WHAT IF Check report

This file was created 2011-12-16 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 pdb2le0.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

Geometric checks

Note: Per-model averages for bond-length check

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

Model 1 : 0.509
Model 2 : 0.506
Model 3 : 0.523
Model 4 : 0.528
Model 5 : 0.524
Model 6 : 0.521
Model 7 : 0.523
Model 8 : 0.505
Model 9 : 0.521
Model 10 : 0.523

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.

  72 PHE   (  72-)  A      CA   CB   CG  109.36   -4.4
  90 HIS   (  90-)  A      CA   CB   CG  109.13   -4.7
 101 HIS   ( 101-)  A      CA   CB   CG  109.45   -4.4
 102 HIS   ( 102-)  A      CA   CB   CG  109.61   -4.2
 103 HIS   ( 103-)  A      CA   CB   CG  109.73   -4.1
 104 HIS   ( 104-)  A      CA   CB   CG  109.42   -4.4
 105 HIS   ( 105-)  A      CA   CB   CG  109.66   -4.1
 106 HIS   ( 106-)  A      CA   CB   CG  109.53   -4.3
 178 PHE   (  72-)  A      CA   CB   CG  109.23   -4.6
 196 HIS   (  90-)  A      CA   CB   CG  109.54   -4.3
 207 HIS   ( 101-)  A      CA   CB   CG  109.35   -4.4
 210 HIS   ( 104-)  A      CA   CB   CG  109.55   -4.3
 212 HIS   ( 106-)  A      CA   CB   CG  109.39   -4.4
 284 PHE   (  72-)  A      CA   CB   CG  108.88   -4.9
 302 HIS   (  90-)  A      CA   CB   CG  109.31   -4.5
 313 HIS   ( 101-)  A      CA   CB   CG  109.53   -4.3
 314 HIS   ( 102-)  A      CA   CB   CG  109.58   -4.2
 316 HIS   ( 104-)  A      CA   CB   CG  109.71   -4.1
 318 HIS   ( 106-)  A      CA   CB   CG  109.33   -4.5
 390 PHE   (  72-)  A      CA   CB   CG  109.58   -4.2
 408 HIS   (  90-)  A      CA   CB   CG  108.55   -5.3
 419 HIS   ( 101-)  A      CA   CB   CG  109.46   -4.3
 420 HIS   ( 102-)  A      CA   CB   CG  109.69   -4.1
 421 HIS   ( 103-)  A      CA   CB   CG  109.75   -4.0
 422 HIS   ( 104-)  A      CA   CB   CG  109.45   -4.3
And so on for a total of 59 lines.

Note: Per-model averages for bond-angle check

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

Model 1 : 0.895
Model 2 : 0.891
Model 3 : 0.884
Model 4 : 0.885
Model 5 : 0.892
Model 6 : 0.897
Model 7 : 0.889
Model 8 : 0.896
Model 9 : 0.889
Model 10 : 0.897

Note: Per-model averages for chirality check

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

Model 1 : 0.709
Model 2 : 0.743
Model 3 : 0.709
Model 4 : 0.724
Model 5 : 0.739
Model 6 : 0.731
Model 7 : 0.728
Model 8 : 0.769
Model 9 : 0.706
Model 10 : 0.740

Torsion-related checks

Note: Per-model averages for Ramachandran check

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

Model 1 : 0.136
Model 2 : -0.143
Model 3 : -0.568
Model 4 : -0.030
Model 5 : -0.086
Model 6 : -0.987
Model 7 : -0.553
Model 8 : -0.673
Model 9 : -0.685
Model 10 : -1.255

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.

 564 THR   (  34-)  A    -3.0
 655 LYS   (  19-)  A    -2.7
1056 HIS   ( 102-)  A 1   -2.7
 458 THR   (  34-)  A    -2.6
 639 PRO   (   3-)  A    -2.6
 354 SER   (  36-)  A    -2.6
 320 LYS   (   2-)  A    -2.6
 949 HIS   ( 101-)  A    -2.6
 884 SER   (  36-)  A    -2.5
 950 HIS   ( 102-)  A    -2.4
 321 PRO   (   3-)  A    -2.4
 409 SER   (  91-)  A    -2.4
 776 THR   (  34-)  A    -2.4
 739 HIS   ( 103-)  A    -2.3
 316 HIS   ( 104-)  A    -2.3
 308 GLY   (  96-)  A    -2.2
 745 PRO   (   3-)  A    -2.2
 944 GLY   (  96-)  A    -2.2
  96 GLY   (  96-)  A    -2.2
 626 GLY   (  96-)  A    -2.2
 331 GLY   (  13-)  A    -2.2
 518 SER   (  94-)  A    -2.2
 649 GLY   (  13-)  A    -2.2
 119 GLY   (  13-)  A    -2.2
 202 GLY   (  96-)  A    -2.2
1050 GLY   (  96-)  A 1   -2.2
 299 LEU   (  87-)  A    -2.1
 755 GLY   (  13-)  A    -2.1
 838 GLY   (  96-)  A    -2.1
 549 LYS   (  19-)  A    -2.1
 254 LEU   (  42-)  A    -2.1
 231 LYS   (  19-)  A    -2.1
 520 GLY   (  96-)  A    -2.1
 829 LEU   (  87-)  A    -2.1
 414 GLY   (  96-)  A    -2.1
  15 LEU   (  15-)  A    -2.1
 960 ASN   (   6-)  A 1   -2.1
 140 THR   (  34-)  A    -2.1
 382 ASN   (  64-)  A    -2.1
 723 LEU   (  87-)  A    -2.1
 439 LEU   (  15-)  A    -2.0
 306 SER   (  94-)  A    -2.0
1053 VAL   (  99-)  A 1   -2.0
 193 LEU   (  87-)  A    -2.0
 227 LEU   (  15-)  A    -2.0
  10 LEU   (  10-)  A    -2.0
 511 LEU   (  87-)  A    -2.0
 437 GLY   (  13-)  A    -2.0

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.

  30 GLY   (  30-)  A  Poor phi/psi
  35 GLY   (  35-)  A  Poor phi/psi
  36 SER   (  36-)  A  Poor phi/psi
  53 MET   (  53-)  A  Poor phi/psi
  64 ASN   (  64-)  A  Poor phi/psi
  97 ALA   (  97-)  A  Poor phi/psi
 122 SER   (  16-)  A  Poor phi/psi
 144 ASN   (  38-)  A  Poor phi/psi
 170 ASN   (  64-)  A  Poor phi/psi
 187 LYS   (  81-)  A  Poor phi/psi
 203 ALA   (  97-)  A  Poor phi/psi
 207 HIS   ( 101-)  A  Poor phi/psi
 209 HIS   ( 103-)  A  Poor phi/psi
 214 LYS   (   2-)  A  Poor phi/psi
 230 ASN   (  18-)  A  Poor phi/psi
 248 SER   (  36-)  A  Poor phi/psi
 276 ASN   (  64-)  A  Poor phi/psi
 293 LYS   (  81-)  A  Poor phi/psi
 309 ALA   (  97-)  A  Poor phi/psi
 313 HIS   ( 101-)  A  Poor phi/psi
 316 HIS   ( 104-)  A  Poor phi/psi
 320 LYS   (   2-)  A  Poor phi/psi
 331 GLY   (  13-)  A  Poor phi/psi
 335 GLN   (  17-)  A  Poor phi/psi
 336 ASN   (  18-)  A  Poor phi/psi
And so on for a total of 81 lines.

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 : -0.273
Model 2 : -0.920
Model 3 : -1.921
Model 4 : -1.237
Model 5 : -0.011
Model 6 : -1.280
Model 7 : -0.561
Model 8 : -1.481
Model 9 : -2.131
Model 10 : -0.773

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 PRO   (   3-)  A      0
   6 ASN   (   6-)  A      0
  12 LEU   (  12-)  A      0
  14 LYS   (  14-)  A      0
  16 SER   (  16-)  A      0
  29 LEU   (  29-)  A      0
  36 SER   (  36-)  A      0
  37 ALA   (  37-)  A      0
  42 LEU   (  42-)  A      0
  44 ILE   (  44-)  A      0
  52 LYS   (  52-)  A      0
  53 MET   (  53-)  A      0
  64 ASN   (  64-)  A      0
  78 ALA   (  78-)  A      0
  79 SER   (  79-)  A      0
  80 ALA   (  80-)  A      0
  81 LYS   (  81-)  A      0
  92 LEU   (  92-)  A      0
  95 TRP   (  95-)  A      0
  97 ALA   (  97-)  A      0
  98 GLU   (  98-)  A      0
 100 LYS   ( 100-)  A      0
 101 HIS   ( 101-)  A      0
 102 HIS   ( 102-)  A      0
 104 HIS   ( 104-)  A      0
And so on for a total of 492 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 : 1.018

Note: Per-model averages for omega angle check

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

Model 1 : 0.828
Model 2 : 1.128
Model 3 : 0.934
Model 4 : 0.960
Model 5 : 1.001
Model 6 : 0.926
Model 7 : 0.942
Model 8 : 1.049
Model 9 : 0.885
Model 10 : 1.264

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!

 649 GLY   (  13-)  A   1.89   18

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].

 215 PRO   (   3-)  A   -64.7 envelop C-beta (-72 degrees)
 321 PRO   (   3-)  A   -58.1 half-chair C-beta/C-alpha (-54 degrees)
 533 PRO   (   3-)  A   -62.5 half-chair C-beta/C-alpha (-54 degrees)
 639 PRO   (   3-)  A   -47.8 half-chair C-beta/C-alpha (-54 degrees)
 745 PRO   (   3-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
 957 PRO   (   3-)  A 1  -65.6 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.

 387 CYS   (  69-)  A      SG  <->  388 GLU   (  70-)  A      N      0.47    2.73
 648 LEU   (  12-)  A      CD1 <->  679 CYS   (  43-)  A      SG     0.42    2.98
 314 HIS   ( 102-)  A      CD2 <->  315 HIS   ( 103-)  A      ND1    0.41    2.69
 865 GLN   (  17-)  A      NE2 <->  922 GLN   (  74-)  A      NE2    0.40    2.45
 123 GLN   (  17-)  A      NE2 <->  176 GLU   (  70-)  A      CD     0.39    2.71
 489 VAL   (  65-)  A      O   <->  519 TRP   (  95-)  A      NE1    0.38    2.32
1004 VAL   (  50-)  A 1    O   <-> 1007 MET   (  53-)  A 1    SD     0.38    2.47
 939 SER   (  91-)  A      O   <->  941 SER   (  93-)  A      N      0.37    2.33
 621 SER   (  91-)  A      O   <->  623 SER   (  93-)  A      N      0.35    2.35
  65 VAL   (  65-)  A      O   <->   95 TRP   (  95-)  A      NE1    0.35    2.35
 171 VAL   (  65-)  A      O   <->  201 TRP   (  95-)  A      NE1    0.33    2.37
 913 VAL   (  65-)  A      O   <->  943 TRP   (  95-)  A      NE1    0.33    2.37
 383 VAL   (  65-)  A      O   <->  413 TRP   (  95-)  A      NE1    0.33    2.37
 573 CYS   (  43-)  A      SG  <->  574 ILE   (  44-)  A      N      0.33    2.87
 595 VAL   (  65-)  A      O   <->  625 TRP   (  95-)  A      NE1    0.33    2.37
 314 HIS   ( 102-)  A      NE2 <->  315 HIS   ( 103-)  A      CE1    0.32    2.78
 705 CYS   (  69-)  A      SG  <->  706 GLU   (  70-)  A      N      0.32    2.88
 277 VAL   (  65-)  A      O   <->  307 TRP   (  95-)  A      NE1    0.32    2.38
 711 ASP   (  75-)  A      OD2 <->  726 HIS   (  90-)  A      NE2    0.32    2.38
 807 VAL   (  65-)  A      O   <->  837 TRP   (  95-)  A      NE1    0.32    2.38
 393 ASP   (  75-)  A      OD2 <->  408 HIS   (  90-)  A      NE2    0.31    2.39
 462 ASN   (  38-)  A      ND2 <->  487 ALA   (  63-)  A      O      0.31    2.39
 493 CYS   (  69-)  A      SG  <->  494 GLU   (  70-)  A      N      0.31    2.89
1029 ASP   (  75-)  A 1    OD2 <-> 1044 HIS   (  90-)  A 1    NE2    0.31    2.39
 600 GLU   (  70-)  A      O   <->  604 GLN   (  74-)  A      NE2    0.31    2.39
And so on for a total of 355 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

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

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

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