WHAT IF Check report

This file was created 2012-01-25 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 pdb2f2d.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 MET   (  33-)  A    Zero
   2 ARG   (  34-)  A    Zero
   3 GLU   (  35-)  A    Zero
   4 TRP   (  36-)  A    Zero
   5 LEU   (  37-)  A    Zero
   6 ASP   (  38-)  A    Zero
   7 ILE   (  39-)  A    Zero
   8 LEU   (  40-)  A    Zero
   9 GLY   (  41-)  A    Zero
  10 ASN   (  42-)  A    Zero
  11 GLY   (  43-)  A    Zero
  12 LEU   (  44-)  A    Zero
  13 LEU   (  45-)  A    Zero
  14 ARG   (  46-)  A    Zero
  15 LYS   (  47-)  A    Zero
  16 LYS   (  48-)  A    Zero
  17 THR   (  49-)  A    Zero
  18 LEU   (  50-)  A    Zero
  19 VAL   (  51-)  A    Zero
  20 PRO   (  52-)  A    Zero
  21 GLY   (  53-)  A    Zero
  22 PRO   (  54-)  A    Zero
  23 PRO   (  55-)  A    Zero
  24 GLY   (  56-)  A    Zero
  25 SER   (  57-)  A    Zero
And so on for a total of 2420 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.

  37 HIS   (  69-)  A      CG   CD2   1.42    5.6
 102 HIS   ( 134-)  A      CG   CD2   1.41    4.6
 158 HIS   (  69-)  A      CG   CD2   1.41    5.1
 223 HIS   ( 134-)  A      CG   CD2   1.41    4.6
 279 HIS   (  69-)  A      CG   CD2   1.41    5.1
 344 HIS   ( 134-)  A      CG   CD2   1.41    4.6
 400 HIS   (  69-)  A      CG   CD2   1.41    5.1
 465 HIS   ( 134-)  A      CG   CD2   1.41    4.7
 521 HIS   (  69-)  A      CG   CD2   1.42    5.4
 586 HIS   ( 134-)  A      CG   CD2   1.41    4.7
 642 HIS   (  69-)  A      CG   CD2   1.41    5.0
 707 HIS   ( 134-)  A      CG   CD2   1.41    4.8
 763 HIS   (  69-)  A      CG   CD2   1.41    5.2
 828 HIS   ( 134-)  A      CG   CD2   1.41    4.7
 884 HIS   (  69-)  A      CG   CD2   1.41    5.3
 949 HIS   ( 134-)  A      CG   CD2   1.41    4.6
1005 HIS   (  69-)  A      CG   CD2   1.41    4.8
1070 HIS   ( 134-)  A      CG   CD2   1.41    4.8
1126 HIS   (  69-)  A 1    CG   CD2   1.41    5.2
1191 HIS   ( 134-)  A 1    CG   CD2   1.41    4.9
1247 HIS   (  69-)  A 1    CG   CD2   1.41    5.3
1312 HIS   ( 134-)  A 1    CG   CD2   1.41    4.9
1368 HIS   (  69-)  A 1    CG   CD2   1.41    5.1
1433 HIS   ( 134-)  A 1    CG   CD2   1.41    4.6
1489 HIS   (  69-)  A 1    CG   CD2   1.41    5.1
1554 HIS   ( 134-)  A 1    CG   CD2   1.41    5.3
1610 HIS   (  69-)  A 1    CG   CD2   1.40    4.4
1675 HIS   ( 134-)  A 1    CG   CD2   1.41    4.6
1731 HIS   (  69-)  A 1    CG   CD2   1.41    5.1
1796 HIS   ( 134-)  A 1    CG   CD2   1.41    4.6
1852 HIS   (  69-)  A 1    CG   CD2   1.41    4.9
1917 HIS   ( 134-)  A 1    CG   CD2   1.41    4.5
1973 HIS   (  69-)  A 1    CG   CD2   1.41    5.0
2038 HIS   ( 134-)  A 1    CG   CD2   1.41    4.7
2094 HIS   (  69-)  A 1    CG   CD2   1.41    5.0
2159 HIS   ( 134-)  A 1    CG   CD2   1.41    5.1
2215 HIS   (  69-)  A 1    CG   CD2   1.41    4.8
2280 HIS   ( 134-)  A 1    CG   CD2   1.41    4.6
2336 HIS   (  69-)  A 2    CG   CD2   1.40    4.4
2401 HIS   ( 134-)  A 2    CG   CD2   1.41    5.3

Note: Per-model averages for bond-length check

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

Model 1 : 1.225
Model 2 : 1.217
Model 3 : 1.240
Model 4 : 1.216
Model 5 : 1.214
Model 6 : 1.221
Model 7 : 1.224
Model 8 : 1.220
Model 9 : 1.223
Model 10 : 1.228
Model 11 : 1.220
Model 12 : 1.220
Model 13 : 1.224
Model 14 : 1.207
Model 15 : 1.223
Model 16 : 1.202
Model 17 : 1.219
Model 18 : 1.225
Model 19 : 1.224
Model 20 : 1.208

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.

  10 ASN   (  42-)  A      CA   CB   CG  118.73    6.1
  37 HIS   (  69-)  A      CA   CB   CG  121.23    7.4
  37 HIS   (  69-)  A      CG   ND1  CE1 100.56   -5.0
  37 HIS   (  69-)  A      ND1  CE1  NE2 120.33    6.6
  37 HIS   (  69-)  A      CE1  NE2  CD2  98.63   -6.4
  37 HIS   (  69-)  A      NE2  CD2  CG  111.67    5.2
  44 ASN   (  76-)  A      CA   CB   CG  116.80    4.2
  56 PHE   (  88-)  A      CA   CB   CG  117.83    4.0
  71 VAL   ( 103-)  A      C    CA   CB  117.86    4.1
  71 VAL   ( 103-)  A      CA   CB   CG1 117.88    4.3
  72 PRO   ( 104-)  A     -CA  -C    N   126.77    6.6
 102 HIS   ( 134-)  A      CG   ND1  CE1  99.86   -5.7
 102 HIS   ( 134-)  A      ND1  CE1  NE2 120.33    6.6
 102 HIS   ( 134-)  A      CE1  NE2  CD2  98.72   -6.3
 102 HIS   ( 134-)  A      NE2  CD2  CG  111.28    4.8
 116 ASP   ( 148-)  A      CA   CB   CG  119.04    6.4
 158 HIS   (  69-)  A      CA   CB   CG  119.17    5.4
 158 HIS   (  69-)  A      CG   ND1  CE1 100.12   -5.5
 158 HIS   (  69-)  A      ND1  CE1  NE2 120.42    6.7
 158 HIS   (  69-)  A      CE1  NE2  CD2  98.68   -6.3
 158 HIS   (  69-)  A      NE2  CD2  CG  111.40    4.9
 167 THR   (  78-)  A      CA   CB   CG2 117.44    4.1
 177 PHE   (  88-)  A      CA   CB   CG  118.79    5.0
 193 PRO   ( 104-)  A     -CA  -C    N   125.12    5.5
 223 HIS   ( 134-)  A      CG   ND1  CE1  99.94   -5.7
And so on for a total of 335 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.361
Model 2 : 1.331
Model 3 : 1.350
Model 4 : 1.356
Model 5 : 1.314
Model 6 : 1.373
Model 7 : 1.332
Model 8 : 1.328
Model 9 : 1.377
Model 10 : 1.365
Model 11 : 1.361
Model 12 : 1.340
Model 13 : 1.360
Model 14 : 1.332
Model 15 : 1.326
Model 16 : 1.333
Model 17 : 1.339
Model 18 : 1.345
Model 19 : 1.373
Model 20 : 1.381

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.

  12 LEU   (  44-)  A      CA    -6.0    24.97    34.19
 416 GLU   (  85-)  A      CA    -6.8    22.86    33.96
 784 LEU   (  90-)  A      CA    -6.2    24.74    34.19
 846 LEU   ( 152-)  A      CA    -6.1    24.79    34.19
1263 GLU   (  85-)  A 1    CA    -8.3    20.41    33.96
1941 LEU   (  37-)  A 1    CA    -7.0    23.55    34.19
2307 LEU   (  40-)  A 2    CA    -7.1    23.38    34.19
The average deviation= 1.337

Note: Per-model averages for chirality check

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

Model 1 : 1.162
Model 2 : 1.152
Model 3 : 1.231
Model 4 : 1.247
Model 5 : 1.080
Model 6 : 1.183
Model 7 : 1.305
Model 8 : 1.165
Model 9 : 1.097
Model 10 : 1.163
Model 11 : 1.231
Model 12 : 1.085
Model 13 : 1.171
Model 14 : 1.083
Model 15 : 1.222
Model 16 : 1.106
Model 17 : 1.184
Model 18 : 1.098
Model 19 : 1.220
Model 20 : 1.273

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.

  68 ASP   ( 100-)  A    4.38
 433 SER   ( 102-)  A    4.28
1517 GLN   (  97-)  A 1   4.28
 552 ASP   ( 100-)  A    4.27
 554 SER   ( 102-)  A    4.24
 428 GLN   (  97-)  A    4.18
2244 ALA   (  98-)  A 1   4.15
1638 GLN   (  97-)  A 1   4.15
2365 ALA   (  98-)  A 2   4.08
  70 SER   ( 102-)  A    4.06

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.

1391 ASP   (  92-)  A 1   4.84
1512 ASP   (  92-)  A 1   4.79
1821 ASP   (  38-)  A 1   4.19
 292 GLU   (  82-)  A    4.07

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.

 730 TRP   (  36-)  A      CB   5.39
 693 TYR   ( 120-)  A      CB   4.19
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -5.566

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 : -5.566

Note: Per-model averages for Ramachandran check

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

Model 1 : -6.205
Model 2 : -5.711
Model 3 : -5.797
Model 4 : -5.041
Model 5 : -5.367
Model 6 : -6.284
Model 7 : -5.330
Model 8 : -5.444
Model 9 : -5.413
Model 10 : -5.673
Model 11 : -5.878
Model 12 : -4.539
Model 13 : -5.596
Model 14 : -5.788
Model 15 : -5.553
Model 16 : -5.848
Model 17 : -5.000
Model 18 : -5.752
Model 19 : -5.059
Model 20 : -6.045

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.

 288 THR   (  78-)  A    -3.6
2224 THR   (  78-)  A 1   -3.5
  46 THR   (  78-)  A    -3.2
2103 THR   (  78-)  A 1   -3.0
 823 PRO   ( 129-)  A    -2.8
2307 LEU   (  40-)  A 2   -2.8
1941 LEU   (  37-)  A 1   -2.7
1590 THR   (  49-)  A 1   -2.7
 107 LEU   ( 139-)  A    -2.6
1263 GLU   (  85-)  A 1   -2.5
 415 PRO   (  84-)  A    -2.5
2149 PRO   ( 124-)  A 1   -2.5
1196 LEU   ( 139-)  A 1   -2.5
 254 LEU   (  44-)  A    -2.5
   3 GLU   (  35-)  A    -2.5
2164 LEU   ( 139-)  A 1   -2.5
1297 LYS   ( 119-)  A 1   -2.5
1817 ARG   (  34-)  A 1   -2.4
2377 GLU   ( 110-)  A 2   -2.4
 731 LEU   (  37-)  A    -2.4
1218 LEU   (  40-)  A 1   -2.4
1755 CYS   (  93-)  A 1   -2.4
 844 PRO   ( 150-)  A    -2.4
 658 GLU   (  85-)  A    -2.4
1842 ARG   (  59-)  A 1   -2.4
And so on for a total of 179 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 ARG   (  34-)  A  Poor phi/psi
   3 GLU   (  35-)  A  Poor phi/psi
  12 LEU   (  44-)  A  Poor phi/psi
  20 PRO   (  52-)  A  omega poor
  23 PRO   (  55-)  A  omega poor
  29 VAL   (  61-)  A  omega poor
  36 VAL   (  68-)  A  omega poor
  42 LEU   (  74-)  A  omega poor
  45 GLY   (  77-)  A  omega poor
  75 ASP   ( 107-)  A  omega poor
  78 GLU   ( 110-)  A  omega poor
  89 CYS   ( 121-)  A  omega poor
  92 PRO   ( 124-)  A  omega poor
  96 SER   ( 128-)  A  PRO omega poor
 102 HIS   ( 134-)  A  Poor phi/psi
 103 ALA   ( 135-)  A  Poor phi/psi
 125 TRP   (  36-)  A  Poor phi/psi
 137 LYS   (  48-)  A  omega poor
 139 LEU   (  50-)  A  omega poor
 144 PRO   (  55-)  A  omega poor
 154 VAL   (  65-)  A  omega poor
 157 VAL   (  68-)  A  omega poor
 182 CYS   (  93-)  A  Poor phi/psi
 193 PRO   ( 104-)  A  omega poor
 207 SER   ( 118-)  A  omega poor
And so on for a total of 378 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 : -3.222

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 : -4.221
Model 2 : -2.755
Model 3 : -2.537
Model 4 : -3.250
Model 5 : -2.963
Model 6 : -3.411
Model 7 : -3.165
Model 8 : -2.136
Model 9 : -4.129
Model 10 : -2.636
Model 11 : -3.234
Model 12 : -2.428
Model 13 : -3.733
Model 14 : -3.053
Model 15 : -3.681
Model 16 : -3.450
Model 17 : -3.389
Model 18 : -2.962
Model 19 : -3.251
Model 20 : -4.060

Warning: Unusual backbone conformations

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

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

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

   3 GLU   (  35-)  A      0
   4 TRP   (  36-)  A      0
   8 LEU   (  40-)  A      0
  10 ASN   (  42-)  A      0
  12 LEU   (  44-)  A      0
  18 LEU   (  50-)  A      0
  19 VAL   (  51-)  A      0
  20 PRO   (  52-)  A      0
  23 PRO   (  55-)  A      0
  25 SER   (  57-)  A      0
  26 SER   (  58-)  A      0
  27 ARG   (  59-)  A      0
  30 LYS   (  62-)  A      0
  44 ASN   (  76-)  A      0
  46 THR   (  78-)  A      0
  47 ARG   (  79-)  A      0
  53 GLU   (  85-)  A      0
  58 LEU   (  90-)  A      0
  61 CYS   (  93-)  A      0
  62 ASP   (  94-)  A      0
  63 VAL   (  95-)  A      0
  75 ASP   ( 107-)  A      0
  76 VAL   ( 108-)  A      0
  88 TYR   ( 120-)  A      0
  89 CYS   ( 121-)  A      0
And so on for a total of 1299 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 : 8.973

Note: Per-model averages for omega angle check

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

Model 1 : 8.739
Model 2 : 8.122
Model 3 : 9.487
Model 4 : 8.905
Model 5 : 8.101
Model 6 : 9.269
Model 7 : 10.368
Model 8 : 8.856
Model 9 : 8.477
Model 10 : 9.233
Model 11 : 9.027
Model 12 : 8.346
Model 13 : 8.750
Model 14 : 7.813
Model 15 : 9.911
Model 16 : 8.662
Model 17 : 10.016
Model 18 : 8.862
Model 19 : 8.950
Model 20 : 8.785

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!

1355 GLY   (  56-)  A 1  3.12   17
 266 GLY   (  56-)  A   3.09   38
1234 GLY   (  56-)  A 1  3.05   13
1476 GLY   (  56-)  A 1  3.03   61
 785 GLY   (  91-)  A   2.88   48
2237 GLY   (  91-)  A 1  2.87   47
 508 GLY   (  56-)  A   2.74   15
1753 GLY   (  91-)  A 1  2.51   48
 750 GLY   (  56-)  A   2.39   80
 629 GLY   (  56-)  A   2.35   32
1718 GLY   (  56-)  A 1  2.34   54
 992 GLY   (  56-)  A   2.33   58
2323 GLY   (  56-)  A 2  2.33   80
1811 GLY   ( 149-)  A 1  2.31   13
2209 GLY   (  63-)  A 1  2.30   24
 145 GLY   (  56-)  A   2.28   37
2358 GLY   (  91-)  A 2  2.22   80
2202 GLY   (  56-)  A 1  2.15   36
1618 GLY   (  77-)  A 1  2.13   19
1255 GLY   (  77-)  A 1  2.11   14
1497 GLY   (  77-)  A 1  2.09   12
1967 GLY   (  63-)  A 1  2.05   80
2189 GLY   (  43-)  A 1  1.99   17
1134 GLY   (  77-)  A 1  1.96   13
 771 GLY   (  77-)  A   1.94   11
 152 GLY   (  63-)  A   1.92   23
 529 GLY   (  77-)  A   1.87   43
 301 GLY   (  91-)  A   1.86   47
  59 GLY   (  91-)  A   1.85   80
1362 GLY   (  63-)  A 1  1.85   67
 803 GLY   ( 109-)  A   1.85   59
 561 GLY   ( 109-)  A   1.77   39
 999 GLY   (  63-)  A   1.76   45
1874 GLY   (  91-)  A 1  1.73   19
 273 GLY   (  63-)  A   1.70   12
1304 GLY   ( 126-)  A 1  1.70   15
 964 GLY   ( 149-)  A   1.68   61
1892 GLY   ( 109-)  A 1  1.67   51
1390 GLY   (  91-)  A 1  1.62   29
1483 GLY   (  63-)  A 1  1.60   43
1327 GLY   ( 149-)  A 1  1.59   22
 319 GLY   ( 109-)  A   1.59   80
2088 GLY   (  63-)  A 1  1.58   14
1148 GLY   (  91-)  A 1  1.55   29
 384 GLY   (  53-)  A   1.53   23
2053 GLY   ( 149-)  A 1  1.51   38
 906 GLY   (  91-)  A   1.50   12

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].

 677 PRO   ( 104-)  A  -115.3 envelop C-gamma (-108 degrees)
1262 PRO   (  84-)  A 1  -53.2 half-chair C-beta/C-alpha (-54 degrees)
2149 PRO   ( 124-)  A 1  -61.3 half-chair C-beta/C-alpha (-54 degrees)
2396 PRO   ( 129-)  A 2  -48.2 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.

 444 MET   ( 113-)  A      SD  <->  469 CYS   ( 138-)  A      SG     0.29    3.16
1657 ALA   ( 116-)  A 1    CB  <-> 1662 CYS   ( 121-)  A 1    SG     0.19    3.21
2388 CYS   ( 121-)  A 2    SG  <-> 2389 TYR   ( 122-)  A 2    N      0.19    3.01
 444 MET   ( 113-)  A      CG  <->  469 CYS   ( 138-)  A      SG     0.18    3.22
 790 ILE   (  96-)  A      CD1 <->  815 CYS   ( 121-)  A      SG     0.18    3.22
 550 ALA   (  98-)  A      CB  <->  573 CYS   ( 121-)  A      SG     0.17    3.23
1049 MET   ( 113-)  A      CG  <-> 1074 CYS   ( 138-)  A      SG     0.16    3.24
1505 GLU   (  85-)  A 1    OE1 <-> 1564 LYS   ( 144-)  A 1    NZ     0.14    2.56
 998 LYS   (  62-)  A      NZ  <-> 1028 ASP   (  92-)  A      OD1    0.14    2.56
1225 LYS   (  47-)  A 1    NZ  <-> 1288 GLU   ( 110-)  A 1    OE2    0.14    2.56
  89 CYS   ( 121-)  A      SG  <->   90 TYR   ( 122-)  A      N      0.14    3.06
 327 ASP   ( 117-)  A      OD2 <->  329 LYS   ( 119-)  A      NZ     0.14    2.56
 537 GLU   (  85-)  A      OE1 <->  596 LYS   ( 144-)  A      NZ     0.13    2.57
2384 ASP   ( 117-)  A 2    OD2 <-> 2386 LYS   ( 119-)  A 2    NZ     0.13    2.57
1830 LYS   (  47-)  A 1    NZ  <-> 1893 GLU   ( 110-)  A 1    OE2    0.13    2.57
2340 SER   (  73-)  A 2    C   <-> 2405 CYS   ( 138-)  A 2    SG     0.13    3.27
1518 ALA   (  98-)  A 1    CB  <-> 1541 CYS   ( 121-)  A 1    SG     0.13    3.27
1658 ASP   ( 117-)  A 1    OD2 <-> 1660 LYS   ( 119-)  A 1    NZ     0.13    2.57
1777 THR   ( 115-)  A 1    OG1 <-> 1800 CYS   ( 138-)  A 1    SG     0.13    2.87
1142 GLU   (  85-)  A 1    OE1 <-> 1201 LYS   ( 144-)  A 1    NZ     0.12    2.58
 815 CYS   ( 121-)  A      SG  <->  816 TYR   ( 122-)  A      N      0.12    3.08
2231 GLU   (  85-)  A 1    OE2 <-> 2290 LYS   ( 144-)  A 1    NZ     0.12    2.58
1021 GLU   (  85-)  A      OE2 <-> 1080 LYS   ( 144-)  A      NZ     0.12    2.58
 257 LYS   (  47-)  A      NZ  <->  320 GLU   ( 110-)  A      OE2    0.12    2.58
 779 GLU   (  85-)  A      OE2 <->  838 LYS   ( 144-)  A      NZ     0.12    2.58
And so on for a total of 172 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


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

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

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