WHAT IF Check report

This file was created 2012-01-05 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 pdb1oca.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   (   1-)  A    Zero
   2 VAL   (   2-)  A    Zero
   3 ASN   (   3-)  A    Zero
   4 PRO   (   4-)  A    Zero
   5 THR   (   5-)  A    Zero
   6 VAL   (   6-)  A    Zero
   7 PHE   (   7-)  A    Zero
   8 PHE   (   8-)  A    Zero
   9 ASP   (   9-)  A    Zero
  10 ILE   (  10-)  A    Zero
  11 ALA   (  11-)  A    Zero
  12 VAL   (  12-)  A    Zero
  13 ASP   (  13-)  A    Zero
  14 GLY   (  14-)  A    Zero
  15 GLU   (  15-)  A    Zero
  16 PRO   (  16-)  A    Zero
  17 LEU   (  17-)  A    Zero
  18 GLY   (  18-)  A    Zero
  19 ARG   (  19-)  A    Zero
  20 VAL   (  20-)  A    Zero
  21 SER   (  21-)  A    Zero
  22 PHE   (  22-)  A    Zero
  23 GLU   (  23-)  A    Zero
  24 LEU   (  24-)  A    Zero
  25 PHE   (  25-)  A    Zero
And so on for a total of 3300 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 : 0.518
Model 2 : 0.511
Model 3 : 0.519
Model 4 : 0.508
Model 5 : 0.514
Model 6 : 0.518
Model 7 : 0.524
Model 8 : 0.521
Model 9 : 0.511
Model 10 : 0.520
Model 11 : 0.515
Model 12 : 0.533
Model 13 : 0.510
Model 14 : 0.515
Model 15 : 0.508
Model 16 : 0.520
Model 17 : 0.513
Model 18 : 0.508
Model 19 : 0.512
Model 20 : 0.518

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.

  36 PHE   (  36-)  A      CA   CB   CG  107.12   -6.7
  67 PHE   (  67-)  A      CA   CB   CG  120.33    6.5
  70 HIS   (  70-)  A      CA   CB   CG  109.51   -4.3
  76 LYS   (  76-)  A     -C    N    CA  132.07    5.8
  82 LYS   (  82-)  A     -C    N    CA  133.88    6.8
  85 ASP   (  85-)  A      CA   CB   CG  119.70    7.1
 106 ASN   ( 106-)  A     -C    N    CA  129.08    4.1
 112 PHE   ( 112-)  A      CA   CB   CG  118.14    4.3
 144 ARG   ( 144-)  A      CD   NE   CZ  129.28    4.2
 148 ARG   ( 148-)  A     -C    N    CA  132.72    6.1
 156 ILE   ( 156-)  A      C    CA   CB  117.99    4.2
 156 ILE   ( 156-)  A      CA   CB   CG1 102.95   -4.4
 177 VAL   (  12-)  A      CA   CB   CG2 117.40    4.1
 180 GLU   (  15-)  A      C    CA   CB  118.26    4.3
 202 ARG   (  37-)  A      CD   NE   CZ  130.08    4.7
 223 PRO   (  58-)  A      N    CA   CB  107.59    4.2
 234 ARG   (  69-)  A      CD   NE   CZ  129.06    4.1
 246 GLU   (  81-)  A      C    CA   CB  118.56    4.5
 288 ASP   ( 123-)  A      CA   CB   CG  116.85    4.2
 309 ARG   ( 144-)  A      CD   NE   CZ  129.75    4.5
 338 PHE   (   8-)  A      CA   CB   CG  118.18    4.4
 365 ASN   (  35-)  A      CA   CB   CG  117.23    4.6
 382 CYS   (  52-)  A     -C    N    CA  132.39    5.9
 396 ASP   (  66-)  A      CA   CB   CG  116.65    4.1
 397 PHE   (  67-)  A     -C    N    CA  131.83    5.6
And so on for a total of 212 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 1.207
Model 2 : 1.163
Model 3 : 1.222
Model 4 : 1.135
Model 5 : 1.171
Model 6 : 1.194
Model 7 : 1.222
Model 8 : 1.211
Model 9 : 1.209
Model 10 : 1.223
Model 11 : 1.148
Model 12 : 1.240
Model 13 : 1.143
Model 14 : 1.211
Model 15 : 1.169
Model 16 : 1.247
Model 17 : 1.207
Model 18 : 1.183
Model 19 : 1.221
Model 20 : 1.237

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.

2642 VAL   (   2-)  A 1    C     -7.0    -9.43     0.15
The average deviation= 1.347

Note: Per-model averages for chirality check

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

Model 1 : 1.077
Model 2 : 1.084
Model 3 : 1.188
Model 4 : 1.056
Model 5 : 1.035
Model 6 : 1.127
Model 7 : 1.124
Model 8 : 1.203
Model 9 : 1.066
Model 10 : 1.164
Model 11 : 1.002
Model 12 : 1.210
Model 13 : 1.070
Model 14 : 1.177
Model 15 : 1.185
Model 16 : 1.070
Model 17 : 1.177
Model 18 : 1.085
Model 19 : 1.177
Model 20 : 1.132

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.

1056 ASP   (  66-)  A    7.13
1221 ASP   (  66-)  A    7.00
3269 GLU   ( 134-)  A 2   5.70
2418 ASN   ( 108-)  A 1   5.68
2706 ASP   (  66-)  A 1   5.56
 438 ASN   ( 108-)  A    5.51
3201 ASP   (  66-)  A 2   5.35
3258 ASP   ( 123-)  A 2   5.30
1551 ASP   (  66-)  A 1   5.30
1533 TYR   (  48-)  A 1   5.27
3295 ASP   ( 160-)  A 2   5.24
1333 ASP   (  13-)  A    5.02
1405 ASP   (  85-)  A    4.97
 288 ASP   ( 123-)  A    4.82
2253 ASN   ( 108-)  A 1   4.80
 543 TYR   (  48-)  A    4.77
 450 GLU   ( 120-)  A    4.76
2028 TYR   (  48-)  A 1   4.66
1278 ASP   ( 123-)  A    4.65
 891 ASP   (  66-)  A    4.60
2046 ASP   (  66-)  A 1   4.54
2774 GLU   ( 134-)  A 1   4.54
2859 HIS   (  54-)  A 1   4.53
2993 GLU   (  23-)  A 1   4.46
 173 PHE   (   8-)  A    4.43
1267 PHE   ( 112-)  A    4.30
 880 ARG   (  55-)  A    4.27
2488 ASP   (  13-)  A 1   4.25
2123 GLU   ( 143-)  A 1   4.14
 353 GLU   (  23-)  A    4.14
1884 ARG   (  69-)  A 1   4.13
1500 GLU   (  15-)  A 1   4.13
2818 ASP   (  13-)  A 1   4.03

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.

 895 HIS   (  70-)  A      CB   6.40
1927 PHE   ( 112-)  A 1    CB   6.12
3171 PHE   (  36-)  A 2    CB   6.07
  36 PHE   (  36-)  A      CB   5.75
 772 PHE   ( 112-)  A      CB   5.59
2529 HIS   (  54-)  A 1    CB   5.44
 730 HIS   (  70-)  A      CB   4.91
2002 PHE   (  22-)  A 1    CB   4.50
2370 PHE   (  60-)  A 1    CB   4.48
1863 TYR   (  48-)  A 1    OH   4.46
1203 TYR   (  48-)  A      CB   4.36
1597 PHE   ( 112-)  A 1    CB   4.23
2193 TYR   (  48-)  A 1    OH   4.09
3018 TYR   (  48-)  A 1    CB   4.09
1538 PHE   (  53-)  A 1    CB   4.06
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.573

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.573

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.897
Model 2 : -3.346
Model 3 : -4.181
Model 4 : -3.544
Model 5 : -3.853
Model 6 : -2.926
Model 7 : -3.327
Model 8 : -3.595
Model 9 : -3.554
Model 10 : -4.018
Model 11 : -2.882
Model 12 : -3.374
Model 13 : -3.691
Model 14 : -3.652
Model 15 : -3.628
Model 16 : -3.905
Model 17 : -3.034
Model 18 : -3.593
Model 19 : -3.803
Model 20 : -3.650

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.

1058 THR   (  68-)  A    -3.4
2686 PHE   (  46-)  A 1   -3.2
 730 HIS   (  70-)  A    -3.2
 565 HIS   (  70-)  A    -3.1
1531 PHE   (  46-)  A 1   -3.1
1597 PHE   ( 112-)  A 1   -2.9
2695 ARG   (  55-)  A 1   -2.8
1225 HIS   (  70-)  A    -2.8
 817 THR   ( 157-)  A    -2.8
 211 PHE   (  46-)  A    -2.7
2388 ILE   (  78-)  A 1   -2.7
1388 THR   (  68-)  A    -2.7
3053 PHE   (  83-)  A 1   -2.7
2551 LYS   (  76-)  A 1   -2.7
1972 THR   ( 157-)  A 1   -2.7
1614 PHE   ( 129-)  A 1   -2.7
2924 THR   ( 119-)  A 1   -2.6
  46 PHE   (  46-)  A    -2.6
 827 VAL   (   2-)  A    -2.6
 731 ASN   (  71-)  A    -2.6
3038 THR   (  68-)  A 1   -2.6
2264 THR   ( 119-)  A 1   -2.6
 543 TYR   (  48-)  A    -2.6
2251 ASN   ( 106-)  A 1   -2.6
 748 PHE   (  88-)  A    -2.6
And so on for a total of 213 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.

  13 ASP   (  13-)  A  Poor phi/psi
  25 PHE   (  25-)  A  Poor phi/psi
  28 LYS   (  28-)  A  Poor phi/psi
  50 GLY   (  50-)  A  omega poor
  51 SER   (  51-)  A  omega poor
  52 CYS   (  52-)  A  Poor phi/psi
  53 PHE   (  53-)  A  omega poor
  60 PHE   (  60-)  A  Poor phi/psi
  70 HIS   (  70-)  A  omega poor
  81 GLU   (  81-)  A  omega poor
  82 LYS   (  82-)  A  Poor phi/psi, omega poor
  84 GLU   (  84-)  A  omega poor
  92 HIS   (  92-)  A  Poor phi/psi, omega poor
 100 MET   ( 100-)  A  omega poor
 110 SER   ( 110-)  A  Poor phi/psi
 112 PHE   ( 112-)  A  omega poor
 119 THR   ( 119-)  A  Poor phi/psi
 127 VAL   ( 127-)  A  omega poor
 146 GLY   ( 146-)  A  omega poor
 148 ARG   ( 148-)  A  Poor phi/psi
 152 THR   ( 152-)  A  omega poor
 156 ILE   ( 156-)  A  omega poor
 167 VAL   (   2-)  A  omega poor
 173 PHE   (   8-)  A  omega poor
 178 ASP   (  13-)  A  Poor phi/psi
And so on for a total of 567 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 : -4.655

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 : -4.156
Model 2 : -3.878
Model 3 : -4.686
Model 4 : -4.984
Model 5 : -4.671
Model 6 : -4.448
Model 7 : -4.059
Model 8 : -4.974
Model 9 : -4.645
Model 10 : -5.432
Model 11 : -4.880
Model 12 : -4.809
Model 13 : -4.586
Model 14 : -4.982
Model 15 : -5.066
Model 16 : -4.191
Model 17 : -4.227
Model 18 : -5.107
Model 19 : -4.644
Model 20 : -4.667

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.

2845 SER   (  40-)  A 1   0.33
 535 SER   (  40-)  A    0.36
 831 VAL   (   6-)  A    0.36
2680 SER   (  40-)  A 1   0.36
1360 SER   (  40-)  A    0.38

Warning: Unusual backbone conformations

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

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

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

  12 VAL   (  12-)  A      0
  16 PRO   (  16-)  A      0
  19 ARG   (  19-)  A      0
  25 PHE   (  25-)  A      0
  28 LYS   (  28-)  A      0
  29 VAL   (  29-)  A      0
  43 GLU   (  43-)  A      0
  44 LYS   (  44-)  A      0
  46 PHE   (  46-)  A      0
  48 TYR   (  48-)  A      0
  49 LYS   (  49-)  A      0
  51 SER   (  51-)  A      0
  52 CYS   (  52-)  A      0
  54 HIS   (  54-)  A      0
  55 ARG   (  55-)  A      0
  58 PRO   (  58-)  A      0
  60 PHE   (  60-)  A      0
  61 MET   (  61-)  A      0
  63 GLN   (  63-)  A      0
  66 ASP   (  66-)  A      0
  67 PHE   (  67-)  A      0
  68 THR   (  68-)  A      0
  69 ARG   (  69-)  A      0
  70 HIS   (  70-)  A      0
  71 ASN   (  71-)  A      0
And so on for a total of 1795 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 : 9.250

Note: Per-model averages for omega angle check

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

Model 1 : 8.255
Model 2 : 9.238
Model 3 : 8.415
Model 4 : 9.338
Model 5 : 8.894
Model 6 : 9.773
Model 7 : 9.093
Model 8 : 9.465
Model 9 : 9.221
Model 10 : 9.868
Model 11 : 8.679
Model 12 : 9.627
Model 13 : 9.094
Model 14 : 9.280
Model 15 : 9.057
Model 16 : 9.848
Model 17 : 9.276
Model 18 : 9.362
Model 19 : 10.575
Model 20 : 8.544

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!

1099 GLY   ( 109-)  A   3.22   10
2786 GLY   ( 146-)  A 1  1.90   10
 150 GLY   ( 150-)  A   1.73   24
 522 ASP   (  27-)  A   1.68   10
 645 GLY   ( 150-)  A   1.65   10
 905 GLY   (  80-)  A   1.55   17
2720 GLY   (  80-)  A 1  1.53   13
 810 GLY   ( 150-)  A   1.51   37

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]

  95 PRO   (  95-)  A    0.17 LOW
 425 PRO   (  95-)  A    0.09 LOW
 590 PRO   (  95-)  A    0.12 LOW
 664 PRO   (   4-)  A    0.15 LOW
 841 PRO   (  16-)  A    0.19 LOW
 920 PRO   (  95-)  A    0.16 LOW
 994 PRO   (   4-)  A    0.17 LOW
1085 PRO   (  95-)  A    0.03 LOW
1415 PRO   (  95-)  A    0.20 LOW
1580 PRO   (  95-)  A 1   0.11 LOW
1654 PRO   (   4-)  A 1   0.20 LOW
1708 PRO   (  58-)  A 1   0.15 LOW
1745 PRO   (  95-)  A 1   0.05 LOW
1831 PRO   (  16-)  A 1   0.17 LOW
1910 PRO   (  95-)  A 1   0.08 LOW
1984 PRO   (   4-)  A 1   0.03 LOW
2075 PRO   (  95-)  A 1   0.09 LOW
2240 PRO   (  95-)  A 1   0.09 LOW
2405 PRO   (  95-)  A 1   0.10 LOW
2479 PRO   (   4-)  A 1   0.20 LOW
2570 PRO   (  95-)  A 1   0.09 LOW
2735 PRO   (  95-)  A 1   0.09 LOW
2809 PRO   (   4-)  A 1   0.15 LOW
3065 PRO   (  95-)  A 1   0.07 LOW
3139 PRO   (   4-)  A 2   0.13 LOW
3165 PRO   (  30-)  A 2   0.14 LOW
3230 PRO   (  95-)  A 2   0.17 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].

  58 PRO   (  58-)  A   112.4 envelop C-beta (108 degrees)
 195 PRO   (  30-)  A  -115.7 envelop C-gamma (-108 degrees)
 223 PRO   (  58-)  A  -143.0 envelop C-delta (-144 degrees)
 388 PRO   (  58-)  A  -142.3 envelop C-delta (-144 degrees)
 499 PRO   (   4-)  A   -64.8 envelop C-beta (-72 degrees)
 525 PRO   (  30-)  A  -112.0 envelop C-gamma (-108 degrees)
 553 PRO   (  58-)  A  -148.7 envelop C-delta (-144 degrees)
 690 PRO   (  30-)  A  -112.1 envelop C-gamma (-108 degrees)
 855 PRO   (  30-)  A   113.1 envelop C-beta (108 degrees)
 883 PRO   (  58-)  A  -143.5 envelop C-delta (-144 degrees)
1171 PRO   (  16-)  A    -3.4 envelop N (0 degrees)
1213 PRO   (  58-)  A  -151.5 envelop C-delta (-144 degrees)
1489 PRO   (   4-)  A 1  -63.9 envelop C-beta (-72 degrees)
1543 PRO   (  58-)  A 1 -128.0 half-chair C-delta/C-gamma (-126 degrees)
1845 PRO   (  30-)  A 1 -113.8 envelop C-gamma (-108 degrees)
1873 PRO   (  58-)  A 1 -132.4 half-chair C-delta/C-gamma (-126 degrees)
2038 PRO   (  58-)  A 1 -115.5 envelop C-gamma (-108 degrees)
2175 PRO   (  30-)  A 1 -112.7 envelop C-gamma (-108 degrees)
2203 PRO   (  58-)  A 1 -116.8 envelop C-gamma (-108 degrees)
2368 PRO   (  58-)  A 1 -124.0 half-chair C-delta/C-gamma (-126 degrees)
2533 PRO   (  58-)  A 1 -132.6 half-chair C-delta/C-gamma (-126 degrees)
2670 PRO   (  30-)  A 1 -145.5 envelop C-delta (-144 degrees)
2698 PRO   (  58-)  A 1 -114.8 envelop C-gamma (-108 degrees)
3028 PRO   (  58-)  A 1 -129.8 half-chair C-delta/C-gamma (-126 degrees)
3193 PRO   (  58-)  A 2 -127.7 half-chair C-delta/C-gamma (-126 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.

 173 PHE   (   8-)  A      CE1 <->  213 TYR   (  48-)  A      CD1    0.34    2.86
 668 PHE   (   8-)  A      CE1 <->  708 TYR   (  48-)  A      CD1    0.31    2.89
1368 TYR   (  48-)  A      CE1 <-> 1432 PHE   ( 112-)  A      CE2    0.26    2.94
2905 MET   ( 100-)  A 1    SD  <-> 2913 ASN   ( 108-)  A 1    CB     0.25    3.15
1356 PHE   (  36-)  A      CE2 <-> 1432 PHE   ( 112-)  A      CE2    0.22    2.98
2032 CYS   (  52-)  A 1    SG  <-> 2135 LYS   ( 155-)  A 1    CE     0.21    3.19
1056 ASP   (  66-)  A      CG  <-> 1101 GLN   ( 111-)  A      NE2    0.20    2.90
2982 VAL   (  12-)  A 1    CG1 <-> 3124 LYS   ( 154-)  A 1    CD     0.20    3.00
1313 ILE   ( 158-)  A      CG2 <-> 1316 CYS   ( 161-)  A      SG     0.20    3.20
  48 TYR   (  48-)  A      CZ  <->  112 PHE   ( 112-)  A      CE2    0.19    3.01
 708 TYR   (  48-)  A      CE2 <->  772 PHE   ( 112-)  A      CE1    0.18    3.02
 187 PHE   (  22-)  A      CD2 <->  263 LEU   (  98-)  A      CD1    0.18    3.02
1534 LYS   (  49-)  A 1    CA  <-> 1646 CYS   ( 161-)  A 1    SG     0.17    3.23
 891 ASP   (  66-)  A      CG  <->  936 GLN   ( 111-)  A      NE2    0.17    2.93
2700 PHE   (  60-)  A 1    CE1 <-> 2761 TRP   ( 121-)  A 1    NE1    0.17    2.93
 925 MET   ( 100-)  A      SD  <->  933 ASN   ( 108-)  A      CB     0.16    3.24
1533 TYR   (  48-)  A 1    CE2 <-> 1643 ILE   ( 158-)  A 1    CD1    0.16    3.04
2080 MET   ( 100-)  A 1    SD  <-> 2088 ASN   ( 108-)  A 1    CB     0.15    3.25
2672 THR   (  32-)  A 1    CG2 <-> 2740 MET   ( 100-)  A 1    SD     0.15    3.25
 213 TYR   (  48-)  A      CD1 <->  323 ILE   ( 158-)  A      CD1    0.15    3.05
 338 PHE   (   8-)  A      CZ  <->  378 TYR   (  48-)  A      CE2    0.15    3.05
 173 PHE   (   8-)  A      CD1 <->  213 TYR   (  48-)  A      CD1    0.15    3.05
1187 THR   (  32-)  A      CG2 <-> 1255 MET   ( 100-)  A      SD     0.14    3.26
 557 CYS   (  62-)  A      SG  <->  638 GLU   ( 143-)  A      CD     0.14    3.26
 100 MET   ( 100-)  A      SD  <->  129 PHE   ( 129-)  A      CE1    0.14    3.26
And so on for a total of 229 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


Warning: Abnormal packing Z-score for sequential residues


Note: Per-model averages for NQA




















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

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