WHAT IF Check report

This file was created 2012-01-31 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 pdb2rmx.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: B; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: B; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: B; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: B; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: B; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: B; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: B; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: B; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: B; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: B; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: B; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: B; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: B; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: B; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: B; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: B; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: B; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: B; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: B; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Note: Ramachandran plot

Chain identifier: B; Model number 20

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 126 PTR   (   8-)  B
 259 PTR   (   8-)  B
 392 PTR   (   8-)  B
 525 PTR   (   8-)  B
 658 PTR   (   8-)  B
 791 PTR   (   8-)  B
 924 PTR   (   8-)  B
1057 PTR   (   8-)  B
1190 PTR   (   8-)  B
1323 PTR   (   8-)  B 1
1456 PTR   (   8-)  B 1
1589 PTR   (   8-)  B 1
1722 PTR   (   8-)  B 1
1855 PTR   (   8-)  B 1
1988 PTR   (   8-)  B 1
2121 PTR   (   8-)  B 1
2254 PTR   (   8-)  B 1
2387 PTR   (   8-)  B 1
2520 PTR   (   8-)  B 1
2653 PTR   (   8-)  B 2

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 GLY   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 GLY   (   4-)  A    Zero
   5 SER   (   5-)  A    Zero
   6 SER   (   6-)  A    Zero
   7 GLY   (   7-)  A    Zero
   8 TRP   (   8-)  A    Zero
   9 TYR   (   9-)  A    Zero
  10 HIS   (  10-)  A    Zero
  11 GLY   (  11-)  A    Zero
  12 HIS   (  12-)  A    Zero
  13 MET   (  13-)  A    Zero
  14 SER   (  14-)  A    Zero
  15 GLY   (  15-)  A    Zero
  16 GLY   (  16-)  A    Zero
  17 GLN   (  17-)  A    Zero
  18 ALA   (  18-)  A    Zero
  19 GLU   (  19-)  A    Zero
  20 THR   (  20-)  A    Zero
  21 LEU   (  21-)  A    Zero
  22 LEU   (  22-)  A    Zero
  23 GLN   (  23-)  A    Zero
  24 ALA   (  24-)  A    Zero
  25 LYS   (  25-)  A    Zero
And so on for a total of 2660 lines.

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.130
Model 2 : 0.130
Model 3 : 0.129
Model 4 : 0.130
Model 5 : 0.128
Model 6 : 0.129
Model 7 : 0.129
Model 8 : 0.129
Model 9 : 0.129
Model 10 : 0.130
Model 11 : 0.131
Model 12 : 0.129
Model 13 : 0.130
Model 14 : 0.129
Model 15 : 0.130
Model 16 : 0.130
Model 17 : 0.130
Model 18 : 0.130
Model 19 : 0.130
Model 20 : 0.129

Note: Per-model averages for bond-angle check

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

Model 1 : 0.330
Model 2 : 0.330
Model 3 : 0.330
Model 4 : 0.330
Model 5 : 0.330
Model 6 : 0.331
Model 7 : 0.331
Model 8 : 0.331
Model 9 : 0.330
Model 10 : 0.331
Model 11 : 0.330
Model 12 : 0.330
Model 13 : 0.332
Model 14 : 0.330
Model 15 : 0.332
Model 16 : 0.330
Model 17 : 0.330
Model 18 : 0.329
Model 19 : 0.332
Model 20 : 0.332

Note: Per-model averages for chirality check

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

Model 1 : 0.281
Model 2 : 0.282
Model 3 : 0.284
Model 4 : 0.283
Model 5 : 0.283
Model 6 : 0.282
Model 7 : 0.282
Model 8 : 0.284
Model 9 : 0.283
Model 10 : 0.282
Model 11 : 0.282
Model 12 : 0.282
Model 13 : 0.281
Model 14 : 0.282
Model 15 : 0.281
Model 16 : 0.283
Model 17 : 0.282
Model 18 : 0.280
Model 19 : 0.281
Model 20 : 0.281

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 : -5.851

Note: Per-model averages for Ramachandran check

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

Model 1 : -5.800
Model 2 : -5.685
Model 3 : -5.227
Model 4 : -5.534
Model 5 : -5.944
Model 6 : -6.358
Model 7 : -6.315
Model 8 : -6.027
Model 9 : -6.130
Model 10 : -5.787
Model 11 : -6.493
Model 12 : -5.125
Model 13 : -5.799
Model 14 : -5.689
Model 15 : -5.393
Model 16 : -5.831
Model 17 : -5.968
Model 18 : -5.963
Model 19 : -6.116
Model 20 : -5.830

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.

2469 THR   (  75-)  A 1   -2.8
 295 TRP   (  29-)  A    -2.7
2423 TRP   (  29-)  A 1   -2.7
 827 TRP   (  29-)  A    -2.7
1891 TRP   (  29-)  A 1   -2.7
 145 HIS   (  12-)  A    -2.7
  29 TRP   (  29-)  A    -2.7
1492 TRP   (  29-)  A 1   -2.7
 561 TRP   (  29-)  A    -2.7
 694 TRP   (  29-)  A    -2.7
 162 TRP   (  29-)  A    -2.7
 960 TRP   (  29-)  A    -2.7
1625 TRP   (  29-)  A 1   -2.7
1226 TRP   (  29-)  A 1   -2.7
2556 TRP   (  29-)  A 2   -2.7
2290 TRP   (  29-)  A 1   -2.6
1359 TRP   (  29-)  A 1   -2.6
2024 TRP   (  29-)  A 1   -2.6
2157 TRP   (  29-)  A 1   -2.6
 428 TRP   (  29-)  A    -2.6
1093 TRP   (  29-)  A    -2.6
1758 TRP   (  29-)  A 1   -2.6
1368 SER   (  38-)  A 1   -2.6
2273 HIS   (  12-)  A 1   -2.6
1149 LEU   (  85-)  A    -2.6
And so on for a total of 209 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.

  29 TRP   (  29-)  A  Poor phi/psi
  36 SER   (  36-)  A  Poor phi/psi
  41 GLY   (  41-)  A  Poor phi/psi
 102 GLY   ( 102-)  A  Poor phi/psi
 110 PRO   ( 110-)  A  Poor phi/psi
 149 GLY   (  16-)  A  Poor phi/psi
 162 TRP   (  29-)  A  Poor phi/psi
 174 GLY   (  41-)  A  Poor phi/psi
 205 GLY   (  72-)  A  Poor phi/psi
 211 GLY   (  78-)  A  Poor phi/psi
 243 PRO   ( 110-)  A  Poor phi/psi
 279 MET   (  13-)  A  Poor phi/psi
 282 GLY   (  16-)  A  Poor phi/psi
 295 TRP   (  29-)  A  Poor phi/psi
 376 PRO   ( 110-)  A  Poor phi/psi
 379 SER   ( 113-)  A  Poor phi/psi
 415 GLY   (  16-)  A  Poor phi/psi
 428 TRP   (  29-)  A  Poor phi/psi
 459 LEU   (  60-)  A  Poor phi/psi
 501 GLY   ( 102-)  A  Poor phi/psi
 561 TRP   (  29-)  A  Poor phi/psi
 592 LEU   (  60-)  A  Poor phi/psi
 634 GLY   ( 102-)  A  Poor phi/psi
 642 PRO   ( 110-)  A  Poor phi/psi
 649 SER   ( 117-)  A  Poor phi/psi
And so on for a total of 99 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 : -5.576

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 : -5.549
Model 2 : -5.873
Model 3 : -5.184
Model 4 : -6.006
Model 5 : -5.384
Model 6 : -5.769
Model 7 : -5.480
Model 8 : -5.454
Model 9 : -5.647
Model 10 : -5.708
Model 11 : -5.721
Model 12 : -5.300
Model 13 : -5.991
Model 14 : -5.618
Model 15 : -5.297
Model 16 : -5.639
Model 17 : -5.953
Model 18 : -5.426
Model 19 : -5.117
Model 20 : -5.404

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.

 171 SER   (  38-)  A    0.36

Warning: Unusual backbone conformations

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

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

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

   8 TRP   (   8-)  A      0
  12 HIS   (  12-)  A      0
  13 MET   (  13-)  A      0
  25 LYS   (  25-)  A      0
  28 PRO   (  28-)  A      0
  29 TRP   (  29-)  A      0
  37 LEU   (  37-)  A      0
  38 SER   (  38-)  A      0
  39 GLN   (  39-)  A      0
  40 PRO   (  40-)  A      0
  42 ASP   (  42-)  A      0
  53 LYS   (  53-)  A      0
  54 ALA   (  54-)  A      0
  56 PRO   (  56-)  A      0
  70 GLU   (  70-)  A      0
  76 VAL   (  76-)  A      0
  80 GLU   (  80-)  A      0
  83 ASP   (  83-)  A      0
  94 LYS   (  94-)  A      0
  95 THR   (  95-)  A      0
 101 SER   ( 101-)  A      0
 109 GLN   ( 109-)  A      0
 113 SER   ( 113-)  A      0
 117 SER   ( 117-)  A      0
 118 GLY   ( 118-)  A      0
And so on for a total of 1155 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 : 0.051

Note: Per-model averages for omega angle check

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

Model 1 : 0.095
Model 2 : 0.097
Model 3 : 0.000
Model 4 : 0.089
Model 5 : 0.140
Model 6 : 0.143
Model 7 : 0.158
Model 8 : 0.000
Model 9 : 0.154
Model 10 : 0.142
Model 11 : 0.000
Model 12 : 0.000
Model 13 : 0.077
Model 14 : 0.137
Model 15 : 0.000
Model 16 : 0.151
Model 17 : 0.103
Model 18 : 0.103
Model 19 : 0.089
Model 20 : 0.057

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!

 204 GLY   (  71-)  A   3.42   10
2598 GLY   (  71-)  A 2  3.29   13
2066 GLY   (  71-)  A 1  3.28   11
2332 GLY   (  71-)  A 1  3.25   11
1933 GLY   (  71-)  A 1  3.22   13
 869 GLY   (  71-)  A   3.07   14
1002 GLY   (  71-)  A   2.93   11
  71 GLY   (  71-)  A   2.63   12
2465 GLY   (  71-)  A 1  2.61   12
2199 GLY   (  71-)  A 1  2.44   10
1135 GLY   (  71-)  A   2.35   11
1268 GLY   (  71-)  A 1  2.34   13
1852 GLY   (   5-)  B 1  2.21   10
1105 GLY   (  41-)  A   1.72   80
2036 GLY   (  41-)  A 1  1.70   80
1577 GLY   ( 114-)  A 1  1.70   14
1637 GLY   (  41-)  A 1  1.68   80
2542 GLY   (  15-)  A 2  1.66   12
1903 GLY   (  41-)  A 1  1.58   80
1744 GLY   (  15-)  A 1  1.57   12
2118 GLY   (   5-)  B 1  1.56   11
 406 GLY   (   7-)  A   1.54   13
2650 GLY   (   5-)  B 2  1.53   19
1736 GLY   (   7-)  A 1  1.52   11
2097 GLY   ( 102-)  A 1  1.51   80

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.

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).

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

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.

1827 GLU   (  98-)  A 1    CD   <->  1833 PHE   ( 104-)  A 1    CE2  0.48    2.72
 763 GLU   (  98-)  A      CD   <->   769 PHE   ( 104-)  A      CE2  0.46    2.74
  98 GLU   (  98-)  A      CD   <->   104 PHE   ( 104-)  A      CE1  0.44    2.76
1827 GLU   (  98-)  A 1    CD   <->  1833 PHE   ( 104-)  A 1    CZ   0.42    2.78
 795 ASN   (  12-)  B      CG   <->   796 LEU   (  13-)  B      N    0.41    2.59
1061 ASN   (  12-)  B      CG   <->  1062 LEU   (  13-)  B      N    0.41    2.59
 763 GLU   (  98-)  A      CD   <->   769 PHE   ( 104-)  A      CZ   0.40    2.80
 529 ASN   (  12-)  B      CG   <->   530 LEU   (  13-)  B      N    0.38    2.62
1859 ASN   (  12-)  B 1    CG   <->  1860 LEU   (  13-)  B 1    N    0.38    2.62
1194 ASN   (  12-)  B      CG   <->  1195 LEU   (  13-)  B      N    0.37    2.63
1327 ASN   (  12-)  B 1    CG   <->  1328 LEU   (  13-)  B 1    N    0.37    2.63
2258 ASN   (  12-)  B 1    CG   <->  2259 LEU   (  13-)  B 1    N    0.36    2.64
2657 ASN   (  12-)  B 2    CG   <->  2658 LEU   (  13-)  B 2    N    0.36    2.64
 662 ASN   (  12-)  B      CG   <->   663 LEU   (  13-)  B      N    0.35    2.65
1803 TYR   (  74-)  A 1    CE2  <->  1814 LEU   (  85-)  A 1    CD2  0.35    2.85
2202 TYR   (  74-)  A 1    CE2  <->  2213 LEU   (  85-)  A 1    CD2  0.34    2.86
 407 TRP   (   8-)  A      CE3  <->   432 VAL   (  33-)  A      CG2  0.34    2.86
 739 TYR   (  74-)  A      CE2  <->   750 LEU   (  85-)  A      CD2  0.33    2.87
2468 TYR   (  74-)  A 1    CE2  <->  2479 LEU   (  85-)  A 1    CD2  0.32    2.88
 340 TYR   (  74-)  A      CE2  <->   351 LEU   (  85-)  A      CD2  0.32    2.88
1161 ILE   (  97-)  A      CG2  <->  1193 LEU   (  11-)  B      CD1  0.31    2.89
 928 ASN   (  12-)  B      CG   <->   929 LEU   (  13-)  B      N    0.31    2.69
  42 ASP   (  42-)  A      C    <->    43 PHE   (  43-)  A      CD1  0.31    2.79
2126 LEU   (  13-)  B 1    N    <->  2127 PRO   (  14-)  B 1    CD   0.31    2.69
1497 ARG   (  34-)  A 1    NH2  <->  1509 SER   (  46-)  A 1    CB   0.30    2.80
And so on for a total of 775 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; 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: B; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: B; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: B; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: B; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: B; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: B; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: B; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: B; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: B; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: B; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: B; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: B; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: B; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: B; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: B; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: B; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: B; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: B; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: B; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Note: Quality value plot

Chain identifier: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; 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: B; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Note: Second generation quality Z-score plot

Chain identifier: B; 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