WHAT IF Check report

This file was created 2012-01-25 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 pdb2k7n.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 MET   (   1-)  A    Zero
1847 MET   (  20-)  A 1   Zero
3666 PRO   (  12-)  A 1   Zero

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.270
Model 2 : 0.285
Model 3 : 0.309
Model 4 : 0.281
Model 5 : 0.277
Model 6 : 0.293
Model 7 : 0.285
Model 8 : 0.268
Model 9 : 0.274
Model 10 : 0.277
Model 11 : 0.277
Model 12 : 0.280
Model 13 : 0.276
Model 14 : 0.272
Model 15 : 0.284
Model 16 : 0.286
Model 17 : 0.284
Model 18 : 0.282
Model 19 : 0.285
Model 20 : 0.281

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.

 395 HIS   ( 192-)  A      CG   ND1  CE1 109.60    4.0
1508 HIS   (  87-)  A      CG   ND1  CE1 109.64    4.0

Note: Per-model averages for bond-angle check

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

Model 1 : 0.451
Model 2 : 0.446
Model 3 : 0.466
Model 4 : 0.465
Model 5 : 0.456
Model 6 : 0.456
Model 7 : 0.466
Model 8 : 0.441
Model 9 : 0.461
Model 10 : 0.452
Model 11 : 0.448
Model 12 : 0.470
Model 13 : 0.445
Model 14 : 0.446
Model 15 : 0.451
Model 16 : 0.453
Model 17 : 0.462
Model 18 : 0.479
Model 19 : 0.460
Model 20 : 0.458

Note: Per-model averages for chirality check

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

Model 1 : 0.492
Model 2 : 0.487
Model 3 : 0.503
Model 4 : 0.513
Model 5 : 0.473
Model 6 : 0.495
Model 7 : 0.509
Model 8 : 0.490
Model 9 : 0.490
Model 10 : 0.470
Model 11 : 0.502
Model 12 : 0.489
Model 13 : 0.481
Model 14 : 0.472
Model 15 : 0.478
Model 16 : 0.468
Model 17 : 0.480
Model 18 : 0.518
Model 19 : 0.505
Model 20 : 0.487

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 : -4.837

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.852
Model 2 : -4.644
Model 3 : -4.668
Model 4 : -4.486
Model 5 : -4.739
Model 6 : -4.836
Model 7 : -4.876
Model 8 : -5.127
Model 9 : -5.287
Model 10 : -5.328
Model 11 : -4.442
Model 12 : -4.529
Model 13 : -4.903
Model 14 : -4.872
Model 15 : -5.022
Model 16 : -5.066
Model 17 : -4.482
Model 18 : -4.445
Model 19 : -5.480
Model 20 : -4.660

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.

3377 PHE   ( 129-)  A 1   -3.4
1020 PRO   (   5-)  A    -3.0
 208 PRO   (   5-)  A    -2.8
1508 HIS   (  87-)  A    -2.8
2441 PRO   (   5-)  A 1   -2.7
4055 LEU   ( 198-)  A 2   -2.7
3783 PHE   ( 129-)  A 1   -2.7
2729 LEU   (  90-)  A 1   -2.7
1652 TYR   (  28-)  A    -2.7
2932 LEU   (  90-)  A 1   -2.7
1040 LEU   (  25-)  A    -2.7
1822 LEU   ( 198-)  A    -2.7
3273 LEU   (  25-)  A 1   -2.7
2055 LEU   (  25-)  A 1   -2.7
1446 LEU   (  25-)  A    -2.7
1010 LEU   ( 198-)  A    -2.7
3040 LEU   ( 198-)  A 1   -2.7
3355 THR   ( 107-)  A 1   -2.7
 198 LEU   ( 198-)  A    -2.7
1852 LEU   (  25-)  A 1   -2.7
2258 LEU   (  25-)  A 1   -2.7
1243 LEU   (  25-)  A    -2.7
1832 PRO   (   5-)  A 1   -2.7
2431 LEU   ( 198-)  A 1   -2.7
1649 LEU   (  25-)  A    -2.7
And so on for a total of 316 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 SER   (   8-)  A  Poor phi/psi
  31 HIS   (  31-)  A  Poor phi/psi
  59 ASP   (  59-)  A  Poor phi/psi
  60 PHE   (  60-)  A  Poor phi/psi
  75 ALA   (  75-)  A  Poor phi/psi
  96 GLY   (  96-)  A  Poor phi/psi
 135 GLY   ( 135-)  A  Poor phi/psi
 150 GLN   ( 150-)  A  Poor phi/psi
 192 HIS   ( 192-)  A  Poor phi/psi
 199 ASP   ( 199-)  A  Poor phi/psi
 207 ILE   (   4-)  A  Poor phi/psi
 263 PHE   (  60-)  A  Poor phi/psi
 269 ASP   (  66-)  A  Poor phi/psi
 278 ALA   (  75-)  A  Poor phi/psi
 291 PRO   (  88-)  A  Poor phi/psi
 295 PHE   (  92-)  A  Poor phi/psi
 299 GLY   (  96-)  A  Poor phi/psi
 338 GLY   ( 135-)  A  Poor phi/psi
 352 SER   ( 149-)  A  Poor phi/psi
 354 ASP   ( 151-)  A  Poor phi/psi
 368 SER   ( 165-)  A  Poor phi/psi
 383 GLY   ( 180-)  A  Poor phi/psi
 402 ASP   ( 199-)  A  Poor phi/psi
 410 ILE   (   4-)  A  Poor phi/psi
 416 GLN   (  10-)  A  Poor phi/psi
And so on for a total of 231 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 : -4.665

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 : -4.827
Model 2 : -4.749
Model 3 : -5.038
Model 4 : -4.569
Model 5 : -4.683
Model 6 : -4.284
Model 7 : -4.769
Model 8 : -4.329
Model 9 : -5.017
Model 10 : -4.514
Model 11 : -4.692
Model 12 : -3.816
Model 13 : -5.403
Model 14 : -5.320
Model 15 : -4.200
Model 16 : -4.649
Model 17 : -4.354
Model 18 : -4.988
Model 19 : -4.801
Model 20 : -4.301

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.

 420 VAL   (  14-)  A    0.36

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
   6 PRO   (   6-)  A      0
   7 ASP   (   7-)  A      0
   8 SER   (   8-)  A      0
  20 MET   (  20-)  A      0
  22 ILE   (  22-)  A      0
  28 TYR   (  28-)  A      0
  29 TRP   (  29-)  A      0
  31 HIS   (  31-)  A      0
  32 ALA   (  32-)  A      0
  45 ARG   (  45-)  A      0
  48 TYR   (  48-)  A      0
  49 ASN   (  49-)  A      0
  51 THR   (  51-)  A      0
  54 HIS   (  54-)  A      0
  58 LYS   (  58-)  A      0
  60 PHE   (  60-)  A      0
  61 MET   (  61-)  A      0
  66 ASP   (  66-)  A      0
  70 THR   (  70-)  A      0
  72 ARG   (  72-)  A      0
  74 GLY   (  74-)  A      0
  75 ALA   (  75-)  A      0
  76 SER   (  76-)  A      0
  78 TYR   (  78-)  A      0
And so on for a total of 2147 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 : 3.727

Note: Per-model averages for omega angle check

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

Model 1 : 3.543
Model 2 : 3.367
Model 3 : 4.062
Model 4 : 3.882
Model 5 : 3.935
Model 6 : 3.659
Model 7 : 3.738
Model 8 : 3.373
Model 9 : 3.737
Model 10 : 3.892
Model 11 : 3.640
Model 12 : 3.537
Model 13 : 3.589
Model 14 : 3.542
Model 15 : 3.581
Model 16 : 3.634
Model 17 : 4.163
Model 18 : 3.993
Model 19 : 3.795
Model 20 : 3.825

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!

3820 GLY   ( 166-)  A 1  3.63   10
 168 GLY   ( 168-)  A   3.35   12
2210 GLY   ( 180-)  A 1  3.33   10
1792 GLY   ( 168-)  A   3.12   11
3224 GLY   ( 179-)  A 1  3.03   13
3622 GLY   ( 171-)  A 1  2.81   10
1389 GLY   ( 171-)  A   2.47   15
3124 GLY   (  79-)  A 1  2.35   11
3420 GLY   ( 172-)  A 1  2.28   12
1297 GLY   (  79-)  A   2.24   11
 995 GLY   ( 183-)  A   2.23   10
2718 GLY   (  79-)  A 1  2.12   13
 891 GLY   (  79-)  A   2.10   13
3560 GLY   ( 109-)  A 1  2.09   12
  79 GLY   (  79-)  A   2.07   19
1500 GLY   (  79-)  A   2.02   13
2312 GLY   (  79-)  A 1  1.99   14
2921 GLY   (  79-)  A 1  1.97   16
3008 GLY   ( 166-)  A 1  1.97   16
2010 GLY   ( 183-)  A 1  1.96   11
 688 GLY   (  79-)  A   1.95   17
2209 GLY   ( 179-)  A 1  1.95   26
1703 GLY   (  79-)  A   1.93   15
1183 GLY   ( 168-)  A   1.89   18
3936 GLY   (  79-)  A 2  1.89   19
2051 GLY   (  21-)  A 1  1.87   16
2413 GLY   ( 180-)  A 1  1.75   37
3733 GLY   (  79-)  A 1  1.74   19
2298 GLY   (  65-)  A 1  1.68   15
3825 GLY   ( 171-)  A 1  1.68   25
3112 PRO   (  67-)  A 1  1.61   10
 224 GLY   (  21-)  A   1.60   16
3217 GLY   ( 172-)  A 1  1.60   19
2840 GLY   ( 201-)  A 1  1.60   80
2404 GLY   ( 171-)  A 1  1.58   17
2297 GLY   (  64-)  A 1  1.56   24
1182 GLY   ( 167-)  A   1.55   18
2457 GLY   (  21-)  A 1  1.54   20
2254 GLY   (  21-)  A 1  1.54   17
1188 GLY   ( 173-)  A   1.54   10
 833 GLY   (  21-)  A   1.54   26
1807 GLY   ( 183-)  A   1.53   10
3878 GLY   (  21-)  A 2  1.53   24
  21 GLY   (  21-)  A   1.52   17
3230 GLY   ( 185-)  A 1  1.52   50
3675 GLY   (  21-)  A 1  1.52   17
4023 GLY   ( 166-)  A 2  1.51   12
1748 GLY   ( 124-)  A   1.50   69

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

   5 PRO   (   5-)  A    47.5 half-chair C-delta/C-gamma (54 degrees)
 105 PRO   ( 105-)  A  -123.9 half-chair C-delta/C-gamma (-126 degrees)
 208 PRO   (   5-)  A     0.4 envelop N (0 degrees)
 392 PRO   ( 189-)  A    39.8 envelop C-delta (36 degrees)
 411 PRO   (   5-)  A    35.7 envelop C-delta (36 degrees)
 412 PRO   (   6-)  A    23.0 half-chair N/C-delta (18 degrees)
 439 PRO   (  33-)  A    48.3 half-chair C-delta/C-gamma (54 degrees)
 511 PRO   ( 105-)  A  -130.4 half-chair C-delta/C-gamma (-126 degrees)
 559 PRO   ( 153-)  A  -114.7 envelop C-gamma (-108 degrees)
 570 PRO   ( 164-)  A    49.1 half-chair C-delta/C-gamma (54 degrees)
 595 PRO   ( 189-)  A    39.3 envelop C-delta (36 degrees)
 642 PRO   (  33-)  A    51.5 half-chair C-delta/C-gamma (54 degrees)
 798 PRO   ( 189-)  A    43.9 envelop C-delta (36 degrees)
 845 PRO   (  33-)  A    45.7 half-chair C-delta/C-gamma (54 degrees)
 917 PRO   ( 105-)  A  -125.0 half-chair C-delta/C-gamma (-126 degrees)
1001 PRO   ( 189-)  A    35.1 envelop C-delta (36 degrees)
1020 PRO   (   5-)  A     6.8 envelop N (0 degrees)
1323 PRO   ( 105-)  A  -113.6 envelop C-gamma (-108 degrees)
1426 PRO   (   5-)  A   -50.5 half-chair C-beta/C-alpha (-54 degrees)
1488 PRO   (  67-)  A   -65.7 envelop C-beta (-72 degrees)
1526 PRO   ( 105-)  A  -132.5 half-chair C-delta/C-gamma (-126 degrees)
1610 PRO   ( 189-)  A    42.2 envelop C-delta (36 degrees)
1629 PRO   (   5-)  A    15.4 half-chair N/C-delta (18 degrees)
1635 PRO   (  11-)  A  -129.1 half-chair C-delta/C-gamma (-126 degrees)
1636 PRO   (  12-)  A    36.5 envelop C-delta (36 degrees)
And so on for a total of 58 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.

4001 MET   ( 144-)  A 2    SD  <-> 4060 LYS   ( 203-)  A 2    NZ     0.35    2.95
2230 MET   ( 200-)  A 1    SD  <-> 2231 GLY   ( 201-)  A 1    N      0.34    2.86
2125 ALA   (  95-)  A 1    CB  <-> 2230 MET   ( 200-)  A 1    SD     0.34    3.06
1247 TRP   (  29-)  A      NE1 <-> 1254 CYS   (  36-)  A      SG     0.33    2.97
2261 TYR   (  28-)  A 1    C   <-> 2269 CYS   (  36-)  A 1    SG     0.29    3.11
1044 TRP   (  29-)  A      CE2 <-> 1051 CYS   (  36-)  A      SG     0.26    3.14
3480 TRP   (  29-)  A 1    CD1 <-> 3487 CYS   (  36-)  A 1    SG     0.26    3.14
2333 MET   ( 100-)  A 1    SD  <-> 2341 ASN   ( 108-)  A 1    CB     0.24    3.16
3471 MET   (  20-)  A 1    SD  <-> 3592 ARG   ( 141-)  A 1    NH1    0.22    3.08
2260 LEU   (  27-)  A 1    CB  <-> 2269 CYS   (  36-)  A 1    SG     0.22    3.18
1450 TRP   (  29-)  A      NE1 <-> 1457 CYS   (  36-)  A      SG     0.21    3.09
  20 MET   (  20-)  A      SD  <->  141 ARG   ( 141-)  A      NH1    0.20    3.10
2668 TRP   (  29-)  A 1    NE1 <-> 2675 CYS   (  36-)  A 1    SG     0.19    3.11
3074 TRP   (  29-)  A 1    CD1 <-> 3081 CYS   (  36-)  A 1    SG     0.19    3.21
3720 ASP   (  66-)  A 1    OD1 <-> 3723 GLY   (  69-)  A 1    N      0.19    2.51
 439 PRO   (  33-)  A      C   <->  442 CYS   (  36-)  A      SG     0.19    3.21
  66 ASP   (  66-)  A      OD1 <->   69 GLY   (  69-)  A      N      0.17    2.53
 232 TRP   (  29-)  A      CD1 <->  239 CYS   (  36-)  A      SG     0.16    3.24
 223 MET   (  20-)  A      SD  <->  344 ARG   ( 141-)  A      NH1    0.16    3.14
2066 CYS   (  36-)  A 1    SG  <-> 2067 LYS   (  37-)  A 1    N      0.15    3.05
3079 LYS   (  34-)  A 1    NZ  <-> 3130 GLU   (  85-)  A 1    OE2    0.14    2.56
1856 TRP   (  29-)  A 1    CD1 <-> 1863 CYS   (  36-)  A 1    SG     0.14    3.26
2592 ASP   ( 156-)  A 1    OD1 <-> 2594 LYS   ( 158-)  A 1    NZ     0.13    2.57
2494 LYS   (  58-)  A 1    NZ  <-> 2582 GLU   ( 146-)  A 1    OE2    0.13    2.57
3396 ASN   ( 148-)  A 1    CG  <-> 3397 SER   ( 149-)  A 1    N      0.13    2.87
And so on for a total of 427 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


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