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 pdb2ke3.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 SER   ( 711-)  A    Zero
   2 LYS   ( 712-)  A    Zero
   3 LEU   ( 713-)  A    Zero
   4 GLU   ( 714-)  A    Zero
   5 GLY   ( 715-)  A    Zero
   6 SER   ( 716-)  A    Zero
   7 GLU   ( 717-)  A    Zero
   8 ASP   ( 718-)  A    Zero
   9 SER   ( 719-)  A    Zero
  10 LEU   ( 720-)  A    Zero
  11 TYR   ( 721-)  A    Zero
  12 SER   ( 722-)  A    Zero
  13 ASP   ( 723-)  A    Zero
  14 TYR   ( 724-)  A    Zero
  15 VAL   ( 725-)  A    Zero
  16 ASP   ( 726-)  A    Zero
  17 VAL   ( 727-)  A    Zero
  18 PHE   ( 728-)  A    Zero
  19 TYR   ( 729-)  A    Zero
  20 ASN   ( 730-)  A    Zero
  21 THR   ( 731-)  A    Zero
  22 LYS   ( 732-)  A    Zero
  23 PRO   ( 733-)  A    Zero
  24 TYR   ( 734-)  A    Zero
  25 LYS   ( 735-)  A    Zero
And so on for a total of 860 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 : 0.158
Model 2 : 0.155
Model 3 : 0.153
Model 4 : 0.158
Model 5 : 0.155
Model 6 : 0.151
Model 7 : 0.158
Model 8 : 0.154
Model 9 : 0.155
Model 10 : 0.155
Model 11 : 0.159
Model 12 : 0.153
Model 13 : 0.152
Model 14 : 0.157
Model 15 : 0.153
Model 16 : 0.153
Model 17 : 0.152
Model 18 : 0.153
Model 19 : 0.153
Model 20 : 0.152

Note: Per-model averages for bond-angle check

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

Model 1 : 0.316
Model 2 : 0.314
Model 3 : 0.316
Model 4 : 0.313
Model 5 : 0.316
Model 6 : 0.320
Model 7 : 0.313
Model 8 : 0.316
Model 9 : 0.315
Model 10 : 0.314
Model 11 : 0.315
Model 12 : 0.318
Model 13 : 0.313
Model 14 : 0.315
Model 15 : 0.315
Model 16 : 0.315
Model 17 : 0.314
Model 18 : 0.314
Model 19 : 0.312
Model 20 : 0.319

Note: Per-model averages for chirality check

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

Model 1 : 0.256
Model 2 : 0.256
Model 3 : 0.260
Model 4 : 0.257
Model 5 : 0.258
Model 6 : 0.256
Model 7 : 0.255
Model 8 : 0.260
Model 9 : 0.259
Model 10 : 0.261
Model 11 : 0.254
Model 12 : 0.256
Model 13 : 0.256
Model 14 : 0.261
Model 15 : 0.261
Model 16 : 0.259
Model 17 : 0.260
Model 18 : 0.257
Model 19 : 0.259
Model 20 : 0.260

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 : -4.612

Note: Per-model averages for Ramachandran check

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

Model 1 : -4.934
Model 2 : -4.895
Model 3 : -4.823
Model 4 : -3.451
Model 5 : -4.311
Model 6 : -4.983
Model 7 : -5.096
Model 8 : -4.683
Model 9 : -5.002
Model 10 : -4.833
Model 11 : -4.585
Model 12 : -3.991
Model 13 : -4.535
Model 14 : -5.161
Model 15 : -4.131
Model 16 : -4.710
Model 17 : -4.612
Model 18 : -3.791
Model 19 : -5.314
Model 20 : -4.404

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.

 613 TYR   ( 721-)  A 1   -3.7
 752 THR   ( 731-)  A 1   -3.6
 570 TYR   ( 721-)  A 1   -3.5
  21 THR   ( 731-)  A    -3.4
 368 TYR   ( 734-)  A    -3.4
 742 TYR   ( 721-)  A 1   -3.3
 365 THR   ( 731-)  A    -3.3
 198 HIS   ( 736-)  A    -3.3
 484 TYR   ( 721-)  A 1   -3.2
 585 HIS   ( 736-)  A 1   -3.2
 239 TYR   ( 734-)  A    -3.2
 327 HIS   ( 736-)  A    -3.2
 800 HIS   ( 736-)  A 1   -3.2
 669 TYR   ( 734-)  A 1   -3.2
 537 THR   ( 731-)  A 1   -3.2
 580 THR   ( 731-)  A 1   -3.1
 583 TYR   ( 734-)  A 1   -3.0
 494 THR   ( 731-)  A 1   -3.0
  53 LEU   ( 720-)  A    -2.8
 671 HIS   ( 736-)  A 1   -2.8
 413 HIS   ( 736-)  A 1   -2.7
  10 LEU   ( 720-)  A    -2.7
 612 LEU   ( 720-)  A 1   -2.7
 538 LYS   ( 732-)  A 1   -2.7
  92 SER   ( 716-)  A    -2.7
And so on for a total of 155 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.

   3 LEU   ( 713-)  A  Poor phi/psi
   8 ASP   ( 718-)  A  Poor phi/psi
  42 GLU   ( 752-)  A  Poor phi/psi
  52 SER   ( 719-)  A  Poor phi/psi
  53 LEU   ( 720-)  A  Poor phi/psi
  63 ASN   ( 730-)  A  Poor phi/psi
  85 GLU   ( 752-)  A  Poor phi/psi
  89 LEU   ( 713-)  A  Poor phi/psi
  92 SER   ( 716-)  A  Poor phi/psi
 106 ASN   ( 730-)  A  Poor phi/psi
 111 LYS   ( 735-)  A  Poor phi/psi
 112 HIS   ( 736-)  A  Poor phi/psi
 113 ARG   ( 737-)  A  Poor phi/psi
 128 GLU   ( 752-)  A  Poor phi/psi
 149 ASN   ( 730-)  A  Poor phi/psi
 151 LYS   ( 732-)  A  Poor phi/psi
 179 GLU   ( 717-)  A  Poor phi/psi
 182 LEU   ( 720-)  A  Poor phi/psi
 192 ASN   ( 730-)  A  Poor phi/psi
 196 TYR   ( 734-)  A  Poor phi/psi
 197 LYS   ( 735-)  A  Poor phi/psi
 198 HIS   ( 736-)  A  Poor phi/psi
 219 GLU   ( 714-)  A  Poor phi/psi
 238 PRO   ( 733-)  A  Poor phi/psi
 239 TYR   ( 734-)  A  Poor phi/psi
And so on for a total of 92 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 : -7.367

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 : -8.410
Model 2 : -6.332
Model 3 : -6.912
Model 4 : -7.144
Model 5 : -7.910
Model 6 : -7.053
Model 7 : -8.095
Model 8 : -7.341
Model 9 : -7.785
Model 10 : -7.672
Model 11 : -7.233
Model 12 : -8.182
Model 13 : -8.111
Model 14 : -6.839
Model 15 : -8.015
Model 16 : -7.774
Model 17 : -6.532
Model 18 : -7.084
Model 19 : -5.965
Model 20 : -6.953

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.

 761 ARG   ( 740-)  A 1   0.36

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 LEU   ( 713-)  A      0
   4 GLU   ( 714-)  A      0
   6 SER   ( 716-)  A      0
   7 GLU   ( 717-)  A      0
   8 ASP   ( 718-)  A      0
  10 LEU   ( 720-)  A      0
  11 TYR   ( 721-)  A      0
  20 ASN   ( 730-)  A      0
  21 THR   ( 731-)  A      0
  23 PRO   ( 733-)  A      0
  24 TYR   ( 734-)  A      0
  42 GLU   ( 752-)  A      0
  43 ASN   ( 753-)  A      0
  44 SER   ( 711-)  A      0
  45 LYS   ( 712-)  A      0
  51 ASP   ( 718-)  A      0
  52 SER   ( 719-)  A      0
  53 LEU   ( 720-)  A      0
  54 TYR   ( 721-)  A      0
  55 SER   ( 722-)  A      0
  61 PHE   ( 728-)  A      0
  62 TYR   ( 729-)  A      0
  63 ASN   ( 730-)  A      0
  64 THR   ( 731-)  A      0
  65 LYS   ( 732-)  A      0
And so on for a total of 443 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 : 0.130

Note: Per-model averages for omega angle check

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

Model 1 : 0.146
Model 2 : 0.147
Model 3 : 0.095
Model 4 : 0.119
Model 5 : 0.108
Model 6 : 0.155
Model 7 : 0.081
Model 8 : 0.122
Model 9 : 0.082
Model 10 : 0.122
Model 11 : 0.137
Model 12 : 0.103
Model 13 : 0.163
Model 14 : 0.156
Model 15 : 0.134
Model 16 : 0.117
Model 17 : 0.102
Model 18 : 0.072
Model 19 : 0.113
Model 20 : 0.107

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!

 392 GLY   ( 715-)  A 1  1.78   37
 306 GLY   ( 715-)  A   1.72   13
  48 GLY   ( 715-)  A   1.54   14

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.

 413 HIS   ( 736-)  A 1    NE2 <->  415 ASP   ( 738-)  A 1    CG     0.25    2.85
 509 MET   ( 746-)  A 1    SD  <->  513 ASN   ( 750-)  A 1    ND2    0.23    3.07
 570 TYR   ( 721-)  A 1    CE2 <->  573 TYR   ( 724-)  A 1    CG     0.20    3.00
  64 THR   ( 731-)  A      C   <->   66 PRO   ( 733-)  A      CD     0.18    3.02
 700 SER   ( 722-)  A 1    O   <->  704 ASP   ( 726-)  A 1    N      0.15    2.55
  65 LYS   ( 732-)  A      N   <->   66 PRO   ( 733-)  A      CD     0.15    2.85
 571 SER   ( 722-)  A 1    O   <->  575 ASP   ( 726-)  A 1    N      0.15    2.55
 614 SER   ( 722-)  A 1    O   <->  618 ASP   ( 726-)  A 1    N      0.15    2.55
 356 SER   ( 722-)  A      O   <->  360 ASP   ( 726-)  A      N      0.14    2.56
 528 SER   ( 722-)  A 1    O   <->  532 ASP   ( 726-)  A 1    N      0.14    2.56
 829 SER   ( 722-)  A 2    O   <->  833 ASP   ( 726-)  A 2    N      0.14    2.56
 141 SER   ( 722-)  A      O   <->  145 ASP   ( 726-)  A      N      0.14    2.56
 442 SER   ( 722-)  A 1    O   <->  446 ASP   ( 726-)  A 1    N      0.14    2.56
 485 SER   ( 722-)  A 1    O   <->  489 ASP   ( 726-)  A 1    N      0.14    2.56
  12 SER   ( 722-)  A      O   <->   16 ASP   ( 726-)  A      N      0.14    2.56
 313 SER   ( 722-)  A      O   <->  317 ASP   ( 726-)  A      N      0.14    2.56
 786 SER   ( 722-)  A 1    O   <->  790 ASP   ( 726-)  A 1    N      0.14    2.56
 743 SER   ( 722-)  A 1    O   <->  747 ASP   ( 726-)  A 1    N      0.14    2.56
 184 SER   ( 722-)  A      O   <->  188 ASP   ( 726-)  A      N      0.14    2.56
 399 SER   ( 722-)  A 1    O   <->  403 ASP   ( 726-)  A 1    N      0.14    2.56
  98 SER   ( 722-)  A      O   <->  102 ASP   ( 726-)  A      N      0.14    2.56
 657 SER   ( 722-)  A 1    O   <->  661 ASP   ( 726-)  A 1    N      0.14    2.56
 521 GLY   ( 715-)  A 1    O   <->  523 GLU   ( 717-)  A 1    N      0.13    2.57
 227 SER   ( 722-)  A      O   <->  231 ASP   ( 726-)  A      N      0.13    2.57
  55 SER   ( 722-)  A      O   <->   59 ASP   ( 726-)  A      N      0.13    2.57
And so on for a total of 163 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.288

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: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure