WHAT IF Check report

This file was created 2011-12-17 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 pdb3pgc.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.853
CA-only RMS fit for the two chains : 0.590

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and E

All-atom RMS fit for the two chains : 0.676
CA-only RMS fit for the two chains : 0.504

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and F

All-atom RMS fit for the two chains : 0.839
CA-only RMS fit for the two chains : 0.400

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and F

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 751 PEG   ( 193-)  E  -

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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  97 ARG   ( 100-)  A      CG
  97 ARG   ( 100-)  A      CD
  97 ARG   ( 100-)  A      NE
  97 ARG   ( 100-)  A      CZ
  97 ARG   ( 100-)  A      NH1
  97 ARG   ( 100-)  A      NH2
  98 GLU   ( 101-)  A      CG
  98 GLU   ( 101-)  A      CD
  98 GLU   ( 101-)  A      OE1
  98 GLU   ( 101-)  A      OE2
 123 LYS   ( 126-)  A      CG
 123 LYS   ( 126-)  A      CD
 123 LYS   ( 126-)  A      CE
 123 LYS   ( 126-)  A      NZ
 242 LYS   (  65-)  B      CG
 242 LYS   (  65-)  B      CD
 242 LYS   (  65-)  B      CE
 242 LYS   (  65-)  B      NZ
 282 ASN   ( 113-)  B      CG
 282 ASN   ( 113-)  B      OD1
 282 ASN   ( 113-)  B      ND2
 297 GLU   ( 128-)  B      CG
 297 GLU   ( 128-)  B      CD
 297 GLU   ( 128-)  B      OE1
 297 GLU   ( 128-)  B      OE2
And so on for a total of 82 lines.

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.

 302 ARG   ( 133-)  B    High
 333 VAL   ( 164-)  B    High
 334 PRO   ( 165-)  B    High
 335 ARG   ( 166-)  B    High
 336 SER   ( 167-)  B    High
 337 GLY   ( 168-)  B    High
 338 GLU   ( 169-)  B    High
 360 ARG   ( 191-)  B    High
 361 SER   ( 192-)  B    High
 376 MET   ( 120-)  C    High
 531 GLU   ( 158-)  D    High
 545 GLU   ( 172-)  D    High
 709 VAL   ( 164-)  E    High
 710 PRO   ( 165-)  E    High
 711 ARG   ( 166-)  E    High
 712 SER   ( 167-)  E    High
 713 GLY   ( 168-)  E    High
 714 GLU   ( 169-)  E    High
 734 ARG   ( 189-)  E    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  47 ARG   (  50-)  A
 271 ARG   (  94-)  B
 302 ARG   ( 133-)  B

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  76 TYR   (  79-)  A
 158 TYR   ( 161-)  A
 292 TYR   ( 123-)  B
 340 TYR   ( 171-)  B
 668 TYR   ( 123-)  E

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  23 PHE   (  26-)  A
  51 PHE   (  54-)  A
 184 PHE   (   7-)  B
 194 PHE   (  17-)  B
 217 PHE   (  40-)  B
 291 PHE   ( 122-)  B
 424 PHE   (  51-)  D
 560 PHE   (   7-)  E
 593 PHE   (  40-)  E
 642 PHE   (  89-)  E
 667 PHE   ( 122-)  E
 700 PHE   ( 155-)  E

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 168 ASP   ( 171-)  A
 243 ASP   (  66-)  B
 554 ASP   ( 181-)  D
 619 ASP   (  66-)  E

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  18 GLU   (  21-)  A
  52 GLU   (  55-)  A
  68 GLU   (  71-)  A
  95 GLU   (  98-)  A
 131 GLU   ( 134-)  A
 163 GLU   ( 166-)  A
 169 GLU   ( 172-)  A
 199 GLU   (  22-)  B
 212 GLU   (  35-)  B
 223 GLU   (  46-)  B
 246 GLU   (  69-)  B
 264 GLU   (  87-)  B
 273 GLU   (  96-)  B
 307 GLU   ( 138-)  B
 331 GLU   ( 162-)  B
 345 GLU   ( 176-)  B
 394 GLU   (  21-)  D
 420 GLU   (  47-)  D
 471 GLU   (  98-)  D
 507 GLU   ( 134-)  D
 531 GLU   ( 158-)  D
 539 GLU   ( 166-)  D
 545 GLU   ( 172-)  D
 599 GLU   (  46-)  E
 640 GLU   (  87-)  E
 649 GLU   (  96-)  E
 683 GLU   ( 138-)  E
 721 GLU   ( 176-)  E

Geometric checks

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  18 GLU   (  21-)  A
  47 ARG   (  50-)  A
  52 GLU   (  55-)  A
  68 GLU   (  71-)  A
  95 GLU   (  98-)  A
 131 GLU   ( 134-)  A
 163 GLU   ( 166-)  A
 168 ASP   ( 171-)  A
 169 GLU   ( 172-)  A
 199 GLU   (  22-)  B
 212 GLU   (  35-)  B
 223 GLU   (  46-)  B
 243 ASP   (  66-)  B
 246 GLU   (  69-)  B
 264 GLU   (  87-)  B
 271 ARG   (  94-)  B
 273 GLU   (  96-)  B
 302 ARG   ( 133-)  B
 307 GLU   ( 138-)  B
 331 GLU   ( 162-)  B
 345 GLU   ( 176-)  B
 394 GLU   (  21-)  D
 420 GLU   (  47-)  D
 471 GLU   (  98-)  D
 507 GLU   ( 134-)  D
 531 GLU   ( 158-)  D
 539 GLU   ( 166-)  D
 545 GLU   ( 172-)  D
 554 ASP   ( 181-)  D
 599 GLU   (  46-)  E
 619 ASP   (  66-)  E
 640 GLU   (  87-)  E
 649 GLU   (  96-)  E
 683 GLU   ( 138-)  E
 721 GLU   ( 176-)  E

Torsion-related checks

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.

 126 THR   ( 129-)  A    -2.9
 488 PRO   ( 115-)  D    -2.8
 110 THR   ( 113-)  A    -2.7
 296 ILE   ( 127-)  B    -2.6
 486 THR   ( 113-)  D    -2.6
 326 THR   ( 157-)  B    -2.5
 447 THR   (  74-)  D    -2.4
 669 PRO   ( 124-)  E    -2.4
 200 ARG   (  23-)  B    -2.4
 548 LEU   ( 175-)  D    -2.4
 502 THR   ( 129-)  D    -2.4
 672 ILE   ( 127-)  E    -2.3
 385 PHE   (  12-)  D    -2.3
 364 ARG   ( 108-)  C    -2.3
  29 PHE   (  32-)  A    -2.3
 277 THR   ( 100-)  B    -2.3
 151 LEU   ( 154-)  A    -2.2
 490 VAL   ( 117-)  D    -2.2
 546 PRO   ( 173-)  D    -2.2
 503 THR   ( 130-)  D    -2.2
 702 THR   ( 157-)  E    -2.2
 519 ARG   ( 146-)  D    -2.2
 127 THR   ( 130-)  A    -2.1
 188 LEU   (  11-)  B    -2.1
 215 VAL   (  38-)  B    -2.1
 334 PRO   ( 165-)  B    -2.1
 465 LEU   (  92-)  D    -2.1
 302 ARG   ( 133-)  B    -2.0
 150 PHE   ( 153-)  A    -2.0
 314 THR   ( 145-)  B    -2.0
 389 PRO   (  16-)  D    -2.0
 143 ARG   ( 146-)  A    -2.0
   9 PHE   (  12-)  A    -2.0
 169 GLU   ( 172-)  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.

   5 ILE   (   8-)  A  omega poor
  12 ASN   (  15-)  A  PRO omega poor
  15 GLN   (  18-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  76 TYR   (  79-)  A  Poor phi/psi
  84 PRO   (  87-)  A  omega poor
  97 ARG   ( 100-)  A  Poor phi/psi
 106 ILE   ( 109-)  A  omega poor
 108 LYS   ( 111-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 112 PRO   ( 115-)  A  Poor phi/psi
 121 ASN   ( 124-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 145 PHE   ( 148-)  A  omega poor
 210 ASN   (  33-)  B  Poor phi/psi
 279 TYR   ( 102-)  B  Poor phi/psi
 292 TYR   ( 123-)  B  PRO omega poor
 322 TRP   ( 153-)  B  Poor phi/psi
 332 THR   ( 163-)  B  omega poor
 334 PRO   ( 165-)  B  omega poor
 370 LEU   ( 114-)  C  omega poor
 388 ASN   (  15-)  D  PRO omega poor
 391 GLN   (  18-)  D  Poor phi/psi
 412 LYS   (  39-)  D  Poor phi/psi
 452 TYR   (  79-)  D  Poor phi/psi
 460 PRO   (  87-)  D  omega poor
 473 ARG   ( 100-)  D  Poor phi/psi
 482 ILE   ( 109-)  D  omega poor
 486 THR   ( 113-)  D  Poor phi/psi, PRO omega poor
 516 HIS   ( 143-)  D  Poor phi/psi
 572 ASN   (  19-)  E  Poor phi/psi
 586 ASN   (  33-)  E  Poor phi/psi
 668 TYR   ( 123-)  E  PRO omega poor
 679 ASN   ( 134-)  E  Poor phi/psi
 698 TRP   ( 153-)  E  Poor phi/psi, omega poor
 708 THR   ( 163-)  E  omega poor
 743 LEU   ( 114-)  F  omega poor
 chi-1/chi-2 correlation Z-score : -3.130

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 : -3.130

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.

 420 GLU   (  47-)  D    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!

   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  23 PHE   (  26-)  A      0
  28 ILE   (  31-)  A      0
  29 PHE   (  32-)  A      0
  36 LYS   (  39-)  A      0
  41 ARG   (  44-)  A      0
  48 PHE   (  51-)  A      0
  74 SER   (  77-)  A      0
  75 ASN   (  78-)  A      0
  76 TYR   (  79-)  A      0
  79 ILE   (  82-)  A      0
  91 ASN   (  94-)  A      0
  95 GLU   (  98-)  A      0
  96 LEU   (  99-)  A      0
 100 ASN   ( 103-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 111 PRO   ( 114-)  A      0
 112 PRO   ( 115-)  A      0
 120 ARG   ( 123-)  A      0
 126 THR   ( 129-)  A      0
 127 THR   ( 130-)  A      0
And so on for a total of 289 lines.

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].

  78 PRO   (  81-)  A    40.5 envelop C-delta (36 degrees)
 170 PRO   ( 173-)  A   111.4 envelop C-beta (108 degrees)
 334 PRO   ( 165-)  B    37.7 envelop C-delta (36 degrees)
 352 PRO   ( 183-)  B   121.5 half-chair C-beta/C-alpha (126 degrees)
 375 PRO   ( 119-)  C  -125.1 half-chair C-delta/C-gamma (-126 degrees)
 460 PRO   (  87-)  D  -119.6 half-chair C-delta/C-gamma (-126 degrees)
 469 PRO   (  96-)  D    46.7 half-chair C-delta/C-gamma (54 degrees)
 488 PRO   ( 115-)  D    29.0 envelop C-delta (36 degrees)
 546 PRO   ( 173-)  D   106.8 envelop C-beta (108 degrees)
 650 PRO   (  97-)  E    47.9 half-chair C-delta/C-gamma (54 degrees)
 656 PRO   ( 103-)  E    36.2 envelop C-delta (36 degrees)
 669 PRO   ( 124-)  E    25.9 half-chair N/C-delta (18 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 205 GLU   (  28-)  B      OE1 <->  248 ARG   (  71-)  B      NE     0.34    2.36  INTRA BL
 384 GLU   (  11-)  D      OE2 <->  435 ASN   (  62-)  D      ND2    0.29    2.41  INTRA BL
 734 ARG   ( 189-)  E      NH1 <->  756 HOH   ( 217 )  E      O      0.28    2.42  INTRA BF
 533 VAL   ( 160-)  D      CG2 <->  550 HIS   ( 177-)  D      CE1    0.24    2.96  INTRA BF
 229 GLU   (  52-)  B      OE2 <->  232 ARG   (  55-)  B      NE     0.22    2.48  INTRA BF
 563 GLN   (  10-)  E      NE2 <->  756 HOH   ( 212 )  E      O      0.21    2.49  INTRA BL
 608 ARG   (  55-)  E      N   <->  609 PRO   (  56-)  E      CD     0.20    2.80  INTRA BF
 246 GLU   (  69-)  B      OE2 <->  686 GLY   ( 141-)  E      N      0.19    2.51  INTRA BF
 640 GLU   (  87-)  E      OE2 <->  645 GLN   (  92-)  E      NE2    0.19    2.51  INTRA BL
 390 ASP   (  17-)  D      OD1 <->  559 ARG   (   6-)  E      NE     0.18    2.52  INTRA BF
 605 GLU   (  52-)  E      OE1 <->  608 ARG   (  55-)  E      NH2    0.17    2.53  INTRA BF
 715 VAL   ( 170-)  E      CG2 <->  734 ARG   ( 189-)  E      NH2    0.17    2.93  INTRA BF
  15 GLN   (  18-)  A      NE2 <->  752 HOH   ( 216 )  A      O      0.17    2.53  INTRA BL
 567 GLU   (  14-)  E      OE2 <->  582 ARG   (  29-)  E      NH1    0.16    2.54  INTRA BF
 669 PRO   ( 124-)  E      O   <->  722 HIS   ( 177-)  E      NE2    0.15    2.55  INTRA BL
 377 GLU   (   4-)  D      OE1 <->  571 PHE   (  18-)  E      CE2    0.15    2.65  INTRA BF
 403 GLU   (  30-)  D      O   <->  698 TRP   ( 153-)  E      NE1    0.14    2.56  INTRA BL
 419 GLU   (  46-)  D      OE2 <->  423 ARG   (  50-)  D      NE     0.14    2.56  INTRA BL
 164 HIS   ( 167-)  A      ND1 <->  166 GLY   ( 169-)  A      N      0.14    2.86  INTRA BL
 540 HIS   ( 167-)  D      O   <->  543 LEU   ( 170-)  D      N      0.14    2.56  INTRA BF
 452 TYR   (  79-)  D      O   <->  454 PRO   (  81-)  D      CD     0.14    2.66  INTRA BF
 218 ASP   (  41-)  B      N   <->  753 HOH   ( 205 )  B      O      0.14    2.56  INTRA BL
 382 GLN   (   9-)  D      NE2 <->  384 GLU   (  11-)  D      OE2    0.14    2.56  INTRA BL
 449 ARG   (  76-)  D      NH1 <->  606 LEU   (  53-)  E      O      0.13    2.57  INTRA BF
 621 LEU   (  68-)  E      CD2 <->  625 ARG   (  72-)  E      NH2    0.12    2.98  INTRA BF
And so on for a total of 95 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 473 ARG   ( 100-)  D      -6.59
  96 LEU   (  99-)  A      -5.87
 151 LEU   ( 154-)  A      -5.80
  95 GLU   (  98-)  A      -5.76
 709 VAL   ( 164-)  E      -5.32
 333 VAL   ( 164-)  B      -5.32
 684 LYS   ( 139-)  E      -5.31
 712 SER   ( 167-)  E      -5.22
 308 LYS   ( 139-)  B      -5.20
  15 GLN   (  18-)  A      -5.18
 391 GLN   (  18-)  D      -5.16
  76 TYR   (  79-)  A      -5.09

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: E

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: F

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 360 ARG   ( 191-)  B   -3.73
 358 ARG   ( 189-)  B   -3.45
 711 ARG   ( 166-)  E   -2.99
 678 ARG   ( 133-)  E   -2.78
  97 ARG   ( 100-)  A   -2.55
 714 GLU   ( 169-)  E   -2.55

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 357 TRP   ( 188-)  B     -  360 ARG   ( 191-)  B        -2.63

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 753 HOH   ( 199 )  B      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  91 ASN   (  94-)  A
 146 HIS   ( 149-)  A
 187 GLN   (  10-)  B
 241 GLN   (  64-)  B
 247 GLN   (  70-)  B
 325 GLN   ( 156-)  B
 522 HIS   ( 149-)  D
 563 GLN   (  10-)  E
 701 GLN   ( 156-)  E

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  42 LEU   (  45-)  A      N
  44 GLU   (  47-)  A      N
 118 TRP   ( 121-)  A      NE1
 120 ARG   ( 123-)  A      NH2
 129 VAL   ( 132-)  A      N
 151 LEU   ( 154-)  A      N
 153 SER   ( 156-)  A      OG
 158 TYR   ( 161-)  A      OH
 165 TRP   ( 168-)  A      N
 187 GLN   (  10-)  B      NE2
 206 ARG   (  29-)  B      NE
 210 ASN   (  33-)  B      ND2
 223 GLU   (  46-)  B      N
 252 VAL   (  75-)  B      N
 269 GLN   (  92-)  B      NE2
 270 ARG   (  93-)  B      N
 271 ARG   (  94-)  B      NE
 319 ASN   ( 150-)  B      ND2
 327 LEU   ( 158-)  B      N
 418 LEU   (  45-)  D      N
 421 PHE   (  48-)  D      N
 422 GLY   (  49-)  D      N
 489 VAL   ( 116-)  D      N
 494 TRP   ( 121-)  D      NE1
 503 THR   ( 130-)  D      N
 505 VAL   ( 132-)  D      N
 509 VAL   ( 136-)  D      N
 563 GLN   (  10-)  E      NE2
 582 ARG   (  29-)  E      NE
 590 SER   (  37-)  E      OG
 599 GLU   (  46-)  E      N
 600 TYR   (  47-)  E      OH
 620 LEU   (  67-)  E      N
 628 VAL   (  75-)  E      N
 703 LEU   ( 158-)  E      N
 711 ARG   ( 166-)  E      N
 736 MET   ( 107-)  F      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

   8 GLU   (  11-)  A      OE1
  12 ASN   (  15-)  A      OD1
  63 ASP   (  66-)  A      OD2
 384 GLU   (  11-)  D      OE1
 439 ASP   (  66-)  D      OD2
 719 GLN   ( 174-)  E      OE1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  18 GLU   (  21-)  A   H-bonding suggests Gln
  63 ASP   (  66-)  A   H-bonding suggests Asn
 159 ASP   ( 162-)  A   H-bonding suggests Asn
 394 GLU   (  21-)  D   H-bonding suggests Gln
 419 GLU   (  46-)  D   H-bonding suggests Gln; Ligand-contact
 471 GLU   (  98-)  D   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.020
  2nd generation packing quality :  -1.274
  Ramachandran plot appearance   :  -1.319
  chi-1/chi-2 rotamer normality  :  -3.130 (poor)
  Backbone conformation          :   0.129

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.590 (tight)
  Omega angle restraints         :   1.098
  Side chain planarity           :   0.322 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.925
  Inside/Outside distribution    :   1.039

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.66


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   1.1
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.590 (tight)
  Omega angle restraints         :   1.098
  Side chain planarity           :   0.322 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.925
  Inside/Outside distribution    :   1.039
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.