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 pdb2dlh.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 GLY   (   1-)  A    Zero
   2 SER   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 GLY   (   4-)  A    Zero
   5 SER   (   5-)  A    Zero
   6 SER   (   6-)  A    Zero
   7 GLY   (   7-)  A    Zero
   8 PRO   (   8-)  A    Zero
   9 VAL   (   9-)  A    Zero
  10 LEU   (  10-)  A    Zero
  11 THR   (  11-)  A    Zero
  12 GLN   (  12-)  A    Zero
  13 THR   (  13-)  A    Zero
  14 SER   (  14-)  A    Zero
  15 GLU   (  15-)  A    Zero
  16 GLN   (  16-)  A    Zero
  17 ALA   (  17-)  A    Zero
  18 PRO   (  18-)  A    Zero
  19 SER   (  19-)  A    Zero
  20 SER   (  20-)  A    Zero
  21 ALA   (  21-)  A    Zero
  22 PRO   (  22-)  A    Zero
  23 ARG   (  23-)  A    Zero
  24 ASP   (  24-)  A    Zero
  25 VAL   (  25-)  A    Zero
And so on for a total of 2420 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 : 0.136
Model 2 : 0.139
Model 3 : 0.138
Model 4 : 0.138
Model 5 : 0.136
Model 6 : 0.139
Model 7 : 0.137
Model 8 : 0.138
Model 9 : 0.139
Model 10 : 0.137
Model 11 : 0.138
Model 12 : 0.138
Model 13 : 0.136
Model 14 : 0.138
Model 15 : 0.139
Model 16 : 0.138
Model 17 : 0.138
Model 18 : 0.138
Model 19 : 0.138
Model 20 : 0.136

Note: Per-model averages for bond-angle check

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

Model 1 : 0.277
Model 2 : 0.280
Model 3 : 0.279
Model 4 : 0.278
Model 5 : 0.280
Model 6 : 0.279
Model 7 : 0.279
Model 8 : 0.279
Model 9 : 0.280
Model 10 : 0.277
Model 11 : 0.280
Model 12 : 0.280
Model 13 : 0.280
Model 14 : 0.277
Model 15 : 0.279
Model 16 : 0.281
Model 17 : 0.277
Model 18 : 0.279
Model 19 : 0.279
Model 20 : 0.280

Note: Per-model averages for chirality check

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

Model 1 : 0.320
Model 2 : 0.323
Model 3 : 0.325
Model 4 : 0.321
Model 5 : 0.324
Model 6 : 0.323
Model 7 : 0.322
Model 8 : 0.323
Model 9 : 0.321
Model 10 : 0.322
Model 11 : 0.322
Model 12 : 0.323
Model 13 : 0.323
Model 14 : 0.324
Model 15 : 0.322
Model 16 : 0.325
Model 17 : 0.322
Model 18 : 0.322
Model 19 : 0.320
Model 20 : 0.322

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 : -4.683

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.468
Model 2 : -4.545
Model 3 : -4.582
Model 4 : -4.033
Model 5 : -5.189
Model 6 : -5.473
Model 7 : -4.923
Model 8 : -4.128
Model 9 : -4.892
Model 10 : -4.882
Model 11 : -4.633
Model 12 : -3.913
Model 13 : -4.507
Model 14 : -4.857
Model 15 : -4.961
Model 16 : -4.865
Model 17 : -4.739
Model 18 : -4.851
Model 19 : -4.647
Model 20 : -4.571

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.

1687 THR   ( 114-)  A 1   -3.6
 374 THR   (  11-)  A    -3.5
 132 THR   (  11-)  A    -3.5
1705 THR   (  11-)  A 1   -3.5
  13 THR   (  13-)  A    -3.5
 840 THR   ( 114-)  A    -3.3
1828 THR   (  13-)  A 1   -3.3
 860 THR   (  13-)  A    -3.3
 616 THR   (  11-)  A    -3.2
1949 THR   (  13-)  A 1   -3.2
2211 THR   (  33-)  A 1   -3.2
 517 THR   (  33-)  A    -3.1
 638 THR   (  33-)  A    -3.1
1606 THR   (  33-)  A 1   -3.0
2189 THR   (  11-)  A 1   -3.0
1929 THR   ( 114-)  A 1   -2.9
1704 LEU   (  10-)  A 1   -2.8
 796 HIS   (  70-)  A    -2.7
2248 HIS   (  70-)  A 1   -2.7
 497 THR   (  13-)  A    -2.7
 554 HIS   (  70-)  A    -2.7
1455 SER   (   3-)  A 1   -2.7
2191 THR   (  13-)  A 1   -2.7
 312 HIS   (  70-)  A    -2.7
2006 HIS   (  70-)  A 1   -2.7
And so on for a total of 315 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.

   4 GLY   (   4-)  A  Poor phi/psi
   9 VAL   (   9-)  A  Poor phi/psi
  24 ASP   (  24-)  A  Poor phi/psi
  46 ASN   (  46-)  A  Poor phi/psi
  69 LYS   (  69-)  A  Poor phi/psi
  76 GLN   (  76-)  A  Poor phi/psi
  82 ASN   (  82-)  A  Poor phi/psi
 123 SER   (   2-)  A  Poor phi/psi
 127 SER   (   6-)  A  Poor phi/psi
 145 ASP   (  24-)  A  Poor phi/psi
 167 ASN   (  46-)  A  Poor phi/psi
 190 LYS   (  69-)  A  Poor phi/psi
 197 GLN   (  76-)  A  Poor phi/psi
 203 ASN   (  82-)  A  Poor phi/psi
 241 SER   ( 120-)  A  Poor phi/psi
 244 SER   (   2-)  A  Poor phi/psi
 248 SER   (   6-)  A  Poor phi/psi
 256 SER   (  14-)  A  Poor phi/psi
 266 ASP   (  24-)  A  Poor phi/psi
 288 ASN   (  46-)  A  Poor phi/psi
 311 LYS   (  69-)  A  Poor phi/psi
 318 GLN   (  76-)  A  Poor phi/psi
 324 ASN   (  82-)  A  Poor phi/psi
 362 SER   ( 120-)  A  Poor phi/psi
 372 VAL   (   9-)  A  Poor phi/psi
And so on for a total of 157 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 : -6.152

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

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

Model 1 : -5.674
Model 2 : -6.121
Model 3 : -6.144
Model 4 : -6.339
Model 5 : -6.092
Model 6 : -6.282
Model 7 : -5.973
Model 8 : -5.792
Model 9 : -6.216
Model 10 : -6.146
Model 11 : -6.125
Model 12 : -6.605
Model 13 : -6.021
Model 14 : -5.929
Model 15 : -6.233
Model 16 : -6.356
Model 17 : -5.967
Model 18 : -6.364
Model 19 : -6.332
Model 20 : -6.321

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 SER   (   3-)  A      0
   5 SER   (   5-)  A      0
   6 SER   (   6-)  A      0
   8 PRO   (   8-)  A      0
   9 VAL   (   9-)  A      0
  10 LEU   (  10-)  A      0
  11 THR   (  11-)  A      0
  12 GLN   (  12-)  A      0
  13 THR   (  13-)  A      0
  14 SER   (  14-)  A      0
  16 GLN   (  16-)  A      0
  17 ALA   (  17-)  A      0
  18 PRO   (  18-)  A      0
  19 SER   (  19-)  A      0
  23 ARG   (  23-)  A      0
  25 VAL   (  25-)  A      0
  29 MET   (  29-)  A      0
  33 THR   (  33-)  A      0
  38 GLN   (  38-)  A      0
  44 GLU   (  44-)  A      0
  45 PRO   (  45-)  A      0
  46 ASN   (  46-)  A      0
  48 GLN   (  48-)  A      0
  50 GLN   (  50-)  A      0
  61 THR   (  61-)  A      0
And so on for a total of 1409 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.000

Note: Per-model averages for omega angle check

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

Model 1 : 0.026
Model 2 : 0.000
Model 3 : 0.145
Model 4 : 0.114
Model 5 : 0.133
Model 6 : 0.112
Model 7 : 0.169
Model 8 : 0.039
Model 9 : 0.069
Model 10 : 0.123
Model 11 : 0.047
Model 12 : 0.202
Model 13 : 0.140
Model 14 : 0.000
Model 15 : 0.000
Model 16 : 0.096
Model 17 : 0.000
Model 18 : 0.092
Model 19 : 0.140
Model 20 : 0.000

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!

1567 GLY   ( 115-)  A 1  2.82   22
 238 GLY   ( 117-)  A   1.95   16
1446 GLY   ( 115-)  A 1  1.85   37
1809 GLY   ( 115-)  A 1  1.78   10
 249 GLY   (   7-)  A   1.75   11
2172 GLY   ( 115-)  A 1  1.70   18

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.

 898 GLY   (  51-)  A      C   <->  943 PHE   (  96-)  A      CE2    0.10    3.10
 656 GLY   (  51-)  A      C   <->  701 PHE   (  96-)  A      CE2    0.10    3.10
 414 GLY   (  51-)  A      C   <->  459 PHE   (  96-)  A      CE2    0.10    3.10
1972 LEU   (  36-)  A 1    CD1 <-> 1973 VAL   (  37-)  A 1    N      0.07    2.93
1624 GLY   (  51-)  A 1    C   <-> 1669 PHE   (  96-)  A 1    CE2    0.07    3.13
1597 ASP   (  24-)  A 1    CG  <-> 1613 LYS   (  40-)  A 1    CE     0.06    3.14
  41 GLU   (  41-)  A      CD  <->   76 GLN   (  76-)  A      NE2    0.06    3.04
1454 SER   (   2-)  A 1    O   <-> 1456 GLY   (   4-)  A 1    N      0.06    2.64
1360 MET   (  29-)  A 1    SD  <-> 1444 GLN   ( 113-)  A 1    N      0.06    3.24
1625 TYR   (  52-)  A 1    N   <-> 1669 PHE   (  96-)  A 1    CE2    0.05    3.05
 426 HIS   (  63-)  A      CG  <->  428 ASN   (  65-)  A      ND2    0.05    3.05
 668 HIS   (  63-)  A      CG  <->  670 ASN   (  65-)  A      ND2    0.05    3.05
1141 TYR   (  52-)  A 1    N   <-> 1185 PHE   (  96-)  A 1    CE2    0.05    3.05
  41 GLU   (  41-)  A      CG  <->   76 GLN   (  76-)  A      NE2    0.05    3.05
2350 GLY   (  51-)  A 2    C   <-> 2395 PHE   (  96-)  A 2    CE2    0.04    3.16
2270 LYS   (  92-)  A 1    NZ  <-> 2285 ASP   ( 107-)  A 1    CG     0.04    3.06
1382 GLY   (  51-)  A 1    C   <-> 1427 PHE   (  96-)  A 1    CE2    0.04    3.16
1031 HIS   (  63-)  A      CG  <-> 1032 VAL   (  64-)  A      N      0.04    2.96
 184 HIS   (  63-)  A      CG  <->  186 ASN   (  65-)  A      ND2    0.04    3.06
1152 HIS   (  63-)  A 1    CG  <-> 1153 VAL   (  64-)  A 1    N      0.04    2.96
2209 SER   (  31-)  A 1    C   <-> 2292 THR   ( 114-)  A 1    CG2    0.04    3.16
1019 GLY   (  51-)  A      C   <-> 1064 PHE   (  96-)  A      CE2    0.03    3.17
  51 GLY   (  51-)  A      C   <->   96 PHE   (  96-)  A      CE2    0.03    3.17
1273 HIS   (  63-)  A 1    CG  <-> 1274 VAL   (  64-)  A 1    N      0.03    2.97
1140 GLY   (  51-)  A 1    C   <-> 1185 PHE   (  96-)  A 1    CE2    0.03    3.17
And so on for a total of 62 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

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