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 pdb2jwx.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

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

1858 TYR   ( 131-)  A 1    CE1  CZ    1.48    4.2
1858 TYR   ( 131-)  A 1    CE2  CZ    1.28   -4.1

Note: Per-model averages for bond-length check

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

Model 1 : 0.456
Model 2 : 0.439
Model 3 : 0.426
Model 4 : 0.473
Model 5 : 0.461
Model 6 : 0.447
Model 7 : 0.465
Model 8 : 0.463
Model 9 : 0.453
Model 10 : 0.469
Model 11 : 0.464
Model 12 : 0.488
Model 13 : 0.451
Model 14 : 0.494
Model 15 : 0.458
Model 16 : 0.448
Model 17 : 0.476
Model 18 : 0.481
Model 19 : 0.476
Model 20 : 0.502

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.

 469 HIS   ( 155-)  A      CG   ND1  CE1 109.62    4.0

Note: Per-model averages for bond-angle check

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

Model 1 : 0.653
Model 2 : 0.632
Model 3 : 0.655
Model 4 : 0.647
Model 5 : 0.656
Model 6 : 0.643
Model 7 : 0.666
Model 8 : 0.649
Model 9 : 0.642
Model 10 : 0.650
Model 11 : 0.644
Model 12 : 0.679
Model 13 : 0.675
Model 14 : 0.679
Model 15 : 0.652
Model 16 : 0.660
Model 17 : 0.661
Model 18 : 0.667
Model 19 : 0.642
Model 20 : 0.666

Note: Per-model averages for chirality check

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

Model 1 : 0.623
Model 2 : 0.629
Model 3 : 0.657
Model 4 : 0.900
Model 5 : 0.643
Model 6 : 1.065
Model 7 : 0.770
Model 8 : 0.709
Model 9 : 0.702
Model 10 : 0.794
Model 11 : 0.640
Model 12 : 0.789
Model 13 : 0.941
Model 14 : 1.040
Model 15 : 0.674
Model 16 : 0.737
Model 17 : 0.857
Model 18 : 0.720
Model 19 : 0.704
Model 20 : 0.712

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 905 TYR   ( 120-)  A    7.64
 591 TYR   ( 120-)  A    5.94
2163 TYR   ( 122-)  A 1   5.80
2004 TYR   ( 120-)  A 1   5.74
2634 TYR   ( 122-)  A 1   4.66

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 : -4.882

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.250
Model 2 : -4.441
Model 3 : -5.334
Model 4 : -4.513
Model 5 : -4.906
Model 6 : -5.078
Model 7 : -4.022
Model 8 : -4.737
Model 9 : -5.133
Model 10 : -5.050
Model 11 : -4.795
Model 12 : -5.102
Model 13 : -4.509
Model 14 : -4.768
Model 15 : -5.461
Model 16 : -4.924
Model 17 : -5.242
Model 18 : -4.469
Model 19 : -5.237
Model 20 : -4.666

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.

2724 PRO   (  55-)  A 1   -3.1
2567 PRO   (  55-)  A 1   -3.1
2367 PRO   (  12-)  A 1   -3.1
1746 PHE   (  19-)  A 1   -3.1
 176 PHE   (  19-)  A    -3.1
1939 PRO   (  55-)  A 1   -3.1
1154 PRO   (  55-)  A    -3.1
1625 PRO   (  55-)  A 1   -3.0
 326 PRO   (  12-)  A    -3.0
 369 PRO   (  55-)  A    -3.0
1072 PRO   ( 130-)  A    -3.0
2485 PRO   ( 130-)  A 1   -3.0
  55 PRO   (  55-)  A    -3.0
2171 PRO   ( 130-)  A 1   -3.0
2328 PRO   ( 130-)  A 1   -3.0
1132 PRO   (  33-)  A    -3.0
1857 PRO   ( 130-)  A 1   -3.0
 526 PRO   (  55-)  A    -3.0
1543 PRO   ( 130-)  A 1   -3.0
1229 PRO   ( 130-)  A    -3.0
3113 PRO   ( 130-)  A 2   -3.0
 444 PRO   ( 130-)  A    -3.0
2980 HIS   ( 154-)  A 1   -3.0
2642 PRO   ( 130-)  A 1   -3.0
1705 HIS   ( 135-)  A 1   -3.0
And so on for a total of 360 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.

   6 ALA   (   6-)  A  Poor phi/psi
   8 GLU   (   8-)  A  Poor phi/psi
   9 ALA   (   9-)  A  Poor phi/psi
  14 ALA   (  14-)  A  Poor phi/psi
  15 LEU   (  15-)  A  Poor phi/psi
  16 ALA   (  16-)  A  Poor phi/psi
  17 ARG   (  17-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  21 ALA   (  21-)  A  Poor phi/psi
  25 PRO   (  25-)  A  Poor phi/psi
  36 TRP   (  36-)  A  Poor phi/psi
  57 SER   (  57-)  A  Poor phi/psi
  63 GLY   (  63-)  A  Poor phi/psi
  85 GLU   (  85-)  A  Poor phi/psi
  93 CYS   (  93-)  A  Poor phi/psi
  95 VAL   (  95-)  A  Poor phi/psi
 121 CYS   ( 121-)  A  Poor phi/psi
 130 PRO   ( 130-)  A  omega poor
 135 HIS   ( 135-)  A  Poor phi/psi
 156 HIS   ( 156-)  A  Poor phi/psi
 165 GLU   (   8-)  A  Poor phi/psi
 167 GLU   (  10-)  A  Poor phi/psi
 175 GLU   (  18-)  A  Poor phi/psi
 182 PRO   (  25-)  A  Poor phi/psi
 188 PRO   (  31-)  A  Poor phi/psi
And so on for a total of 339 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 : -5.319

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 : -4.846
Model 2 : -5.096
Model 3 : -4.884
Model 4 : -5.519
Model 5 : -5.482
Model 6 : -5.408
Model 7 : -5.237
Model 8 : -5.263
Model 9 : -5.614
Model 10 : -5.520
Model 11 : -5.607
Model 12 : -5.839
Model 13 : -5.427
Model 14 : -5.410
Model 15 : -5.832
Model 16 : -4.576
Model 17 : -4.763
Model 18 : -6.005
Model 19 : -5.279
Model 20 : -4.772

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 GLN   (   3-)  A      0
   5 PRO   (   5-)  A      0
   6 ALA   (   6-)  A      0
   7 GLU   (   7-)  A      0
   8 GLU   (   8-)  A      0
   9 ALA   (   9-)  A      0
  10 GLU   (  10-)  A      0
  11 GLN   (  11-)  A      0
  12 PRO   (  12-)  A      0
  14 ALA   (  14-)  A      0
  15 LEU   (  15-)  A      0
  16 ALA   (  16-)  A      0
  17 ARG   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 PHE   (  19-)  A      0
  20 LEU   (  20-)  A      0
  21 ALA   (  21-)  A      0
  22 ALA   (  22-)  A      0
  24 GLU   (  24-)  A      0
  25 PRO   (  25-)  A      0
  29 PRO   (  29-)  A      0
  30 ALA   (  30-)  A      0
  31 PRO   (  31-)  A      0
  34 GLU   (  34-)  A      0
  35 GLU   (  35-)  A      0
And so on for a total of 1818 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 5.908
Model 2 : 6.220
Model 3 : 5.962
Model 4 : 5.983
Model 5 : 5.947
Model 6 : 5.904
Model 7 : 5.828
Model 8 : 5.788
Model 9 : 6.048
Model 10 : 5.742
Model 11 : 6.158
Model 12 : 5.802
Model 13 : 5.827
Model 14 : 6.115
Model 15 : 5.899
Model 16 : 6.234
Model 17 : 5.734
Model 18 : 6.066
Model 19 : 5.973
Model 20 : 5.821

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!

 527 GLY   (  56-)  A   2.57   20
1940 GLY   (  56-)  A 1  2.55   10
 370 GLY   (  56-)  A   2.48   37
1312 GLY   (  56-)  A   2.37   42
1155 GLY   (  56-)  A   2.32   38
 998 GLY   (  56-)  A   2.32   32
1626 GLY   (  56-)  A 1  2.25   80
 213 GLY   (  56-)  A   2.20   12
2882 GLY   (  56-)  A 1  2.19   13
2411 GLY   (  56-)  A 1  2.17   80
  56 GLY   (  56-)  A   2.15   80
 684 GLY   (  56-)  A   2.14   80
3039 GLY   (  56-)  A 2  2.00   58
 841 GLY   (  56-)  A   1.98   77
2097 GLY   (  56-)  A 1  1.91   22
1783 GLY   (  56-)  A 1  1.75   15
1469 GLY   (  56-)  A 1  1.71   69

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]

 134 PRO   ( 134-)  A    0.17 LOW
 575 PRO   ( 104-)  A    0.16 LOW
1026 PRO   (  84-)  A    0.20 LOW
1076 PRO   ( 134-)  A    0.08 LOW
1360 PRO   ( 104-)  A    0.12 LOW
1517 PRO   ( 104-)  A 1   0.07 LOW
1968 PRO   (  84-)  A 1   0.18 LOW
2175 PRO   ( 134-)  A 1   0.20 LOW
2302 PRO   ( 104-)  A 1   0.08 LOW
2459 PRO   ( 104-)  A 1   0.06 LOW
3087 PRO   ( 104-)  A 2   0.11 LOW
3117 PRO   ( 134-)  A 2   0.14 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].

  12 PRO   (  12-)  A    39.4 envelop C-delta (36 degrees)
  29 PRO   (  29-)  A    29.8 envelop C-delta (36 degrees)
  33 PRO   (  33-)  A    27.3 envelop C-delta (36 degrees)
  52 PRO   (  52-)  A   -37.1 envelop C-alpha (-36 degrees)
  54 PRO   (  54-)  A  -118.9 half-chair C-delta/C-gamma (-126 degrees)
  55 PRO   (  55-)  A   129.8 half-chair C-beta/C-alpha (126 degrees)
  84 PRO   (  84-)  A    33.0 envelop C-delta (36 degrees)
 130 PRO   ( 130-)  A    21.4 half-chair N/C-delta (18 degrees)
 133 PRO   ( 133-)  A   116.2 envelop C-beta (108 degrees)
 169 PRO   (  12-)  A   -23.9 half-chair C-alpha/N (-18 degrees)
 184 PRO   (  27-)  A    45.7 half-chair C-delta/C-gamma (54 degrees)
 186 PRO   (  29-)  A  -116.1 envelop C-gamma (-108 degrees)
 209 PRO   (  52-)  A   -43.7 envelop C-alpha (-36 degrees)
 212 PRO   (  55-)  A  -124.4 half-chair C-delta/C-gamma (-126 degrees)
 281 PRO   ( 124-)  A   -11.6 half-chair C-alpha/N (-18 degrees)
 287 PRO   ( 130-)  A    11.9 half-chair N/C-delta (18 degrees)
 290 PRO   ( 133-)  A   113.4 envelop C-beta (108 degrees)
 291 PRO   ( 134-)  A  -124.9 half-chair C-delta/C-gamma (-126 degrees)
 318 PRO   (   4-)  A    19.6 half-chair N/C-delta (18 degrees)
 326 PRO   (  12-)  A   139.0 envelop C-alpha (144 degrees)
 341 PRO   (  27-)  A  -112.6 envelop C-gamma (-108 degrees)
 343 PRO   (  29-)  A  -129.2 half-chair C-delta/C-gamma (-126 degrees)
 345 PRO   (  31-)  A  -112.2 envelop C-gamma (-108 degrees)
 366 PRO   (  52-)  A   -37.8 envelop C-alpha (-36 degrees)
 369 PRO   (  55-)  A   138.4 envelop C-alpha (144 degrees)
And so on for a total of 188 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.

1192 CYS   (  93-)  A      SG  <-> 1196 GLN   (  97-)  A      NE2    0.39    2.91
2625 MET   ( 113-)  A 1    SD  <-> 2651 CYS   ( 139-)  A 1    SG     0.32    3.13
2122 GLN   (  81-)  A 1    NE2 <-> 2163 TYR   ( 122-)  A 1    OH     0.31    2.39
 429 THR   ( 115-)  A      CG2 <->  453 CYS   ( 139-)  A      SG     0.29    3.11
2397 ASN   (  42-)  A 1    ND2 <-> 2400 LEU   (  45-)  A 1    N      0.22    2.63
1217 SER   ( 118-)  A      O   <-> 1222 GLY   ( 123-)  A      N      0.21    2.49
2156 THR   ( 115-)  A 1    CG2 <-> 2180 CYS   ( 139-)  A 1    SG     0.21    3.19
2002 SER   ( 118-)  A 1    O   <-> 2007 GLY   ( 123-)  A 1    N      0.21    2.49
 900 THR   ( 115-)  A      CG2 <->  924 CYS   ( 139-)  A      SG     0.21    3.19
1845 SER   ( 118-)  A 1    O   <-> 1850 GLY   ( 123-)  A 1    N      0.20    2.50
1769 ASN   (  42-)  A 1    ND2 <-> 1772 LEU   (  45-)  A 1    N      0.20    2.65
1999 THR   ( 115-)  A 1    CG2 <-> 2023 CYS   ( 139-)  A 1    SG     0.20    3.20
 118 SER   ( 118-)  A      O   <->  123 GLY   ( 123-)  A      N      0.20    2.50
 275 SER   ( 118-)  A      O   <->  280 GLY   ( 123-)  A      N      0.20    2.50
2787 SER   ( 118-)  A 1    O   <-> 2792 GLY   ( 123-)  A 1    N      0.20    2.50
 903 SER   ( 118-)  A      O   <->  908 GLY   ( 123-)  A      N      0.20    2.50
2291 CYS   (  93-)  A 1    SG  <-> 2295 GLN   (  97-)  A 1    NE2    0.20    3.10
2159 SER   ( 118-)  A 1    O   <-> 2164 GLY   ( 123-)  A 1    N      0.20    2.50
2542 ALA   (  30-)  A 1    N   <-> 2543 PRO   (  31-)  A 1    CD     0.20    2.80
3101 SER   ( 118-)  A 2    O   <-> 3106 GLY   ( 123-)  A 2    N      0.20    2.50
 577 MET   ( 106-)  A      SD  <->  615 LEU   ( 144-)  A      CB     0.20    3.20
1688 SER   ( 118-)  A 1    O   <-> 1693 GLY   ( 123-)  A 1    N      0.20    2.50
2944 SER   ( 118-)  A 1    O   <-> 2949 GLY   ( 123-)  A 1    N      0.19    2.51
1060 SER   ( 118-)  A      O   <-> 1065 GLY   ( 123-)  A      N      0.19    2.51
 270 MET   ( 113-)  A      CG  <->  296 CYS   ( 139-)  A      SG     0.19    3.21
And so on for a total of 868 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