WHAT IF Check report

This file was created 2012-01-30 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 pdb2kz5.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.

 365 MET   (   1-)  A    Zero
1200 ARG   (  17-)  A 1   Zero
1255 GLY   (  72-)  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 : 0.562
Model 2 : 0.587
Model 3 : 0.581
Model 4 : 0.580
Model 5 : 0.592
Model 6 : 0.583
Model 7 : 0.577
Model 8 : 0.575
Model 9 : 0.576
Model 10 : 0.567
Model 11 : 0.573
Model 12 : 0.577
Model 13 : 0.580
Model 14 : 0.585
Model 15 : 0.581
Model 16 : 0.571
Model 17 : 0.580
Model 18 : 0.579
Model 19 : 0.579
Model 20 : 0.589

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.

   4 HIS   (   4-)  A      CG   ND1  CE1 109.66    4.1
   5 HIS   (   5-)  A      CG   ND1  CE1 109.67    4.1
  97 HIS   (   6-)  A      CG   ND1  CE1 109.64    4.0
 101 HIS   (  10-)  A      CG   ND1  CE1 109.64    4.0
 185 HIS   (   3-)  A      CG   ND1  CE1 109.62    4.0
 276 HIS   (   3-)  A      CG   ND1  CE1 109.61    4.0
 368 HIS   (   4-)  A      CG   ND1  CE1 109.62    4.0
 370 HIS   (   6-)  A      CG   ND1  CE1 109.72    4.1
 371 HIS   (   7-)  A      CG   ND1  CE1 109.60    4.0
 462 HIS   (   7-)  A      CG   ND1  CE1 109.71    4.1
 644 HIS   (   7-)  A      CG   ND1  CE1 109.64    4.0
 731 HIS   (   3-)  A      CG   ND1  CE1 109.71    4.1
 735 HIS   (   7-)  A      CG   ND1  CE1 109.61    4.0
1006 HIS   (   5-)  A 1    CG   ND1  CE1 109.61    4.0
1009 HIS   (   8-)  A 1    CG   ND1  CE1 109.62    4.0
1190 HIS   (   7-)  A 1    CG   ND1  CE1 109.66    4.1
1372 HIS   (   7-)  A 1    CG   ND1  CE1 109.75    4.2
1466 HIS   (  10-)  A 1    CG   ND1  CE1 109.60    4.0
1553 HIS   (   6-)  A 1    CG   ND1  CE1 109.73    4.1
1555 HIS   (   8-)  A 1    CG   ND1  CE1 109.64    4.0
1641 HIS   (   3-)  A 1    CG   ND1  CE1 109.63    4.0
1733 HIS   (   4-)  A 2    CG   ND1  CE1 109.61    4.0
1734 HIS   (   5-)  A 2    CG   ND1  CE1 109.68    4.1
1735 HIS   (   6-)  A 2    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 : 0.578
Model 2 : 0.578
Model 3 : 0.572
Model 4 : 0.576
Model 5 : 0.597
Model 6 : 0.578
Model 7 : 0.580
Model 8 : 0.571
Model 9 : 0.574
Model 10 : 0.575
Model 11 : 0.575
Model 12 : 0.577
Model 13 : 0.562
Model 14 : 0.575
Model 15 : 0.577
Model 16 : 0.575
Model 17 : 0.585
Model 18 : 0.580
Model 19 : 0.583
Model 20 : 0.585

Note: Per-model averages for chirality check

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

Model 1 : 0.370
Model 2 : 0.368
Model 3 : 0.331
Model 4 : 0.348
Model 5 : 0.368
Model 6 : 0.353
Model 7 : 0.346
Model 8 : 0.350
Model 9 : 0.354
Model 10 : 0.352
Model 11 : 0.345
Model 12 : 0.335
Model 13 : 0.331
Model 14 : 0.339
Model 15 : 0.367
Model 16 : 0.324
Model 17 : 0.362
Model 18 : 0.372
Model 19 : 0.344
Model 20 : 0.357

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -2.923
Model 2 : -3.306
Model 3 : -2.145
Model 4 : -2.091
Model 5 : -2.796
Model 6 : -3.189
Model 7 : -1.591
Model 8 : -1.560
Model 9 : -4.211
Model 10 : -2.909
Model 11 : -2.755
Model 12 : -2.487
Model 13 : -2.540
Model 14 : -3.131
Model 15 : -3.397
Model 16 : -3.219
Model 17 : -2.765
Model 18 : -3.773
Model 19 : -2.740
Model 20 : -3.210

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.

1561 PRO   (  14-)  A 1   -2.8
 924 PRO   (  14-)  A 1   -2.8
1635 THR   (  88-)  A 1   -2.8
 809 TYR   (  81-)  A    -2.7
1743 PRO   (  14-)  A 2   -2.7
 651 PRO   (  14-)  A    -2.6
 105 PRO   (  14-)  A    -2.6
1308 PRO   (  34-)  A 1   -2.4
1490 PRO   (  34-)  A 1   -2.4
1180 THR   (  88-)  A 1   -2.3
 826 HIS   (   7-)  A 1   -2.3
 266 ARG   (  84-)  A    -2.3
 560 PRO   (  14-)  A    -2.3
1380 THR   (  15-)  A 1   -2.2
 457 GLY   (   2-)  A    -2.2
1110 GLY   (  18-)  A 1   -2.2
1672 PRO   (  34-)  A 1   -2.2
 580 PRO   (  34-)  A    -2.2
 730 GLY   (   2-)  A    -2.2
1763 PRO   (  34-)  A 2   -2.2
1747 GLY   (  18-)  A 2   -2.2
  18 GLY   (  18-)  A    -2.2
 998 THR   (  88-)  A 1   -2.2
  34 PRO   (  34-)  A    -2.2
 200 GLY   (  18-)  A    -2.2
 203 GLY   (  21-)  A    -2.2
 639 GLY   (   2-)  A    -2.2
  14 PRO   (  14-)  A    -2.2
1564 ARG   (  17-)  A 1   -2.1
 840 GLY   (  21-)  A 1   -2.1
1022 GLY   (  21-)  A 1   -2.1
1634 GLU   (  87-)  A 1   -2.1
 837 GLY   (  18-)  A 1   -2.1
1035 PRO   (  34-)  A 1   -2.1
1566 GLU   (  19-)  A 1   -2.0
 275 GLY   (   2-)  A    -2.0
1543 GLU   (  87-)  A 1   -2.0
 918 HIS   (   8-)  A 1   -2.0
 821 GLY   (   2-)  A 1   -2.0
1656 GLY   (  18-)  A 1   -2.0

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.

   3 HIS   (   3-)  A  Poor phi/psi
  32 LYS   (  32-)  A  Poor phi/psi
  95 HIS   (   4-)  A  Poor phi/psi
 111 ALA   (  20-)  A  Poor phi/psi
 123 LYS   (  32-)  A  Poor phi/psi
 175 ARG   (  84-)  A  Poor phi/psi
 176 LYS   (  85-)  A  Poor phi/psi
 177 LEU   (  86-)  A  Poor phi/psi
 186 HIS   (   4-)  A  Poor phi/psi
 214 LYS   (  32-)  A  Poor phi/psi
 305 LYS   (  32-)  A  Poor phi/psi
 367 HIS   (   3-)  A  omega poor
 377 LYS   (  13-)  A  Poor phi/psi
 396 LYS   (  32-)  A  Poor phi/psi
 467 ALA   (  12-)  A  Poor phi/psi
 487 LYS   (  32-)  A  Poor phi/psi
 559 LYS   (  13-)  A  Poor phi/psi
 560 PRO   (  14-)  A  Poor phi/psi
 578 LYS   (  32-)  A  Poor phi/psi
 628 ARG   (  82-)  A  Poor phi/psi
 656 GLU   (  19-)  A  Poor phi/psi
 669 LYS   (  32-)  A  Poor phi/psi
 693 PRO   (  56-)  A  Poor phi/psi
 734 HIS   (   6-)  A  Poor phi/psi
 748 ALA   (  20-)  A  Poor phi/psi
And so on for a total of 63 lines.

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 : -1.498
Model 2 : -1.496
Model 3 : -1.471
Model 4 : -1.840
Model 5 : -1.059
Model 6 : -0.779
Model 7 : -1.068
Model 8 : -0.818
Model 9 : -2.295
Model 10 : -0.737
Model 11 : -0.432
Model 12 : -1.737
Model 13 : -1.248
Model 14 : -1.478
Model 15 : -1.182
Model 16 : -1.328
Model 17 : -0.545
Model 18 : -1.133
Model 19 : -0.544
Model 20 : -1.132

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.

1425 SER   (  60-)  A 1   0.35

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 HIS   (   3-)  A      0
   4 HIS   (   4-)  A      0
  17 ARG   (  17-)  A      0
  19 GLU   (  19-)  A      0
  20 ALA   (  20-)  A      0
  31 MET   (  31-)  A      0
  55 TYR   (  55-)  A      0
  84 ARG   (  84-)  A      0
  90 VAL   (  90-)  A      0
  91 GLN   (  91-)  A      0
  92 MET   (   1-)  A      0
  93 GLY   (   2-)  A      0
  94 HIS   (   3-)  A      0
  95 HIS   (   4-)  A      0
  96 HIS   (   5-)  A      0
  99 HIS   (   8-)  A      0
 110 GLU   (  19-)  A      0
 122 MET   (  31-)  A      0
 123 LYS   (  32-)  A      0
 145 ARG   (  54-)  A      0
 146 TYR   (  55-)  A      0
 173 ARG   (  82-)  A      0
 174 LYS   (  83-)  A      0
 175 ARG   (  84-)  A      0
 176 LYS   (  85-)  A      0
And so on for a total of 619 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 : 3.506

Note: Per-model averages for omega angle check

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

Model 1 : 3.713
Model 2 : 3.312
Model 3 : 3.678
Model 4 : 3.510
Model 5 : 3.777
Model 6 : 3.236
Model 7 : 3.241
Model 8 : 3.732
Model 9 : 3.623
Model 10 : 3.573
Model 11 : 3.555
Model 12 : 3.046
Model 13 : 3.235
Model 14 : 3.404
Model 15 : 3.627
Model 16 : 2.768
Model 17 : 3.562
Model 18 : 3.598
Model 19 : 4.285
Model 20 : 3.308

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!

  18 GLY   (  18-)  A   1.80   18
 200 GLY   (  18-)  A   1.66   48
 746 GLY   (  18-)  A   1.60   31

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].

  14 PRO   (  14-)  A   -65.9 envelop C-beta (-72 degrees)
  34 PRO   (  34-)  A    28.4 envelop C-delta (36 degrees)
 105 PRO   (  14-)  A   -53.6 half-chair C-beta/C-alpha (-54 degrees)
 378 PRO   (  14-)  A    44.4 envelop C-delta (36 degrees)
 560 PRO   (  14-)  A   -65.7 envelop C-beta (-72 degrees)
 602 PRO   (  56-)  A    48.3 half-chair C-delta/C-gamma (54 degrees)
 651 PRO   (  14-)  A   -55.2 half-chair C-beta/C-alpha (-54 degrees)
 693 PRO   (  56-)  A    51.9 half-chair C-delta/C-gamma (54 degrees)
 924 PRO   (  14-)  A 1  -44.0 envelop C-alpha (-36 degrees)
1288 PRO   (  14-)  A 1  -48.1 half-chair C-beta/C-alpha (-54 degrees)
1308 PRO   (  34-)  A 1  -64.0 envelop C-beta (-72 degrees)
1379 PRO   (  14-)  A 1  -49.6 half-chair C-beta/C-alpha (-54 degrees)
1470 PRO   (  14-)  A 1   36.1 envelop C-delta (36 degrees)
1490 PRO   (  34-)  A 1  -64.9 envelop C-beta (-72 degrees)
1561 PRO   (  14-)  A 1  -56.2 half-chair C-beta/C-alpha (-54 degrees)
1743 PRO   (  14-)  A 2  -33.7 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.

1366 MET   (   1-)  A 1    SD  <-> 1367 GLY   (   2-)  A 1    N      0.29    2.91
 102 MET   (  11-)  A      SD  <->  103 ALA   (  12-)  A      N      0.23    2.97
 496 VAL   (  41-)  A      O   <->  528 LYS   (  73-)  A      NZ     0.20    2.50
 568 SER   (  22-)  A      O   <->  572 ARG   (  26-)  A      NH1    0.14    2.56
 259 ALA   (  77-)  A      O   <->  263 TYR   (  81-)  A      N      0.14    2.56
 225 LEU   (  43-)  A      O   <->  251 ARG   (  69-)  A      NH2    0.13    2.57
1497 VAL   (  41-)  A 1    O   <-> 1529 LYS   (  73-)  A 1    NZ     0.11    2.59
  40 ILE   (  40-)  A      O   <->   69 ARG   (  69-)  A      NH1    0.11    2.59
1592 VAL   (  45-)  A 1    O   <-> 1596 ASN   (  49-)  A 1    ND2    0.10    2.60
 161 ARG   (  70-)  A      O   <->  165 ASN   (  74-)  A      N      0.10    2.60
 222 ILE   (  40-)  A      O   <->  251 ARG   (  69-)  A      NH2    0.10    2.60
1113 GLY   (  21-)  A 1    O   <-> 1115 ARG   (  23-)  A 1    NH2    0.10    2.60
1226 LEU   (  43-)  A 1    O   <-> 1252 ARG   (  69-)  A 1    NH2    0.09    2.61
1412 ASP   (  47-)  A 1    O   <-> 1416 LEU   (  51-)  A 1    N      0.09    2.61
1769 ILE   (  40-)  A 2    O   <-> 1798 ARG   (  69-)  A 2    NH1    0.09    2.61
 749 GLY   (  21-)  A      O   <->  754 ARG   (  26-)  A      NH1    0.09    2.61
1772 LEU   (  43-)  A 2    O   <-> 1798 ARG   (  69-)  A 2    NH1    0.08    2.62
1230 ASP   (  47-)  A 1    O   <-> 1234 LEU   (  51-)  A 1    N      0.08    2.62
1483 ARG   (  27-)  A 1    NH1 <-> 1523 ASP   (  67-)  A 1    OD1    0.07    2.63
 665 ALA   (  28-)  A      O   <->  669 LYS   (  32-)  A      N      0.07    2.63
1215 LYS   (  32-)  A 1    O   <-> 1244 GLN   (  61-)  A 1    NE2    0.06    2.64
 889 ARG   (  70-)  A 1    O   <->  893 ASN   (  74-)  A 1    N      0.06    2.64
1571 ASP   (  24-)  A 1    OD1 <-> 1622 LYS   (  75-)  A 1    NZ     0.06    2.64
1735 HIS   (   6-)  A 2    CG  <-> 1736 HIS   (   7-)  A 2    N      0.06    2.94
 990 ASN   (  80-)  A 1    OD1 <->  993 LYS   (  83-)  A 1    NZ     0.06    2.64
And so on for a total of 74 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: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure