   (  13-)  A   1.55   80
 217 GLY   ( 100-)  A   1.54   11
1836 GLY   (  81-)  A 1  1.54   11
1036 GLY   ( 100-)  A   1.54   11
1270 GLY   ( 100-)  A 1  1.51   18
1479 GLN   (  75-)  A 1  1.50   10

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.

1599 LYS   (  78-)  A 1    C   <-> 1635 LEU   ( 114-)  A 1    CD1    0.17    3.03
1241 ASP   (  71-)  A 1    CG  <-> 1245 GLN   (  75-)  A 1    NE2    0.16    2.94
 539 ASP   (  71-)  A      CG  <->  543 GLN   (  75-)  A      NE2    0.16    2.94
1716 LYS   (  78-)  A 1    C   <-> 1752 LEU   ( 114-)  A 1    CD1    0.15    3.05
2177 ASP   (  71-)  A 1    CG  <-> 2181 GLN   (  75-)  A 1    NE2    0.15    2.95
 546 LYS   (  78-)  A      C   <->  582 LEU   ( 114-)  A      CD1    0.14    3.06
 663 LYS   (  78-)  A      C   <->  699 LEU   ( 114-)  A      CD1    0.14    3.06
2294 ASP   (  71-)  A 2    CG  <-> 2298 GLN   (  75-)  A 2    NE2    0.14    2.96
 312 LYS   (  78-)  A      C   <->  348 LEU   ( 114-)  A      CD2    0.13    3.07
1131 LYS   (  78-)  A 1    C   <-> 1167 LEU   ( 114-)  A 1    CD2    0.13    3.07
 847 ARG   (  28-)  A      C   <->  880 LEU   (  61-)  A      CD2    0.11    3.09
  40 TRP   (  40-)  A      CH2 <->  111 GLU   ( 111-)  A      CD     0.11    3.09
 153 HIS   (  36-)  A      CE1 <->  172 ASP   (  55-)  A      C      0.11    3.09
2017 ARG   (  28-)  A 1    C   <-> 2050 LEU   (  61-)  A 1    CD2    0.11    3.09
1377 GLN   (  90-)  A 1    CD  <-> 1378 LEU   (  91-)  A 1    CD1    0.11    3.09
1783 ARG   (  28-)  A 1    C   <-> 1816 LEU   (  61-)  A 1    CD2    0.11    3.09
1260 GLN   (  90-)  A 1    CD  <-> 1261 LEU   (  91-)  A 1    CD2    0.11    3.09
2134 ARG   (  28-)  A 1    C   <-> 2167 LEU   (  61-)  A 1    CD2    0.11    3.09
1026 GLN   (  90-)  A      CD  <-> 1027 LEU   (  91-)  A      CD2    0.10    3.10
1845 GLN   (  90-)  A 1    CD  <-> 1846 LEU   (  91-)  A 1    CD2    0.10    3.10
1549 ARG   (  28-)  A 1    C   <-> 1582 LEU   (  61-)  A 1    CD2    0.10    3.10
1962 GLN   (  90-)  A 1    CD  <-> 1963 LEU   (  91-)  A 1    CD2    0.10    3.10
 964 ARG   (  28-)  A      C   <->  997 LEU   (  61-)  A      CD2    0.10    3.10
1795 TRP   (  40-)  A 1    CH2 <-> 1866 GLU   ( 111-)  A 1    CD     0.10    3.10
2079 GLN   (  90-)  A 1    CD  <-> 2080 LEU   (  91-)  A 1    CD1    0.10    3.10
And so on for a total of 254 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


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: 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