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 pdb1xke.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.

1798 GLU   ( 108-)  A 1
2375 LEU   (  35-)  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 GLY   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 GLY   (   3-)  A    Zero
   4 GLU   (   4-)  A    Zero
   5 GLU   (   5-)  A    Zero
   6 ASP   (   6-)  A    Zero
   7 GLU   (   7-)  A    Zero
   8 LYS   (   8-)  A    Zero
   9 VAL   (   9-)  A    Zero
  10 LEU   (  10-)  A    Zero
  11 TYR   (  11-)  A    Zero
  12 SER   (  12-)  A    Zero
  13 GLN   (  13-)  A    Zero
  14 ARG   (  14-)  A    Zero
  15 VAL   (  15-)  A    Zero
  16 LYS   (  16-)  A    Zero
  17 LEU   (  17-)  A    Zero
  18 PHE   (  18-)  A    Zero
  19 ARG   (  19-)  A    Zero
  20 PHE   (  20-)  A    Zero
  21 ASP   (  21-)  A    Zero
  22 ALA   (  22-)  A    Zero
  23 GLU   (  23-)  A    Zero
  24 VAL   (  24-)  A    Zero
  25 SER   (  25-)  A    Zero
And so on for a total of 2600 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.

   5 GLU   (   5-)  A      N    CA    1.37   -4.5
   7 GLU   (   7-)  A      N    CA    1.37   -4.5
  20 PHE   (  20-)  A      N   -C     1.23   -4.7
  21 ASP   (  21-)  A      CA   C     1.44   -4.1
  21 ASP   (  21-)  A      N   -C     1.23   -4.9
  22 ALA   (  22-)  A      N   -C     1.22   -5.4
  29 GLU   (  29-)  A      N    CA    1.38   -4.4
  35 LEU   (  35-)  A      N    CA    1.36   -5.3
  35 LEU   (  35-)  A      N   -C     1.25   -4.0
  36 LYS   (  36-)  A      N    CA    1.38   -4.0
  36 LYS   (  36-)  A      N   -C     1.25   -4.0
  46 LEU   (  46-)  A      N    CA    1.37   -4.5
  47 ARG   (  47-)  A      N   -C     1.24   -4.5
  48 MET   (  48-)  A      N   -C     1.24   -4.2
  50 MET   (  50-)  A      N    CA    1.33   -6.9
  51 ARG   (  51-)  A      N   -C     1.19   -7.2
  52 ARG   (  52-)  A      N    CA    1.36   -5.1
  53 GLU   (  53-)  A      CA   C     1.44   -4.3
  62 HIS   (  62-)  A      N   -C     1.23   -4.9
  68 MET   (  68-)  A      N    CA    1.37   -4.7
  70 LEU   (  70-)  A      N    CA    1.37   -4.8
  71 LYS   (  71-)  A      N   -C     1.23   -4.9
  77 ASP   (  77-)  A      N    CA    1.38   -4.1
  81 MET   (  81-)  A      N    CA    1.37   -4.7
  82 TRP   (  82-)  A      N    CA    1.37   -4.5
And so on for a total of 778 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 1.523
RMS-deviation in bond distances: 0.030

Note: Per-model averages for bond-length check

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

Model 1 : 1.526
Model 2 : 1.490
Model 3 : 1.545
Model 4 : 1.491
Model 5 : 1.561
Model 6 : 1.495
Model 7 : 1.510
Model 8 : 1.458
Model 9 : 1.511
Model 10 : 1.522
Model 11 : 1.513
Model 12 : 1.544
Model 13 : 1.554
Model 14 : 1.527
Model 15 : 1.544
Model 16 : 1.499
Model 17 : 1.543
Model 18 : 1.541
Model 19 : 1.536
Model 20 : 1.551

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 ASP   (   6-)  A      CA   CB   CG  118.77    6.2
  21 ASP   (  21-)  A      CA   CB   CG  107.79   -4.8
  26 GLN   (  26-)  A     -C    N    CA  113.51   -4.5
  51 ARG   (  51-)  A      CA   CB   CG  122.53    4.2
  56 LEU   (  56-)  A      N    CA   CB   99.92   -6.2
  57 LYS   (  57-)  A      N    CA   CB  103.27   -4.3
  87 PHE   (  87-)  A      CA   CB   CG  117.98    4.2
  89 ASP   (  89-)  A     -C    N    CA  130.31    4.8
 122 LEU   ( 122-)  A      N    CA   CB  101.12   -5.5
 136 ASP   (   6-)  A      CA   CB   CG  118.16    5.6
 151 ASP   (  21-)  A      CA   CB   CG  108.12   -4.5
 156 GLN   (  26-)  A     -C    N    CA  112.91   -4.9
 177 ARG   (  47-)  A      C    CA   CB  101.92   -4.3
 185 VAL   (  55-)  A      N    CA   CB  103.64   -4.0
 186 LEU   (  56-)  A      N    CA   CB  102.23   -4.9
 217 PHE   (  87-)  A     -C    N    CA  129.25    4.2
 252 LEU   ( 122-)  A      N    CA   CB  101.17   -5.5
 266 ASP   (   6-)  A      CA   CB   CG  116.62    4.0
 281 ASP   (  21-)  A      CA   CB   CG  108.06   -4.5
 286 GLN   (  26-)  A     -C    N    CA  112.24   -5.3
 311 ARG   (  51-)  A      CA   CB   CG  122.70    4.3
 316 LEU   (  56-)  A      N    CA   CB  100.25   -6.0
 382 LEU   ( 122-)  A      N    CA   CB  101.12   -5.5
 382 LEU   ( 122-)  A      C    CA   CB  102.26   -4.1
 411 ASP   (  21-)  A      N    CA   CB  117.37    4.0
And so on for a total of 166 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.089
Model 2 : 1.066
Model 3 : 1.060
Model 4 : 1.099
Model 5 : 1.092
Model 6 : 1.069
Model 7 : 1.066
Model 8 : 1.125
Model 9 : 1.033
Model 10 : 1.061
Model 11 : 1.080
Model 12 : 1.084
Model 13 : 1.044
Model 14 : 1.085
Model 15 : 1.052
Model 16 : 1.073
Model 17 : 1.058
Model 18 : 1.086
Model 19 : 1.046
Model 20 : 1.071

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.

 122 LEU   ( 122-)  A      CA     6.9    44.81    34.19
 252 LEU   ( 122-)  A      CA     7.2    45.19    34.19
 382 LEU   ( 122-)  A      CA     7.2    45.23    34.19
 512 LEU   ( 122-)  A      CA     6.4    44.02    34.19
 642 LEU   ( 122-)  A      CA     6.7    44.37    34.19
 772 LEU   ( 122-)  A      CA     7.2    45.16    34.19
 867 PHE   (  87-)  A      CA    -6.1    24.24    33.98
 902 LEU   ( 122-)  A      CA     7.5    45.64    34.19
1032 LEU   ( 122-)  A      CA     6.2    43.73    34.19
1162 LEU   ( 122-)  A      CA     6.3    43.84    34.19
1292 LEU   ( 122-)  A 1    CA     7.4    45.49    34.19
1329 GLU   (  29-)  A 1    CA    -6.9    22.71    33.96
1422 LEU   ( 122-)  A 1    CA     7.3    45.36    34.19
1552 LEU   ( 122-)  A 1    CA     6.6    44.32    34.19
1682 LEU   ( 122-)  A 1    CA     6.9    44.76    34.19
1812 LEU   ( 122-)  A 1    CA     6.3    43.81    34.19
1942 LEU   ( 122-)  A 1    CA     7.3    45.30    34.19
1979 GLU   (  29-)  A 1    CA    -6.3    23.58    33.96
2072 LEU   ( 122-)  A 1    CA     6.9    44.78    34.19
2202 LEU   ( 122-)  A 1    CA     7.9    46.32    34.19
2332 LEU   ( 122-)  A 1    CA     6.8    44.65    34.19
2462 LEU   ( 122-)  A 1    CA     7.4    45.54    34.19
2584 PHE   ( 114-)  A 2    CA    -8.2    20.83    33.98
2592 LEU   ( 122-)  A 2    CA     6.8    44.64    34.19
The average deviation= 1.572

Note: Per-model averages for chirality check

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

Model 1 : 1.314
Model 2 : 1.365
Model 3 : 1.329
Model 4 : 1.378
Model 5 : 1.337
Model 6 : 1.393
Model 7 : 1.378
Model 8 : 1.366
Model 9 : 1.326
Model 10 : 1.380
Model 11 : 1.399
Model 12 : 1.319
Model 13 : 1.368
Model 14 : 1.349
Model 15 : 1.344
Model 16 : 1.359
Model 17 : 1.337
Model 18 : 1.364
Model 19 : 1.360
Model 20 : 1.419

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

1290 LEU   ( 120-)  A 1   5.40
1030 LEU   ( 120-)  A    4.96
1940 LEU   ( 120-)  A 1   4.79
 510 LEU   ( 120-)  A    4.78
 250 LEU   ( 120-)  A    4.68
 380 LEU   ( 120-)  A    4.66
 770 LEU   ( 120-)  A    4.64
2200 LEU   ( 120-)  A 1   4.63
 577 LYS   (  57-)  A    4.54
1680 LEU   ( 120-)  A 1   4.41
 317 LYS   (  57-)  A    4.39
2527 LYS   (  57-)  A 2   4.39
1160 LEU   ( 120-)  A    4.37
 900 LEU   ( 120-)  A    4.36
1877 LYS   (  57-)  A 1   4.33
1550 LEU   ( 120-)  A 1   4.29
2267 LYS   (  57-)  A 1   4.22
2330 LEU   ( 120-)  A 1   4.21
2460 LEU   ( 120-)  A 1   4.21
1487 LYS   (  57-)  A 1   4.19
1097 LYS   (  57-)  A    4.17
 746 GLN   (  96-)  A    4.15
 640 LEU   ( 120-)  A    4.15
1810 LEU   ( 120-)  A 1   4.06
2397 LYS   (  57-)  A 1   4.06
1639 ALA   (  79-)  A 1   4.05
2070 LEU   ( 120-)  A 1   4.02

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.

2532 HIS   (  62-)  A 2    CB   4.45
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.385

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : -0.953
Model 2 : -1.261
Model 3 : -0.679
Model 4 : -1.455
Model 5 : -1.078
Model 6 : -0.785
Model 7 : -1.759
Model 8 : -1.795
Model 9 : -1.869
Model 10 : -1.650
Model 11 : -1.872
Model 12 : -1.601
Model 13 : -0.971
Model 14 : -1.563
Model 15 : -1.552
Model 16 : -1.048
Model 17 : -1.274
Model 18 : -1.783
Model 19 : -1.518
Model 20 : -1.232

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.

1257 PHE   (  87-)  A 1   -3.5
1647 PHE   (  87-)  A 1   -3.4
1127 PHE   (  87-)  A    -3.4
2427 PHE   (  87-)  A 1   -3.3
 728 ARG   (  78-)  A    -2.8
 598 ARG   (  78-)  A    -2.6
1118 ARG   (  78-)  A    -2.6
1378 ARG   (  78-)  A 1   -2.6
2548 ARG   (  78-)  A 2   -2.5
1508 ARG   (  78-)  A 1   -2.5
2144 ILE   (  64-)  A 1   -2.4
1195 SER   (  25-)  A 1   -2.4
  87 PHE   (  87-)  A    -2.4
 155 SER   (  25-)  A    -2.4
 988 ARG   (  78-)  A    -2.4
 217 PHE   (  87-)  A    -2.4
1975 SER   (  25-)  A 1   -2.4
 747 LEU   (  97-)  A    -2.4
 935 SER   (  25-)  A    -2.4
 463 LEU   (  73-)  A    -2.4
1754 ILE   (  64-)  A 1   -2.4
 194 ILE   (  64-)  A    -2.4
1917 LEU   (  97-)  A 1   -2.4
1743 GLU   (  53-)  A 1   -2.4
  64 ILE   (  64-)  A    -2.3
And so on for a total of 167 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 SER   (   2-)  A  Poor phi/psi
   5 GLU   (   5-)  A  Poor phi/psi
   6 ASP   (   6-)  A  Poor phi/psi
  43 ASN   (  43-)  A  Poor phi/psi
  56 LEU   (  56-)  A  Poor phi/psi
  57 LYS   (  57-)  A  omega poor
  79 ALA   (  79-)  A  omega poor
  89 ASP   (  89-)  A  Poor phi/psi
  91 ASP   (  91-)  A  Poor phi/psi, omega poor
 132 SER   (   2-)  A  Poor phi/psi
 136 ASP   (   6-)  A  Poor phi/psi
 173 ASN   (  43-)  A  Poor phi/psi
 183 GLU   (  53-)  A  Poor phi/psi
 186 LEU   (  56-)  A  Poor phi/psi
 187 LYS   (  57-)  A  omega poor
 216 ASP   (  86-)  A  omega poor
 217 PHE   (  87-)  A  Poor phi/psi
 221 ASP   (  91-)  A  Poor phi/psi
 250 LEU   ( 120-)  A  omega poor
 266 ASP   (   6-)  A  Poor phi/psi
 303 ASN   (  43-)  A  Poor phi/psi
 316 LEU   (  56-)  A  Poor phi/psi
 317 LYS   (  57-)  A  omega poor
 351 ASP   (  91-)  A  Poor phi/psi
 395 GLU   (   5-)  A  Poor phi/psi
And so on for a total of 163 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 : -4.503

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -4.533
Model 2 : -4.870
Model 3 : -4.235
Model 4 : -4.845
Model 5 : -4.638
Model 6 : -5.143
Model 7 : -4.327
Model 8 : -4.179
Model 9 : -4.191
Model 10 : -4.114
Model 11 : -4.502
Model 12 : -3.487
Model 13 : -4.947
Model 14 : -5.320
Model 15 : -4.642
Model 16 : -4.503
Model 17 : -4.373
Model 18 : -4.930
Model 19 : -4.407
Model 20 : -3.869

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!

   5 GLU   (   5-)  A      0
   6 ASP   (   6-)  A      0
  11 TYR   (  11-)  A      0
  14 ARG   (  14-)  A      0
  24 VAL   (  24-)  A      0
  26 GLN   (  26-)  A      0
  30 ARG   (  30-)  A      0
  32 LEU   (  32-)  A      0
  34 ASN   (  34-)  A      0
  40 ASN   (  40-)  A      0
  42 VAL   (  42-)  A      0
  43 ASN   (  43-)  A      0
  53 GLU   (  53-)  A      0
  55 VAL   (  55-)  A      0
  56 LEU   (  56-)  A      0
  59 CYS   (  59-)  A      0
  66 THR   (  66-)  A      0
  67 THR   (  67-)  A      0
  68 MET   (  68-)  A      0
  74 SER   (  74-)  A      0
  77 ASP   (  77-)  A      0
  78 ARG   (  78-)  A      0
  79 ALA   (  79-)  A      0
  80 TRP   (  80-)  A      0
  87 PHE   (  87-)  A      0
And so on for a total of 1298 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 5.752
Model 2 : 5.706
Model 3 : 5.724
Model 4 : 6.384
Model 5 : 5.736
Model 6 : 6.672
Model 7 : 6.349
Model 8 : 6.139
Model 9 : 6.073
Model 10 : 6.260
Model 11 : 5.446
Model 12 : 5.984
Model 13 : 6.352
Model 14 : 5.796
Model 15 : 6.079
Model 16 : 6.075
Model 17 : 6.479
Model 18 : 6.163
Model 19 : 6.582
Model 20 : 5.876

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!

2503 GLY   (  33-)  A 2  1.55   23

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

1144 PRO   ( 104-)  A    0.12 LOW
1815 PRO   ( 125-)  A 1   0.19 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 202 PRO   (  72-)  A   -54.7 half-chair C-beta/C-alpha (-54 degrees)
 462 PRO   (  72-)  A   -55.8 half-chair C-beta/C-alpha (-54 degrees)
 982 PRO   (  72-)  A   -55.1 half-chair C-beta/C-alpha (-54 degrees)
1112 PRO   (  72-)  A    39.2 envelop C-delta (36 degrees)
1242 PRO   (  72-)  A 1   42.0 envelop C-delta (36 degrees)
1372 PRO   (  72-)  A 1  -65.1 envelop C-beta (-72 degrees)
2339 PRO   ( 129-)  A 1 -119.0 half-chair C-delta/C-gamma (-126 degrees)
2542 PRO   (  72-)  A 2  -50.6 half-chair C-beta/C-alpha (-54 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.

2408 MET   (  68-)  A 1    SD  <-> 2422 TRP   (  82-)  A 1    NE1    0.37    2.93
1187 LEU   (  17-)  A 1    CB  <-> 1220 MET   (  50-)  A 1    SD     0.34    3.06
 601 MET   (  81-)  A      SD  <->  616 GLN   (  96-)  A      NE2    0.27    3.03
1088 MET   (  48-)  A      SD  <-> 1102 HIS   (  62-)  A      ND1    0.26    3.04
 290 ARG   (  30-)  A      NE  <->  319 CYS   (  59-)  A      SG     0.25    3.05
  62 HIS   (  62-)  A      NE2 <->   68 MET   (  68-)  A      SD     0.25    3.05
 198 MET   (  68-)  A      SD  <->  212 TRP   (  82-)  A      CB     0.22    3.18
1611 ARG   (  51-)  A 1    CG  <-> 1618 VAL   (  58-)  A 1    N      0.22    2.88
1222 ARG   (  52-)  A 1    NE  <-> 1229 CYS   (  59-)  A 1    SG     0.22    3.08
1781 ASP   (  91-)  A 1    N   <-> 1782 ALA   (  92-)  A 1    N      0.21    2.39        B3
1628 MET   (  68-)  A 1    SD  <-> 1629 ASN   (  69-)  A 1    N      0.20    3.00
1868 MET   (  48-)  A 1    SD  <-> 1902 TRP   (  82-)  A 1    NE1    0.19    3.11
1092 ARG   (  52-)  A      NE  <-> 1099 CYS   (  59-)  A      SG     0.19    3.11
2391 ARG   (  51-)  A 1    CG  <-> 2398 VAL   (  58-)  A 1    N      0.19    2.91
1521 ASP   (  91-)  A 1    N   <-> 1522 ALA   (  92-)  A 1    N      0.19    2.41        B3
1317 LEU   (  17-)  A 1    CB  <-> 1350 MET   (  50-)  A 1    SD     0.18    3.22
2027 ASP   (  77-)  A 1    N   <-> 2028 ARG   (  78-)  A 1    N      0.18    2.42        B3
 178 MET   (  48-)  A      SD  <->  244 PHE   ( 114-)  A      CE1    0.18    3.22
1091 ARG   (  51-)  A      CG  <-> 1098 VAL   (  58-)  A      N      0.18    2.92
1368 MET   (  68-)  A 1    SD  <-> 1382 TRP   (  82-)  A 1    CB     0.17    3.23
 915 GLU   (   5-)  A      CG  <->  916 ASP   (   6-)  A      N      0.17    2.83
2018 MET   (  68-)  A 1    SD  <-> 2032 TRP   (  82-)  A 1    CB     0.17    3.23
2411 LYS   (  71-)  A 1    NZ  <-> 2421 MET   (  81-)  A 1    SD     0.16    3.14
 568 MET   (  48-)  A      SD  <->  634 PHE   ( 114-)  A      CE2    0.16    3.24
1472 VAL   (  42-)  A 1    N   <-> 1473 ASN   (  43-)  A 1    N      0.16    2.44        B3
And so on for a total of 1042 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


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