WHAT IF Check report

This file was created 2012-01-19 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 pdb1zgg.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: 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.

 857 GLU   ( 107-)  A
 946 LYS   (  46-)  A
2464 HIS   (  64-)  A 1

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 MET   (   1-)  A    Zero
   2 ASP   (   2-)  A    Zero
   3 ILE   (   3-)  A    Zero
   4 ILE   (   4-)  A    Zero
   5 PHE   (   5-)  A    Zero
   6 VAL   (   6-)  A    Zero
   7 CYS   (   7-)  A    Zero
   8 THR   (   8-)  A    Zero
   9 GLY   (   9-)  A    Zero
  10 ASN   (  10-)  A    Zero
  11 THR   (  11-)  A    Zero
  12 CYS   (  12-)  A    Zero
  13 ARG   (  13-)  A    Zero
  14 SER   (  14-)  A    Zero
  15 PRO   (  15-)  A    Zero
  16 MET   (  16-)  A    Zero
  17 ALA   (  17-)  A    Zero
  18 GLU   (  18-)  A    Zero
  19 ALA   (  19-)  A    Zero
  20 LEU   (  20-)  A    Zero
  21 PHE   (  21-)  A    Zero
  22 LYS   (  22-)  A    Zero
  23 SER   (  23-)  A    Zero
  24 ILE   (  24-)  A    Zero
  25 ALA   (  25-)  A    Zero
And so on for a total of 3000 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 : 0.526
Model 2 : 0.527
Model 3 : 0.524
Model 4 : 0.524
Model 5 : 0.526
Model 6 : 0.527
Model 7 : 0.529
Model 8 : 0.525
Model 9 : 0.528
Model 10 : 0.525
Model 11 : 0.527
Model 12 : 0.530
Model 13 : 0.531
Model 14 : 0.533
Model 15 : 0.528
Model 16 : 0.530
Model 17 : 0.524
Model 18 : 0.530
Model 19 : 0.529
Model 20 : 0.527

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.

  21 PHE   (  21-)  A      CA   CB   CG  109.29   -4.5
  87 HIS   (  87-)  A      CB   CG   ND1 128.58    4.7
 150 ARG   ( 150-)  A     -C    N    CA  130.41    4.8
 171 PHE   (  21-)  A      CA   CB   CG  109.13   -4.7
 266 VAL   ( 116-)  A      CA   CB   CG1 117.65    4.2
 310 ASN   (  10-)  A     -C    N    CA  129.32    4.2
 321 PHE   (  21-)  A      CA   CB   CG  108.73   -5.1
 335 ARG   (  35-)  A      CD   NE   CZ  132.12    5.8
 340 PHE   (  40-)  A      CA   CB   CG  119.21    5.4
 387 HIS   (  87-)  A      CB   CG   ND1 128.76    4.8
 387 HIS   (  87-)  A      CB   CG   CD2 123.89   -4.0
 471 PHE   (  21-)  A      CA   CB   CG  109.66   -4.1
 537 HIS   (  87-)  A      CB   CG   ND1 129.08    5.0
 549 ARG   (  99-)  A     -C    N    CA  129.03    4.1
 566 VAL   ( 116-)  A      CA   CB   CG1 117.56    4.2
 687 HIS   (  87-)  A      CB   CG   ND1 128.69    4.7
 771 PHE   (  21-)  A      CA   CB   CG  109.13   -4.7
 837 HIS   (  87-)  A      CB   CG   ND1 127.73    4.1
 910 ASN   (  10-)  A     -C    N    CA  129.85    4.5
 911 THR   (  11-)  A     -C    N    CA  129.14    4.1
 987 HIS   (  87-)  A      CB   CG   ND1 128.58    4.7
1100 HIS   (  50-)  A      CB   CG   ND1 128.08    4.3
1181 ARG   ( 131-)  A      CD   NE   CZ  130.14    4.7
1210 ASN   (  10-)  A     -C    N    CA  129.15    4.1
1221 PHE   (  21-)  A      CA   CB   CG  109.34   -4.5
And so on for a total of 58 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.076
Model 2 : 1.031
Model 3 : 1.077
Model 4 : 1.047
Model 5 : 1.028
Model 6 : 1.042
Model 7 : 1.057
Model 8 : 1.052
Model 9 : 1.055
Model 10 : 1.070
Model 11 : 1.073
Model 12 : 1.055
Model 13 : 1.033
Model 14 : 1.046
Model 15 : 1.046
Model 16 : 1.045
Model 17 : 1.061
Model 18 : 1.052
Model 19 : 1.070
Model 20 : 1.060

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

2882 VAL   (  32-)  A 2    CB     6.4   -24.60   -32.96
The average deviation= 1.182

Note: Per-model averages for chirality check

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

Model 1 : 0.994
Model 2 : 0.932
Model 3 : 0.975
Model 4 : 0.948
Model 5 : 0.948
Model 6 : 0.974
Model 7 : 0.913
Model 8 : 0.983
Model 9 : 0.978
Model 10 : 0.943
Model 11 : 0.945
Model 12 : 1.007
Model 13 : 0.935
Model 14 : 0.943
Model 15 : 0.951
Model 16 : 0.929
Model 17 : 0.950
Model 18 : 0.998
Model 19 : 0.953
Model 20 : 0.994

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.

1349 ARG   ( 149-)  A    4.20

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

1627 TYR   ( 127-)  A 1    OH   4.24
1221 PHE   (  21-)  A      CB   4.10
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.155

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -0.970
Model 2 : -1.024
Model 3 : -1.521
Model 4 : -1.499
Model 5 : -0.950
Model 6 : -1.318
Model 7 : -1.077
Model 8 : -0.967
Model 9 : -1.010
Model 10 : -1.684
Model 11 : -1.341
Model 12 : -0.802
Model 13 : -1.093
Model 14 : -0.815
Model 15 : -0.838
Model 16 : -1.400
Model 17 : -1.304
Model 18 : -1.092
Model 19 : -1.033
Model 20 : -1.365

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.

 911 THR   (  11-)  A    -2.6
2669 PRO   ( 119-)  A 1   -2.6
1661 THR   (  11-)  A 1   -2.6
2909 HIS   (  59-)  A 2   -2.6
 248 TYR   (  98-)  A    -2.6
2484 THR   (  84-)  A 1   -2.6
  98 TYR   (  98-)  A    -2.6
1559 HIS   (  59-)  A 1   -2.6
 809 HIS   (  59-)  A    -2.6
2159 HIS   (  59-)  A 1   -2.6
2309 HIS   (  59-)  A 1   -2.5
1259 HIS   (  59-)  A    -2.5
2759 HIS   (  59-)  A 1   -2.5
2009 HIS   (  59-)  A 1   -2.5
1109 HIS   (  59-)  A    -2.5
2882 VAL   (  32-)  A 2   -2.5
2648 TYR   (  98-)  A 1   -2.5
2459 HIS   (  59-)  A 1   -2.5
2609 HIS   (  59-)  A 1   -2.5
 659 HIS   (  59-)  A    -2.5
  59 HIS   (  59-)  A    -2.5
2219 PRO   ( 119-)  A 1   -2.5
2519 PRO   ( 119-)  A 1   -2.5
1019 PRO   ( 119-)  A    -2.4
1748 TYR   (  98-)  A 1   -2.4
And so on for a total of 90 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.

  10 ASN   (  10-)  A  Poor phi/psi
  13 ARG   (  13-)  A  Poor phi/psi
  32 VAL   (  32-)  A  omega poor
  43 PRO   (  43-)  A  Poor phi/psi
  44 ASN   (  44-)  A  omega poor
  59 HIS   (  59-)  A  Poor phi/psi
  70 THR   (  70-)  A  omega poor
  94 GLN   (  94-)  A  omega poor
  97 ARG   (  97-)  A  omega poor
 148 ASP   ( 148-)  A  omega poor
 149 ARG   ( 149-)  A  Poor phi/psi
 160 ASN   (  10-)  A  Poor phi/psi
 163 ARG   (  13-)  A  Poor phi/psi
 182 VAL   (  32-)  A  omega poor
 185 ARG   (  35-)  A  omega poor
 193 PRO   (  43-)  A  Poor phi/psi
 194 ASN   (  44-)  A  omega poor
 197 ALA   (  47-)  A  Poor phi/psi
 209 HIS   (  59-)  A  Poor phi/psi
 220 THR   (  70-)  A  omega poor
 247 ARG   (  97-)  A  omega poor
 298 ASP   ( 148-)  A  Poor phi/psi, omega poor
 310 ASN   (  10-)  A  Poor phi/psi
 313 ARG   (  13-)  A  Poor phi/psi
 332 VAL   (  32-)  A  omega poor
And so on for a total of 197 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.548

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 : -3.859
Model 2 : -3.429
Model 3 : -3.889
Model 4 : -2.997
Model 5 : -3.592
Model 6 : -3.922
Model 7 : -3.938
Model 8 : -3.395
Model 9 : -3.065
Model 10 : -3.062
Model 11 : -3.313
Model 12 : -3.691
Model 13 : -3.853
Model 14 : -3.047
Model 15 : -3.077
Model 16 : -3.467
Model 17 : -3.574
Model 18 : -3.687
Model 19 : -3.712
Model 20 : -4.382

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.

  23 SER   (  23-)  A    0.33
1373 SER   (  23-)  A 1   0.33
2423 SER   (  23-)  A 1   0.33
2573 SER   (  23-)  A 1   0.33
2723 SER   (  23-)  A 1   0.33
2873 SER   (  23-)  A 2   0.36
1223 SER   (  23-)  A    0.36
1523 SER   (  23-)  A 1   0.36
2273 SER   (  23-)  A 1   0.36
1007 GLU   ( 107-)  A    0.38
1757 GLU   ( 107-)  A 1   0.39

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!

   7 CYS   (   7-)  A      0
   8 THR   (   8-)  A      0
  10 ASN   (  10-)  A      0
  12 CYS   (  12-)  A      0
  13 ARG   (  13-)  A      0
  28 GLU   (  28-)  A      0
  31 ASN   (  31-)  A      0
  33 ASN   (  33-)  A      0
  35 ARG   (  35-)  A      0
  36 SER   (  36-)  A      0
  40 PHE   (  40-)  A      0
  41 ALA   (  41-)  A      0
  46 LYS   (  46-)  A      0
  58 LYS   (  58-)  A      0
  59 HIS   (  59-)  A      0
  60 ILE   (  60-)  A      0
  61 ALA   (  61-)  A      0
  63 ASN   (  63-)  A      0
  64 HIS   (  64-)  A      0
  66 SER   (  66-)  A      0
  78 ASP   (  78-)  A      0
  83 MET   (  83-)  A      0
  85 HIS   (  85-)  A      0
  97 ARG   (  97-)  A      0
  98 TYR   (  98-)  A      0
And so on for a total of 1115 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.408

Note: Per-model averages for omega angle check

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

Model 1 : 8.024
Model 2 : 7.347
Model 3 : 7.327
Model 4 : 7.183
Model 5 : 7.233
Model 6 : 7.567
Model 7 : 7.136
Model 8 : 7.302
Model 9 : 7.105
Model 10 : 7.536
Model 11 : 7.554
Model 12 : 7.230
Model 13 : 7.906
Model 14 : 7.502
Model 15 : 6.866
Model 16 : 7.616
Model 17 : 7.519
Model 18 : 7.267
Model 19 : 7.818
Model 20 : 7.473

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!

2196 GLY   (  96-)  A 1  2.72   12
 546 GLY   (  96-)  A   2.49   10
 499 PRO   (  49-)  A   2.22   11
 696 GLY   (  96-)  A   2.21   10
 199 PRO   (  49-)  A   2.15   12
2449 PRO   (  49-)  A 1  2.10   10
1249 PRO   (  49-)  A   2.01   11
 349 PRO   (  49-)  A   1.88   13
2299 PRO   (  49-)  A 1  1.87   12
 649 PRO   (  49-)  A   1.86   13
1849 PRO   (  49-)  A 1  1.84   12
2749 PRO   (  49-)  A 1  1.68   11
2899 PRO   (  49-)  A 2  1.67   12
 799 PRO   (  49-)  A   1.66   12
2942 ALA   (  92-)  A 2  1.60   46
1592 ALA   (  92-)  A 1  1.57   46

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.

2563 ARG   (  13-)  A 1    NH1 <-> 2633 MET   (  83-)  A 1    SD     0.22    3.08
2263 ARG   (  13-)  A 1    NH1 <-> 2333 MET   (  83-)  A 1    SD     0.21    3.09
 163 ARG   (  13-)  A      NH1 <->  233 MET   (  83-)  A      SD     0.17    3.13
 463 ARG   (  13-)  A      NH1 <->  533 MET   (  83-)  A      SD     0.15    3.15
 913 ARG   (  13-)  A      NH1 <->  983 MET   (  83-)  A      SD     0.14    3.16
1063 ARG   (  13-)  A      NH1 <-> 1133 MET   (  83-)  A      SD     0.14    3.16
1363 ARG   (  13-)  A 1    NH1 <-> 1433 MET   (  83-)  A 1    SD     0.14    3.16
1213 ARG   (  13-)  A      NH1 <-> 1283 MET   (  83-)  A      SD     0.14    3.16
1208 THR   (   8-)  A      N   <-> 1287 HIS   (  87-)  A      NE2    0.12    2.88
  13 ARG   (  13-)  A      NH1 <->   83 MET   (  83-)  A      SD     0.12    3.18
 394 GLN   (  94-)  A      NE2 <->  395 PHE   (  95-)  A      CZ     0.12    2.98
 674 MET   (  74-)  A      SD  <->  701 LYS   ( 101-)  A      CE     0.12    3.28
1513 ARG   (  13-)  A 1    NH1 <-> 1583 MET   (  83-)  A 1    SD     0.11    3.19
2257 CYS   (   7-)  A 1    SG  <-> 2333 MET   (  83-)  A 1    CG     0.10    3.30
 694 GLN   (  94-)  A      NE2 <->  695 PHE   (  95-)  A      CZ     0.10    3.00
2344 GLN   (  94-)  A 1    NE2 <-> 2345 PHE   (  95-)  A 1    CZ     0.10    3.00
1744 GLN   (  94-)  A 1    NE2 <-> 1745 PHE   (  95-)  A 1    CZ     0.10    3.00
1294 GLN   (  94-)  A      NE2 <-> 1295 PHE   (  95-)  A      CZ     0.10    3.00
2194 GLN   (  94-)  A 1    NE2 <-> 2195 PHE   (  95-)  A 1    CZ     0.09    3.01
1894 GLN   (  94-)  A 1    NE2 <-> 1895 PHE   (  95-)  A 1    CZ     0.09    3.01
1444 GLN   (  94-)  A 1    NE2 <-> 1445 PHE   (  95-)  A 1    CZ     0.08    3.02
 313 ARG   (  13-)  A      NH1 <->  383 MET   (  83-)  A      SD     0.08    3.22
 309 GLY   (   9-)  A      C   <->  312 CYS   (  12-)  A      SG     0.08    3.32
 544 GLN   (  94-)  A      NE2 <->  545 PHE   (  95-)  A      CZ     0.08    3.02
 994 GLN   (  94-)  A      NE2 <->  995 PHE   (  95-)  A      CZ     0.08    3.02
And so on for a total of 81 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


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