WHAT IF Check report

This file was created 2012-08-23 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 pdb2lj4.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

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.

 839 TYR   (  37-)  A      CE1  CZ    1.48    4.1

Note: Per-model averages for bond-length check

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

Model 1 : 0.285
Model 2 : 0.299
Model 3 : 0.288
Model 4 : 0.283
Model 5 : 0.283
Model 6 : 0.277
Model 7 : 0.280
Model 8 : 0.354
Model 9 : 0.300
Model 10 : 0.272
Model 11 : 0.287
Model 12 : 0.277
Model 13 : 0.293
Model 14 : 0.281
Model 15 : 0.289
Model 16 : 0.306
Model 17 : 0.286
Model 18 : 0.295
Model 19 : 0.275
Model 20 : 0.275

Note: Per-model averages for bond-angle check

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

Model 1 : 0.470
Model 2 : 0.477
Model 3 : 0.468
Model 4 : 0.472
Model 5 : 0.458
Model 6 : 0.480
Model 7 : 0.469
Model 8 : 0.495
Model 9 : 0.471
Model 10 : 0.479
Model 11 : 0.464
Model 12 : 0.482
Model 13 : 0.477
Model 14 : 0.464
Model 15 : 0.453
Model 16 : 0.469
Model 17 : 0.481
Model 18 : 0.460
Model 19 : 0.471
Model 20 : 0.465

Note: Per-model averages for chirality check

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

Model 1 : 0.478
Model 2 : 0.488
Model 3 : 0.488
Model 4 : 0.491
Model 5 : 0.486
Model 6 : 0.485
Model 7 : 0.481
Model 8 : 0.713
Model 9 : 0.504
Model 10 : 0.483
Model 11 : 0.462
Model 12 : 0.491
Model 13 : 0.489
Model 14 : 0.503
Model 15 : 0.459
Model 16 : 0.489
Model 17 : 0.499
Model 18 : 0.473
Model 19 : 0.500
Model 20 : 0.480

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.

 839 TYR   (  37-)  A    4.01

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 : -3.300

Note: Per-model averages for Ramachandran check

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

Model 1 : -3.367
Model 2 : -3.145
Model 3 : -3.605
Model 4 : -3.360
Model 5 : -3.473
Model 6 : -3.371
Model 7 : -2.679
Model 8 : -3.398
Model 9 : -3.095
Model 10 : -3.464
Model 11 : -3.037
Model 12 : -3.105
Model 13 : -3.318
Model 14 : -3.339
Model 15 : -3.082
Model 16 : -3.590
Model 17 : -3.468
Model 18 : -3.162
Model 19 : -3.459
Model 20 : -3.477

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.

 208 LEU   (  96-)  A    -2.5
1818 LEU   (  96-)  A 1   -2.5
 783 LEU   (  96-)  A    -2.4
1170 PRO   (  23-)  A 1   -2.4
 480 PRO   (  23-)  A    -2.4
1588 LEU   (  96-)  A 1   -2.4
 323 LEU   (  96-)  A    -2.4
1473 LEU   (  96-)  A 1   -2.4
  93 LEU   (  96-)  A    -2.4
2278 LEU   (  96-)  A 2   -2.4
1013 LEU   (  96-)  A    -2.4
 898 LEU   (  96-)  A    -2.4
1703 LEU   (  96-)  A 1   -2.4
2205 PRO   (  23-)  A 2   -2.3
1128 LEU   (  96-)  A 1   -2.3
1224 LEU   (  77-)  A 1   -2.3
2048 LEU   (  96-)  A 1   -2.3
2163 LEU   (  96-)  A 1   -2.3
1454 LEU   (  77-)  A 1   -2.3
1569 LEU   (  77-)  A 1   -2.3
2147 PHE   (  80-)  A 1   -2.3
1457 PHE   (  80-)  A 1   -2.3
 104 THR   ( 107-)  A    -2.3
 994 LEU   (  77-)  A    -2.3
1917 PHE   (  80-)  A 1   -2.3
And so on for a total of 99 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   (   5-)  A  Poor phi/psi
  18 ARG   (  21-)  A  Poor phi/psi
  20 PRO   (  23-)  A  Poor phi/psi
  82 MET   (  85-)  A  Poor phi/psi
 109 HIS   ( 112-)  A  omega poor
 133 ARG   (  21-)  A  Poor phi/psi
 135 PRO   (  23-)  A  Poor phi/psi
 196 GLU   (  84-)  A  Poor phi/psi
 197 MET   (  85-)  A  Poor phi/psi
 224 HIS   ( 112-)  A  omega poor
 232 SER   (   5-)  A  Poor phi/psi
 248 ARG   (  21-)  A  Poor phi/psi
 250 PRO   (  23-)  A  Poor phi/psi
 251 VAL   (  24-)  A  Poor phi/psi
 312 MET   (  85-)  A  Poor phi/psi
 339 HIS   ( 112-)  A  omega poor
 363 ARG   (  21-)  A  Poor phi/psi
 365 PRO   (  23-)  A  Poor phi/psi
 417 GLY   (  75-)  A  Poor phi/psi
 427 MET   (  85-)  A  Poor phi/psi
 454 HIS   ( 112-)  A  omega poor
 462 SER   (   5-)  A  Poor phi/psi
 478 ARG   (  21-)  A  Poor phi/psi
 487 ASP   (  30-)  A  Poor phi/psi
 542 MET   (  85-)  A  Poor phi/psi
And so on for a total of 114 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 : -3.949

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

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

Model 1 : -3.868
Model 2 : -3.047
Model 3 : -4.831
Model 4 : -4.144
Model 5 : -4.161
Model 6 : -3.344
Model 7 : -4.259
Model 8 : -4.197
Model 9 : -3.806
Model 10 : -3.832
Model 11 : -4.144
Model 12 : -4.238
Model 13 : -3.515
Model 14 : -4.657
Model 15 : -4.049
Model 16 : -4.049
Model 17 : -3.489
Model 18 : -4.253
Model 19 : -3.772
Model 20 : -3.322

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.

1195 SER   (  48-)  A 1   0.36
1540 SER   (  48-)  A 1   0.36
 735 SER   (  48-)  A    0.37
1310 SER   (  48-)  A 1   0.39
2230 SER   (  48-)  A 2   0.39

Warning: Unusual backbone conformations

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

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

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

   3 GLU   (   6-)  A      0
  14 PHE   (  17-)  A      0
  15 SER   (  18-)  A      0
  17 SER   (  20-)  A      0
  18 ARG   (  21-)  A      0
  20 PRO   (  23-)  A      0
  25 THR   (  28-)  A      0
  27 ASP   (  30-)  A      0
  28 SER   (  31-)  A      0
  29 THR   (  32-)  A      0
  30 ALA   (  33-)  A      0
  50 SER   (  53-)  A      0
  62 ARG   (  65-)  A      0
  64 ASP   (  67-)  A      0
  65 CYS   (  68-)  A      0
  70 SER   (  73-)  A      0
  76 PHE   (  79-)  A      0
  79 SER   (  82-)  A      0
  82 MET   (  85-)  A      0
  92 ALA   (  95-)  A      0
  94 LYS   (  97-)  A      0
  95 ILE   (  98-)  A      0
 101 ILE   ( 104-)  A      0
 106 SER   ( 109-)  A      0
 108 LEU   ( 111-)  A      0
And so on for a total of 911 lines.

Note: Per-model averages for omega angle check

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

Model 1 : 4.215
Model 2 : 4.183
Model 3 : 4.181
Model 4 : 4.300
Model 5 : 4.356
Model 6 : 4.220
Model 7 : 4.160
Model 8 : 4.397
Model 9 : 4.406
Model 10 : 4.212
Model 11 : 4.135
Model 12 : 4.280
Model 13 : 4.414
Model 14 : 4.463
Model 15 : 4.064
Model 16 : 4.469
Model 17 : 4.279
Model 18 : 4.018
Model 19 : 4.350
Model 20 : 4.029

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!

2030 GLY   (  78-)  A 1  2.30   10
1570 GLY   (  78-)  A 1  2.00   13
1800 GLY   (  78-)  A 1  1.92   12
1685 GLY   (  78-)  A 1  1.58   17

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].

  20 PRO   (  23-)  A   -65.0 envelop C-beta (-72 degrees)
 480 PRO   (  23-)  A   -64.5 envelop C-beta (-72 degrees)
1055 PRO   (  23-)  A 1  -66.0 envelop C-beta (-72 degrees)
1170 PRO   (  23-)  A 1  -59.6 half-chair C-beta/C-alpha (-54 degrees)
1285 PRO   (  23-)  A 1  -63.2 envelop C-beta (-72 degrees)
1630 PRO   (  23-)  A 1   51.5 half-chair C-delta/C-gamma (54 degrees)
2205 PRO   (  23-)  A 2  -63.1 envelop C-beta (-72 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.

2079 HIS   (  12-)  A 1    NE2 <-> 2135 CYS   (  68-)  A 1    SG     0.34    2.96
   9 HIS   (  12-)  A      NE2 <->   65 CYS   (  68-)  A      SG     0.34    2.96
 469 HIS   (  12-)  A      NE2 <->  525 CYS   (  68-)  A      SG     0.32    2.98
1159 HIS   (  12-)  A 1    NE2 <-> 1215 CYS   (  68-)  A 1    SG     0.31    2.99
 699 HIS   (  12-)  A      NE2 <->  755 CYS   (  68-)  A      SG     0.30    3.00
 124 HIS   (  12-)  A      NE2 <->  180 CYS   (  68-)  A      SG     0.27    3.03
1504 HIS   (  12-)  A 1    NE2 <-> 1560 CYS   (  68-)  A 1    SG     0.27    3.03
 584 HIS   (  12-)  A      NE2 <->  640 CYS   (  68-)  A      SG     0.27    3.03
2194 HIS   (  12-)  A 2    NE2 <-> 2250 CYS   (  68-)  A 2    SG     0.26    3.04
1619 HIS   (  12-)  A 1    NE2 <-> 1675 CYS   (  68-)  A 1    SG     0.26    3.04
 354 HIS   (  12-)  A      NE2 <->  410 CYS   (  68-)  A      SG     0.24    3.06
1849 HIS   (  12-)  A 1    NE2 <-> 1905 CYS   (  68-)  A 1    SG     0.24    3.06
1964 HIS   (  12-)  A 1    NE2 <-> 2020 CYS   (  68-)  A 1    SG     0.24    3.06
1044 HIS   (  12-)  A 1    NE2 <-> 1100 CYS   (  68-)  A 1    SG     0.23    3.07
1851 LEU   (  14-)  A 1    CD2 <-> 1905 CYS   (  68-)  A 1    SG     0.23    3.17
1215 CYS   (  68-)  A 1    SG  <-> 1216 GLY   (  69-)  A 1    N      0.22    2.98
 931 LEU   (  14-)  A      CD2 <->  985 CYS   (  68-)  A      SG     0.21    3.19
1046 LEU   (  14-)  A 1    CD2 <-> 1100 CYS   (  68-)  A 1    SG     0.21    3.19
 372 ASP   (  30-)  A      CG  <->  373 SER   (  31-)  A      N      0.20    2.80
1736 LEU   (  14-)  A 1    CD2 <-> 1790 CYS   (  68-)  A 1    SG     0.19    3.21
1732 ALA   (  10-)  A 1    N   <-> 1802 PHE   (  80-)  A 1    CZ     0.18    2.92
 467 ALA   (  10-)  A      N   <->  537 PHE   (  80-)  A      CZ     0.18    2.92
 525 CYS   (  68-)  A      SG  <->  526 GLY   (  69-)  A      N      0.18    3.02
 352 ALA   (  10-)  A      N   <->  422 PHE   (  80-)  A      CZ     0.18    2.92
 180 CYS   (  68-)  A      SG  <->  181 GLY   (  69-)  A      N      0.17    3.03
And so on for a total of 415 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

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