WHAT IF Check report

This file was created 2011-12-17 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 pdb2ofn.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

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.290
Model 2 : 0.281
Model 3 : 0.280
Model 4 : 0.303
Model 5 : 0.288
Model 6 : 0.286
Model 7 : 0.274
Model 8 : 0.298
Model 9 : 0.279
Model 10 : 0.290
Model 11 : 0.293
Model 12 : 0.281
Model 13 : 0.295
Model 14 : 0.285
Model 15 : 0.289
Model 16 : 0.284
Model 17 : 0.284
Model 18 : 0.275
Model 19 : 0.282
Model 20 : 0.284

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.

1688 HIS   (  68-)  A 1    CG   ND1  CE1 109.67    4.1
1890 HIS   ( 135-)  A 1    CG   ND1  CE1 109.61    4.0

Note: Per-model averages for bond-angle check

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

Model 1 : 0.538
Model 2 : 0.541
Model 3 : 0.521
Model 4 : 0.521
Model 5 : 0.536
Model 6 : 0.524
Model 7 : 0.529
Model 8 : 0.542
Model 9 : 0.526
Model 10 : 0.539
Model 11 : 0.527
Model 12 : 0.523
Model 13 : 0.541
Model 14 : 0.536
Model 15 : 0.536
Model 16 : 0.529
Model 17 : 0.539
Model 18 : 0.528
Model 19 : 0.536
Model 20 : 0.548

Note: Per-model averages for chirality check

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

Model 1 : 0.468
Model 2 : 0.442
Model 3 : 0.441
Model 4 : 0.456
Model 5 : 0.453
Model 6 : 0.443
Model 7 : 0.450
Model 8 : 0.475
Model 9 : 0.456
Model 10 : 0.466
Model 11 : 0.445
Model 12 : 0.442
Model 13 : 0.467
Model 14 : 0.452
Model 15 : 0.444
Model 16 : 0.438
Model 17 : 0.459
Model 18 : 0.449
Model 19 : 0.442
Model 20 : 0.454

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 : -3.540

Note: Per-model averages for Ramachandran check

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

Model 1 : -2.753
Model 2 : -3.948
Model 3 : -3.353
Model 4 : -2.655
Model 5 : -3.868
Model 6 : -3.245
Model 7 : -3.011
Model 8 : -3.591
Model 9 : -3.770
Model 10 : -3.724
Model 11 : -3.616
Model 12 : -3.493
Model 13 : -3.873
Model 14 : -3.620
Model 15 : -4.079
Model 16 : -3.048
Model 17 : -3.569
Model 18 : -3.864
Model 19 : -3.732
Model 20 : -3.994

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.

2420 PHE   ( 125-)  A 1   -3.3
1893 THR   (   3-)  A 1   -3.2
2428 HIS   ( 133-)  A 1   -3.2
1340 PHE   ( 125-)  A 1   -3.2
 272 THR   (   2-)  A    -3.1
1353 THR   (   3-)  A 1   -3.1
1731 PRO   ( 111-)  A 1   -3.1
1610 PHE   ( 125-)  A 1   -3.0
 651 PRO   ( 111-)  A    -3.0
 665 PHE   ( 125-)  A    -3.0
1055 ILE   ( 110-)  A    -3.0
1325 ILE   ( 110-)  A 1   -3.0
2001 PRO   ( 111-)  A 1   -3.0
1880 PHE   ( 125-)  A 1   -3.0
 650 ILE   ( 110-)  A    -3.0
2675 ILE   ( 110-)  A 2   -3.0
2541 PRO   ( 111-)  A 1   -3.0
1596 PRO   ( 111-)  A 1   -2.9
2000 ILE   ( 110-)  A 1   -2.9
 111 PRO   ( 111-)  A    -2.9
2135 ILE   ( 110-)  A 1   -2.9
2690 PHE   ( 125-)  A 2   -2.9
2676 PRO   ( 111-)  A 2   -2.9
1460 ILE   ( 110-)  A 1   -2.9
2015 PHE   ( 125-)  A 1   -2.9
And so on for a total of 267 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.

  12 LEU   (  12-)  A  Poor phi/psi
  16 GLY   (  16-)  A  Poor phi/psi
  70 GLU   (  70-)  A  Poor phi/psi
 113 ASN   ( 113-)  A  Poor phi/psi
 147 LEU   (  12-)  A  Poor phi/psi
 162 ASP   (  27-)  A  Poor phi/psi
 186 THR   (  51-)  A  Poor phi/psi
 205 GLU   (  70-)  A  Poor phi/psi
 246 PRO   ( 111-)  A  Poor phi/psi
 272 THR   (   2-)  A  Poor phi/psi
 274 GLU   (   4-)  A  Poor phi/psi
 286 GLY   (  16-)  A  Poor phi/psi
 340 GLU   (  70-)  A  Poor phi/psi
 383 ASN   ( 113-)  A  Poor phi/psi
 384 SER   ( 114-)  A  Poor phi/psi
 399 GLU   ( 129-)  A  Poor phi/psi
 417 LEU   (  12-)  A  Poor phi/psi
 434 GLY   (  29-)  A  Poor phi/psi
 514 SER   ( 109-)  A  Poor phi/psi
 518 ASN   ( 113-)  A  Poor phi/psi
 534 GLU   ( 129-)  A  Poor phi/psi
 543 THR   (   3-)  A  Poor phi/psi
 546 GLU   (   6-)  A  Poor phi/psi
 552 LEU   (  12-)  A  Poor phi/psi
 591 THR   (  51-)  A  Poor phi/psi
And so on for a total of 130 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 : -4.774

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 : -4.638
Model 2 : -4.718
Model 3 : -5.183
Model 4 : -4.804
Model 5 : -4.494
Model 6 : -4.849
Model 7 : -3.927
Model 8 : -5.357
Model 9 : -4.942
Model 10 : -4.758
Model 11 : -4.927
Model 12 : -4.018
Model 13 : -4.850
Model 14 : -4.711
Model 15 : -4.749
Model 16 : -4.957
Model 17 : -5.032
Model 18 : -4.979
Model 19 : -4.692
Model 20 : -4.893

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!

   5 GLN   (   5-)  A      0
  11 GLU   (  11-)  A      0
  12 LEU   (  12-)  A      0
  15 ASP   (  15-)  A      0
  28 GLU   (  28-)  A      0
  30 GLU   (  30-)  A      0
  31 GLU   (  31-)  A      0
  32 ASN   (  32-)  A      0
  36 LYS   (  36-)  A      0
  45 VAL   (  45-)  A      0
  47 LYS   (  47-)  A      0
  48 LEU   (  48-)  A      0
  50 SER   (  50-)  A      0
  51 THR   (  51-)  A      0
  56 ASP   (  56-)  A      0
  69 LEU   (  69-)  A      0
  70 GLU   (  70-)  A      0
  71 GLN   (  71-)  A      0
  76 LYS   (  76-)  A      0
  85 MET   (  85-)  A      0
  88 ASN   (  88-)  A      0
  89 GLU   (  89-)  A      0
  99 TYR   (  99-)  A      0
 101 TYR   ( 101-)  A      0
 104 GLU   ( 104-)  A      0
And so on for a total of 1392 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 : 3.951

Note: Per-model averages for omega angle check

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

Model 1 : 3.816
Model 2 : 3.814
Model 3 : 3.906
Model 4 : 4.291
Model 5 : 4.286
Model 6 : 3.702
Model 7 : 3.948
Model 8 : 3.629
Model 9 : 3.821
Model 10 : 4.444
Model 11 : 3.934
Model 12 : 3.406
Model 13 : 4.261
Model 14 : 3.839
Model 15 : 3.879
Model 16 : 3.978
Model 17 : 3.865
Model 18 : 3.932
Model 19 : 3.956
Model 20 : 4.301

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!

1376 GLY   (  26-)  A 1  2.54   35
 287 GLY   (  17-)  A   2.33   15
 827 GLY   (  17-)  A   2.20   11
2312 GLY   (  17-)  A 1  2.17   67
1106 GLY   (  26-)  A   2.07   24
 692 GLY   (  17-)  A   2.03   70
  17 GLY   (  17-)  A   2.03   13
 161 GLY   (  26-)  A   2.01   39
 557 GLY   (  17-)  A   2.00   20
2042 GLY   (  17-)  A 1  1.97   14
2177 GLY   (  17-)  A 1  1.95   49
2582 GLY   (  17-)  A 2  1.93   20
 152 GLY   (  17-)  A   1.90   27
2407 GLY   ( 112-)  A 1  1.88   12
1772 GLY   (  17-)  A 1  1.88   43
1781 GLY   (  26-)  A 1  1.87   54
1502 GLY   (  17-)  A 1  1.81   39
 962 GLY   (  17-)  A   1.77   80
2447 GLY   (  17-)  A 1  1.76   35
1232 GLY   (  17-)  A 1  1.70   38
1936 GLY   (  46-)  A 1  1.67   20
 512 GLY   ( 107-)  A   1.65   10
 422 GLY   (  17-)  A   1.64   46
 701 GLY   (  26-)  A   1.63   20
1241 GLY   (  26-)  A 1  1.57   10
2677 GLY   ( 112-)  A 2  1.55   10
1320 GLY   ( 105-)  A 1  1.54   27
 736 ARG   (  61-)  A   1.52   18
2341 GLY   (  46-)  A 1  1.51   35

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]

 381 PRO   ( 111-)  A    0.17 LOW

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].

  64 PRO   (  64-)  A    43.0 envelop C-delta (36 degrees)
 111 PRO   ( 111-)  A   -43.6 envelop C-alpha (-36 degrees)
 169 PRO   (  34-)  A   -61.7 half-chair C-beta/C-alpha (-54 degrees)
 246 PRO   ( 111-)  A   -55.2 half-chair C-beta/C-alpha (-54 degrees)
 439 PRO   (  34-)  A   -31.9 envelop C-alpha (-36 degrees)
 469 PRO   (  64-)  A    17.9 half-chair N/C-delta (18 degrees)
 516 PRO   ( 111-)  A   -44.6 envelop C-alpha (-36 degrees)
 651 PRO   ( 111-)  A   -14.6 half-chair C-alpha/N (-18 degrees)
 739 PRO   (  64-)  A    46.0 half-chair C-delta/C-gamma (54 degrees)
 786 PRO   ( 111-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 921 PRO   ( 111-)  A   -62.7 half-chair C-beta/C-alpha (-54 degrees)
 979 PRO   (  34-)  A    26.2 half-chair N/C-delta (18 degrees)
1009 PRO   (  64-)  A    20.0 half-chair N/C-delta (18 degrees)
1056 PRO   ( 111-)  A     2.7 envelop N (0 degrees)
1191 PRO   ( 111-)  A   -44.5 envelop C-alpha (-36 degrees)
1414 PRO   (  64-)  A 1   43.6 envelop C-delta (36 degrees)
1461 PRO   ( 111-)  A 1    9.1 half-chair N/C-delta (18 degrees)
1596 PRO   ( 111-)  A 1  -12.9 half-chair C-alpha/N (-18 degrees)
1731 PRO   ( 111-)  A 1  -13.8 half-chair C-alpha/N (-18 degrees)
1866 PRO   ( 111-)  A 1  -55.9 half-chair C-beta/C-alpha (-54 degrees)
1924 PRO   (  34-)  A 1   31.0 envelop C-delta (36 degrees)
1954 PRO   (  64-)  A 1   45.3 half-chair C-delta/C-gamma (54 degrees)
2001 PRO   ( 111-)  A 1  -27.7 envelop C-alpha (-36 degrees)
2194 PRO   (  34-)  A 1   29.5 envelop C-delta (36 degrees)
2271 PRO   ( 111-)  A 1   -6.9 envelop N (0 degrees)
2329 PRO   (  34-)  A 1   32.8 envelop C-delta (36 degrees)
2359 PRO   (  64-)  A 1   26.7 half-chair N/C-delta (18 degrees)
2541 PRO   ( 111-)  A 1   -6.2 envelop N (0 degrees)
2629 PRO   (  64-)  A 2   46.5 half-chair C-delta/C-gamma (54 degrees)
2676 PRO   ( 111-)  A 2  -28.4 envelop C-alpha (-36 degrees)

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.

1165 MET   (  85-)  A      SD  <-> 1171 CYS   (  91-)  A      N      0.20    3.10
 625 MET   (  85-)  A      SD  <->  631 CYS   (  91-)  A      SG     0.16    3.29
1659 GLU   (  39-)  A 1    OE1 <-> 1688 HIS   (  68-)  A 1    ND1    0.15    2.55
 465 ASP   (  60-)  A      CG  <->  466 ARG   (  61-)  A      N      0.14    2.86
2203 HIS   (  43-)  A 1    ND1 <-> 2281 GLU   ( 121-)  A 1    OE1    0.14    2.56
1794 GLU   (  39-)  A 1    OE1 <-> 1881 ARG   ( 126-)  A 1    NH1    0.13    2.57
2526 GLU   (  96-)  A 1    CD  <-> 2527 SER   (  97-)  A 1    N      0.13    2.87
2209 GLU   (  49-)  A 1    OE2 <-> 2254 ARG   (  94-)  A 1    NH1    0.13    2.57
1129 GLU   (  49-)  A      OE2 <-> 1174 ARG   (  94-)  A      NH2    0.13    2.57
2380 MET   (  85-)  A 1    SD  <-> 2415 ILE   ( 120-)  A 1    CG2    0.12    3.28
1251 LYS   (  36-)  A 1    NZ  <-> 1285 GLU   (  70-)  A 1    OE2    0.12    2.58
 870 ASP   (  60-)  A      CG  <->  871 ARG   (  61-)  A      N      0.12    2.88
 374 GLU   ( 104-)  A      OE2 <->  376 CYS   ( 106-)  A      SG     0.12    2.88
 458 LYS   (  53-)  A      NZ  <->  461 ASP   (  56-)  A      OD1    0.12    2.58
 268 HIS   ( 133-)  A      NE2 <-> 2702 HIS   ( 135-)  A      O''    0.12    2.58
 891 CYS   (  81-)  A      SG  <->  901 CYS   (  91-)  A      SG     0.12    3.33
 914 GLU   ( 104-)  A      OE1 <->  916 CYS   ( 106-)  A      SG     0.11    2.89
 994 GLU   (  49-)  A      OE2 <-> 1039 ARG   (  94-)  A      NH2    0.11    2.59
 895 MET   (  85-)  A      SD  <->  930 ILE   ( 120-)  A      CG2    0.11    3.29
 548 GLU   (   8-)  A      OE1 <->  549 LYS   (   9-)  A      NZ     0.11    2.59
1841 ARG   (  86-)  A 1    NH1 <-> 1844 GLU   (  89-)  A 1    OE1    0.11    2.59
2445 ASP   (  15-)  A 1    OD2 <-> 2450 LYS   (  20-)  A 1    NZ     0.11    2.59
 621 CYS   (  81-)  A      SG  <->  631 CYS   (  91-)  A      SG     0.11    3.34
 183 LEU   (  48-)  A      O   <->  187 GLY   (  52-)  A      N      0.11    2.59
1808 LYS   (  53-)  A 1    NZ  <-> 1811 ASP   (  56-)  A 1    OD1    0.11    2.59
And so on for a total of 246 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