WHAT IF Check report

This file was created 2011-12-21 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 pdb1clh.ent

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

  48 ARG   (  48-)  A  1
 595 SER   (  98-)  A  4
1179 GLU   (  19-)  A  8
1443 GLN   ( 117-)  A  9

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

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

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 ALA   (   1-)  A    Zero
   2 LYS   (   2-)  A    Zero
   3 GLY   (   3-)  A    Zero
   4 ASP   (   4-)  A    Zero
   5 PRO   (   5-)  A    Zero
   6 HIS   (   6-)  A    Zero
   7 VAL   (   7-)  A    Zero
   8 LEU   (   8-)  A    Zero
   9 LEU   (   9-)  A    Zero
  10 THR   (  10-)  A    Zero
  11 THR   (  11-)  A    Zero
  12 SER   (  12-)  A    Zero
  13 ALA   (  13-)  A    Zero
  14 GLY   (  14-)  A    Zero
  15 ASN   (  15-)  A    Zero
  16 ILE   (  16-)  A    Zero
  17 GLU   (  17-)  A    Zero
  18 LEU   (  18-)  A    Zero
  19 GLU   (  19-)  A    Zero
  20 LEU   (  20-)  A    Zero
  21 ASP   (  21-)  A    Zero
  22 LYS   (  22-)  A    Zero
  23 GLN   (  23-)  A    Zero
  24 LYS   (  24-)  A    Zero
  25 ALA   (  25-)  A    Zero
And so on for a total of 1988 lines.

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.

   6 HIS   (   6-)  A      CG   CD2   1.40    4.2
   6 HIS   (   6-)  A      ND1  CE1   1.37    4.1
  47 HIS   (  47-)  A      CG   CD2   1.40    4.1
  47 HIS   (  47-)  A      ND1  CE1   1.37    4.2
 114 HIS   ( 115-)  A      CG   CD2   1.40    4.0
 114 HIS   ( 115-)  A      ND1  CE1   1.37    4.3
 143 HIS   ( 144-)  A      CG   CD2   1.40    4.3
 143 HIS   ( 144-)  A      ND1  CE1   1.37    4.2
 171 HIS   (   6-)  A      CG   CD2   1.40    4.1
 171 HIS   (   6-)  A      ND1  CE1   1.37    4.2
 212 HIS   (  47-)  A      CG   CD2   1.40    4.1
 212 HIS   (  47-)  A      ND1  CE1   1.37    4.2
 280 HIS   ( 115-)  A      CG   CD2   1.40    4.1
 280 HIS   ( 115-)  A      ND1  CE1   1.37    4.2
 309 HIS   ( 144-)  A      CG   CD2   1.40    4.2
 309 HIS   ( 144-)  A      ND1  CE1   1.37    4.2
 337 HIS   (   6-)  A      CG   CD2   1.40    4.1
 337 HIS   (   6-)  A      ND1  CE1   1.37    4.2
 378 HIS   (  47-)  A      CG   CD2   1.40    4.1
 378 HIS   (  47-)  A      ND1  CE1   1.37    4.3
 446 HIS   ( 115-)  A      CG   CD2   1.40    4.1
 446 HIS   ( 115-)  A      ND1  CE1   1.37    4.2
 475 HIS   ( 144-)  A      CG   CD2   1.40    4.4
 475 HIS   ( 144-)  A      ND1  CE1   1.37    4.2
 503 HIS   (   6-)  A      CG   CD2   1.40    4.1
And so on for a total of 95 lines.

Note: Per-model averages for bond-length check

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

Model 1 : 0.659
Model 2 : 0.646
Model 3 : 0.650
Model 4 : 0.652
Model 5 : 0.652
Model 6 : 0.653
Model 7 : 0.644
Model 8 : 0.656
Model 9 : 0.643
Model 10 : 0.655
Model 11 : 0.657
Model 12 : 0.661

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.

   6 HIS   (   6-)  A      CG   ND1  CE1  98.55   -7.0
   6 HIS   (   6-)  A      ND1  CE1  NE2 120.33    6.6
   6 HIS   (   6-)  A      CE1  NE2  CD2  99.74   -5.5
   6 HIS   (   6-)  A      CD2  CG   ND1 111.34    5.2
  47 HIS   (  47-)  A      CG   ND1  CE1  98.48   -7.1
  47 HIS   (  47-)  A      ND1  CE1  NE2 120.33    6.6
  47 HIS   (  47-)  A      CE1  NE2  CD2  99.75   -5.5
  47 HIS   (  47-)  A      CD2  CG   ND1 111.47    5.4
 114 HIS   ( 115-)  A      CG   ND1  CE1  98.39   -7.2
 114 HIS   ( 115-)  A      ND1  CE1  NE2 120.35    6.7
 114 HIS   ( 115-)  A      CE1  NE2  CD2  99.69   -5.5
 114 HIS   ( 115-)  A      CD2  CG   ND1 111.47    5.4
 114 HIS   ( 115-)  A      CB   CG   CD2 123.72   -4.1
 124 PHE   ( 125-)  A      CA   CB   CG  109.72   -4.1
 143 HIS   ( 144-)  A      CG   ND1  CE1  98.72   -6.9
 143 HIS   ( 144-)  A      ND1  CE1  NE2 120.30    6.6
 143 HIS   ( 144-)  A      CE1  NE2  CD2  99.75   -5.5
 143 HIS   ( 144-)  A      CD2  CG   ND1 111.07    5.0
 171 HIS   (   6-)  A      CG   ND1  CE1  98.49   -7.1
 171 HIS   (   6-)  A      ND1  CE1  NE2 120.40    6.7
 171 HIS   (   6-)  A      CE1  NE2  CD2  99.69   -5.5
 171 HIS   (   6-)  A      CD2  CG   ND1 111.38    5.3
 212 HIS   (  47-)  A      CG   ND1  CE1  98.44   -7.2
 212 HIS   (  47-)  A      ND1  CE1  NE2 120.40    6.7
 212 HIS   (  47-)  A      CE1  NE2  CD2  99.73   -5.5
And so on for a total of 205 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.097
Model 2 : 1.085
Model 3 : 1.080
Model 4 : 1.093
Model 5 : 1.079
Model 6 : 1.083
Model 7 : 1.085
Model 8 : 1.092
Model 9 : 1.087
Model 10 : 1.086
Model 11 : 1.074
Model 12 : 1.101

Note: Per-model averages for chirality check

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

Model 1 : 0.776
Model 2 : 0.730
Model 3 : 0.745
Model 4 : 0.779
Model 5 : 0.737
Model 6 : 0.750
Model 7 : 0.760
Model 8 : 0.764
Model 9 : 0.760
Model 10 : 0.749
Model 11 : 0.755
Model 12 : 0.768

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 : -8.511

Note: Per-model averages for Ramachandran check

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

Model 1 : -8.137
Model 2 : -8.604
Model 3 : -8.920
Model 4 : -8.329
Model 5 : -9.078
Model 6 : -8.631
Model 7 : -8.675
Model 8 : -7.675
Model 9 : -8.334
Model 10 : -8.555
Model 11 : -8.678
Model 12 : -8.483

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.

1633 THR   ( 143-)  A 1   -3.6
1965 THR   ( 143-)  A 1   -3.5
 971 THR   ( 143-)  A    -3.4
 639 THR   ( 143-)  A    -3.4
 474 THR   ( 143-)  A    -3.3
 258 THR   (  93-)  A    -3.3
 142 THR   ( 143-)  A    -3.3
1467 THR   ( 143-)  A    -3.2
1799 THR   ( 143-)  A 1   -3.2
 805 THR   ( 143-)  A    -3.2
 599 PHE   ( 103-)  A    -3.1
 875 HIS   (  47-)  A    -3.1
 308 THR   ( 143-)  A    -3.1
1302 THR   ( 143-)  A    -3.1
 943 HIS   ( 115-)  A    -3.1
 765 PHE   ( 103-)  A    -3.1
1263 PHE   ( 103-)  A    -3.0
 456 PHE   ( 125-)  A    -3.0
 434 PHE   ( 103-)  A    -3.0
1137 THR   ( 143-)  A    -3.0
1925 PHE   ( 103-)  A 1   -3.0
1119 PHE   ( 125-)  A    -3.0
1593 PHE   ( 103-)  A 1   -2.9
1615 PHE   ( 125-)  A 1   -2.9
  70 PRO   (  71-)  A    -2.9
And so on for a total of 257 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.

   2 LYS   (   2-)  A  Poor phi/psi
  21 ASP   (  21-)  A  Poor phi/psi
  22 LYS   (  22-)  A  Poor phi/psi
  38 SER   (  38-)  A  Poor phi/psi
  40 PHE   (  40-)  A  Poor phi/psi
  43 ASN   (  43-)  A  omega poor
  44 THR   (  44-)  A  Poor phi/psi
  45 THR   (  45-)  A  Poor phi/psi
  47 HIS   (  47-)  A  Poor phi/psi
  51 GLY   (  52-)  A  Poor phi/psi
  55 GLN   (  56-)  A  Poor phi/psi, omega poor
  61 GLU   (  62-)  A  Poor phi/psi
  63 MET   (  64-)  A  Poor phi/psi
  66 LYS   (  67-)  A  Poor phi/psi
  68 PRO   (  69-)  A  Poor phi/psi
  69 ASN   (  70-)  A  Poor phi/psi
  72 ILE   (  73-)  A  Poor phi/psi
  73 LYS   (  74-)  A  Poor phi/psi
  75 GLU   (  76-)  A  Poor phi/psi
  77 ASP   (  78-)  A  Poor phi/psi
  79 GLY   (  80-)  A  Poor phi/psi
  80 LEU   (  81-)  A  Poor phi/psi
  82 ASN   (  83-)  A  Poor phi/psi
  90 ALA   (  91-)  A  Poor phi/psi
  91 ARG   (  92-)  A  Poor phi/psi
And so on for a total of 566 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 : -3.102
Model 2 : -2.189
Model 3 : -3.261
Model 4 : -3.201
Model 5 : -2.732
Model 6 : -2.616
Model 7 : -2.468
Model 8 : -3.075
Model 9 : -1.641
Model 10 : -3.277
Model 11 : -3.124
Model 12 : -3.320

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.

 864 VAL   (  36-)  A    0.36
1518 SER   (  28-)  A 1   0.38
 201 VAL   (  36-)  A    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   4 ASP   (   4-)  A      0
  13 ALA   (  13-)  A      0
  15 ASN   (  15-)  A      0
  21 ASP   (  21-)  A      0
  22 LYS   (  22-)  A      0
  37 ASN   (  37-)  A      0
  38 SER   (  38-)  A      0
  40 PHE   (  40-)  A      0
  41 TYR   (  41-)  A      0
  42 ASN   (  42-)  A      0
  43 ASN   (  43-)  A      0
  44 THR   (  44-)  A      0
  45 THR   (  45-)  A      0
  46 PHE   (  46-)  A      0
  47 HIS   (  47-)  A      0
  48 ARG   (  48-)  A      0
  49 ILE   (  50-)  A      0
  50 PRO   (  51-)  A      0
  52 PHE   (  53-)  A      0
  53 MET   (  54-)  A      0
  55 GLN   (  56-)  A      0
  57 GLY   (  58-)  A      0
  59 PHE   (  60-)  A      0
  60 THR   (  61-)  A      0
  61 GLU   (  62-)  A      0
And so on for a total of 1325 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.269

Note: Per-model averages for omega angle check

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

Model 1 : 6.161
Model 2 : 5.182
Model 3 : 5.265
Model 4 : 5.796
Model 5 : 5.035
Model 6 : 6.816
Model 7 : 5.340
Model 8 : 5.193
Model 9 : 5.571
Model 10 : 5.641
Model 11 : 5.398
Model 12 : 5.870

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!

1493 GLY   (   3-)  A 1  2.65   21
   3 GLY   (   3-)  A   2.59   19
1052 GLY   (  58-)  A   2.43   10

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].

 234 PRO   (  69-)  A    99.7 envelop C-beta (108 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.

1410 ARG   (  85-)  A      CB  <-> 1432 VAL   ( 107-)  A      O      1.95    0.85
 747 ARG   (  85-)  A      CB  <->  769 VAL   ( 107-)  A      O      1.78    1.02
  84 ARG   (  85-)  A      CB  <->  106 VAL   ( 107-)  A      O      1.62    1.18
1054 PHE   (  60-)  A      CE1 <-> 1061 LYS   (  67-)  A      NZ     1.51    1.59
1025 ASN   (  31-)  A      O   <-> 1028 ASP   (  34-)  A      OD1    1.48    0.92
  73 LYS   (  74-)  A      O   <->   75 GLU   (  76-)  A      OE2    1.43    0.97
1410 ARG   (  85-)  A      CB  <-> 1432 VAL   ( 107-)  A      C      1.42    1.78
  84 ARG   (  85-)  A      CB  <->  106 VAL   ( 107-)  A      C      1.42    1.78
1274 ASP   ( 114-)  A      O   <-> 1275 HIS   ( 115-)  A      ND1    1.37    1.23
1387 GLU   (  62-)  A      OE1 <-> 1388 GLN   (  63-)  A      OE1    1.35    1.05
1417 ARG   (  92-)  A      CB  <-> 1420 ASP   (  95-)  A      OD2    1.34    1.46
 973 ASP   ( 145-)  A      OD1 <->  978 GLN   ( 150-)  A      OE1    1.32    1.08
 336 PRO   (   5-)  A      O   <->  337 HIS   (   6-)  A      CD2    1.27    1.43
 747 ARG   (  85-)  A      CB  <->  769 VAL   ( 107-)  A      C      1.26    1.94
1013 GLU   (  19-)  A      CG  <-> 1121 LYS   ( 127-)  A      O      1.26    1.54
 503 HIS   (   6-)  A      NE2 <->  516 GLU   (  19-)  A      CG     1.25    1.85
 769 VAL   ( 107-)  A      CG1 <->  794 MET   ( 132-)  A      CE     1.23    1.97
1070 GLU   (  76-)  A      OE2 <-> 1086 ARG   (  92-)  A      CD     1.22    1.58
1252 ARG   (  92-)  A      CG  <-> 1259 ALA   (  99-)  A      N      1.22    1.88
1741 ARG   (  85-)  A 1    CB  <-> 1763 VAL   ( 107-)  A 1    C      1.22    1.98
1402 ALA   (  77-)  A      C   <-> 1440 HIS   ( 115-)  A      CD2    1.22    1.98
 350 GLU   (  19-)  A      OE1 <->  458 LYS   ( 127-)  A      NZ     1.20    1.50
1252 ARG   (  92-)  A      CB  <-> 1259 ALA   (  99-)  A      CA     1.19    2.01
 587 MET   (  90-)  A      CE  <->  598 GLN   ( 102-)  A      OE1    1.19    1.61
 170 PRO   (   5-)  A      O   <->  171 HIS   (   6-)  A      CD2    1.19    1.51
And so on for a total of 3754 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

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Error: Abnormal average packing environment

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

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

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