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 pdb3pgd.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 : 0.261
CA-only RMS fit for the two chains : 0.091

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 : 0.192
CA-only RMS fit for the two chains : 0.066

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
 123 LYS   ( 126-)  A      CG
 123 LYS   ( 126-)  A      CD
 123 LYS   ( 126-)  A      CE
 123 LYS   ( 126-)  A      NZ
 155 GLU   ( 158-)  A      CG
 155 GLU   ( 158-)  A      CD
 155 GLU   ( 158-)  A      OE1
 155 GLU   ( 158-)  A      OE2
 201 GLU   (  22-)  B      CG
 201 GLU   (  22-)  B      CD
 201 GLU   (  22-)  B      OE1
 201 GLU   (  22-)  B      OE2
 284 LYS   ( 105-)  B      CG
 284 LYS   ( 105-)  B      CD
 284 LYS   ( 105-)  B      CE
 284 LYS   ( 105-)  B      NZ
 379 GLU   (   3-)  D      CG
 379 GLU   (   3-)  D      CD
 379 GLU   (   3-)  D      OE1
 379 GLU   (   3-)  D      OE2
 476 ARG   ( 100-)  D      CG
 476 ARG   ( 100-)  D      CD
 476 ARG   ( 100-)  D      NE
 476 ARG   ( 100-)  D      CZ
 476 ARG   ( 100-)  D      NH1
 476 ARG   ( 100-)  D      NH2
 534 GLU   ( 158-)  D      CG
 534 GLU   ( 158-)  D      CD
 534 GLU   ( 158-)  D      OE1
 534 GLU   ( 158-)  D      OE2
 663 LYS   ( 105-)  E      CG
 663 LYS   ( 105-)  E      CD
 663 LYS   ( 105-)  E      CE
 663 LYS   ( 105-)  E      NZ

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.

  95 GLU   (  98-)  A    High
 120 ARG   ( 123-)  A    High
 177 PHE   ( 180-)  A    High
 178 ASP   ( 181-)  A    High
 248 GLU   (  69-)  B    High
 284 LYS   ( 105-)  B    High
 285 THR   ( 106-)  B    High
 286 ASN   ( 113-)  B    High
 306 ARG   ( 133-)  B    High
 335 GLU   ( 162-)  B    High
 337 VAL   ( 164-)  B    High
 338 PRO   ( 165-)  B    High
 339 ARG   ( 166-)  B    High
 362 ARG   ( 189-)  B    High
 378 MET   ( 120-)  C    High
 474 GLU   (  98-)  D    High
 499 ARG   ( 123-)  D    High
 556 PHE   ( 180-)  D    High
 557 ASP   ( 181-)  D    High
 627 GLU   (  69-)  E    High
 663 LYS   ( 105-)  E    High
 664 THR   ( 106-)  E    High
 665 ASN   ( 113-)  E    High
 685 ARG   ( 133-)  E    High
 714 GLU   ( 162-)  E    High
 716 VAL   ( 164-)  E    High
 717 PRO   ( 165-)  E    High
 718 ARG   ( 166-)  E    High
 741 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.

 202 ARG   (  23-)  B
 234 ARG   (  55-)  B
 339 ARG   ( 166-)  B
 362 ARG   ( 189-)  B

Warning: Tyrosine convention problem

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

  10 TYR   (  13-)  A
 281 TYR   ( 102-)  B
 389 TYR   (  13-)  D
 660 TYR   ( 102-)  E
 723 TYR   ( 171-)  E

Warning: Phenylalanine convention problem

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

  29 PHE   (  32-)  A
 186 PHE   (   7-)  B
 197 PHE   (  18-)  B
 268 PHE   (  89-)  B
 408 PHE   (  32-)  D
 427 PHE   (  51-)  D
 513 PHE   ( 137-)  D
 565 PHE   (   7-)  E
 575 PHE   (  17-)  E
 576 PHE   (  18-)  E
 647 PHE   (  89-)  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.

 156 ASP   ( 159-)  A
 178 ASP   ( 181-)  A
 401 ASP   (  25-)  D
 535 ASP   ( 159-)  D

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.

  68 GLU   (  71-)  A
 131 GLU   ( 134-)  A
 163 GLU   ( 166-)  A
 214 GLU   (  35-)  B
 275 GLU   (  96-)  B
 301 GLU   ( 128-)  B
 335 GLU   ( 162-)  B
 422 GLU   (  46-)  D
 423 GLU   (  47-)  D
 447 GLU   (  71-)  D
 510 GLU   ( 134-)  D
 542 GLU   ( 166-)  D
 580 GLU   (  22-)  E
 593 GLU   (  35-)  E
 654 GLU   (  96-)  E
 680 GLU   ( 128-)  E
 714 GLU   ( 162-)  E

Geometric checks

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.

  94 VAL   (  97-)  A      C    CA   CB  102.33   -4.1
 140 HIS   ( 143-)  A      CG   ND1  CE1 109.80    4.2
 164 HIS   ( 167-)  A      CG   ND1  CE1 109.64    4.0
 174 HIS   ( 177-)  A      CG   ND1  CE1 109.61    4.0
 260 HIS   (  81-)  B      CG   ND1  CE1 109.60    4.0
 553 HIS   ( 177-)  D      CG   ND1  CE1 109.69    4.1

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.

  68 GLU   (  71-)  A
 131 GLU   ( 134-)  A
 156 ASP   ( 159-)  A
 163 GLU   ( 166-)  A
 178 ASP   ( 181-)  A
 202 ARG   (  23-)  B
 214 GLU   (  35-)  B
 234 ARG   (  55-)  B
 275 GLU   (  96-)  B
 301 GLU   ( 128-)  B
 335 GLU   ( 162-)  B
 339 ARG   ( 166-)  B
 362 ARG   ( 189-)  B
 401 ASP   (  25-)  D
 422 GLU   (  46-)  D
 423 GLU   (  47-)  D
 447 GLU   (  71-)  D
 510 GLU   ( 134-)  D
 535 ASP   ( 159-)  D
 542 GLU   ( 166-)  D
 580 GLU   (  22-)  E
 593 GLU   (  35-)  E
 654 GLU   (  96-)  E
 680 GLU   ( 128-)  E
 714 GLU   ( 162-)  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.

 715 THR   ( 163-)  E    -2.6
  13 PRO   (  16-)  A    -2.6
 489 THR   ( 113-)  D    -2.6
 336 THR   ( 163-)  B    -2.6
 110 THR   ( 113-)  A    -2.5
 529 PHE   ( 153-)  D    -2.4
 206 LEU   (  27-)  B    -2.4
 392 PRO   (  16-)  D    -2.4
 330 THR   ( 157-)  B    -2.3
 597 ARG   (  39-)  E    -2.2
 716 VAL   ( 164-)  E    -2.2
 337 VAL   ( 164-)  B    -2.2
 596 VAL   (  38-)  E    -2.2
 218 ARG   (  39-)  B    -2.1
 217 VAL   (  38-)  B    -2.1
 506 THR   ( 130-)  D    -2.1
 150 PHE   ( 153-)  A    -2.1
 709 THR   ( 157-)  E    -2.1
 131 GLU   ( 134-)  A    -2.1
 569 LEU   (  11-)  E    -2.1
 279 THR   ( 100-)  B    -2.1
 283 SER   ( 104-)  B    -2.1
 510 GLU   ( 134-)  D    -2.0
 697 THR   ( 145-)  E    -2.0
 309 GLN   ( 136-)  B    -2.0
 169 GLU   ( 172-)  A    -2.0
 318 THR   ( 145-)  B    -2.0
 658 THR   ( 100-)  E    -2.0
 190 LEU   (  11-)  B    -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.

  12 ASN   (  15-)  A  PRO omega poor
  15 GLN   (  18-)  A  Poor phi/psi
  49 ALA   (  52-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  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
 121 ASN   ( 124-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 177 PHE   ( 180-)  A  Poor phi/psi
 181 ASP   (   2-)  B  Poor phi/psi
 213 GLN   (  34-)  B  Poor phi/psi
 296 TYR   ( 123-)  B  PRO omega poor
 297 PRO   ( 124-)  B  Poor phi/psi
 307 ASN   ( 134-)  B  Poor phi/psi
 308 GLY   ( 135-)  B  omega poor
 326 TRP   ( 153-)  B  Poor phi/psi
 391 ASN   (  15-)  D  PRO omega poor
 394 GLN   (  18-)  D  Poor phi/psi
 454 ASN   (  78-)  D  Poor phi/psi
 455 TYR   (  79-)  D  Poor phi/psi
 463 PRO   (  87-)  D  omega poor
 472 PRO   (  96-)  D  omega poor
 476 ARG   ( 100-)  D  Poor phi/psi
 485 ILE   ( 109-)  D  omega poor
 487 LYS   ( 111-)  D  Poor phi/psi
 489 THR   ( 113-)  D  PRO omega poor
 491 PRO   ( 115-)  D  Poor phi/psi, omega poor
 500 ASN   ( 124-)  D  Poor phi/psi
 519 HIS   ( 143-)  D  Poor phi/psi
 556 PHE   ( 180-)  D  Poor phi/psi
 560 ASP   (   2-)  E  Poor phi/psi
 592 GLN   (  34-)  E  Poor phi/psi
 675 TYR   ( 123-)  E  PRO omega poor
 686 ASN   ( 134-)  E  Poor phi/psi
 687 GLY   ( 135-)  E  omega poor
 705 TRP   ( 153-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.912

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.

 267 SER   (  88-)  B    0.35
 646 SER   (  88-)  E    0.37

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
  14 ASP   (  17-)  A      0
  15 GLN   (  18-)  A      0
  16 SER   (  19-)  A      0
  23 PHE   (  26-)  A      0
  28 ILE   (  31-)  A      0
  29 PHE   (  32-)  A      0
  30 HIS   (  33-)  A      0
  41 ARG   (  44-)  A      0
  48 PHE   (  51-)  A      0
  76 TYR   (  79-)  A      0
  91 ASN   (  94-)  A      0
  95 GLU   (  98-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 112 PRO   ( 115-)  A      0
 120 ARG   ( 123-)  A      0
 121 ASN   ( 124-)  A      0
 126 THR   ( 129-)  A      0
 127 THR   ( 130-)  A      0
And so on for a total of 280 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].

 377 PRO   ( 119-)  C    25.3 half-chair N/C-delta (18 degrees)
 756 PRO   ( 119-)  F    23.6 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.

 610 GLU   (  52-)  E      CG  <->  613 ARG   (  55-)  E      NH2    0.37    2.73  INTRA BF
  25 GLY   (  28-)  A      O   <->  143 ARG   ( 146-)  A      NH2    0.34    2.36  INTRA BL
 404 GLY   (  28-)  D      O   <->  522 ARG   ( 146-)  D      NH2    0.32    2.38  INTRA BL
 140 HIS   ( 143-)  A      ND1 <->  191 LYS   (  12-)  B      NZ     0.30    2.70  INTRA BL
 640 ASN   (  82-)  E      ND2 <->  762 HOH   ( 219 )  E      O      0.26    2.44  INTRA BL
 613 ARG   (  55-)  E      N   <->  614 PRO   (  56-)  E      CD     0.25    2.75  INTRA BL
 568 GLN   (  10-)  E      NE2 <->  762 HOH   ( 210 )  E      O      0.23    2.47  INTRA BL
 234 ARG   (  55-)  B      N   <->  235 PRO   (  56-)  B      CD     0.19    2.81  INTRA BL
 434 GLY   (  58-)  D      C   <->  746 MET   ( 109-)  F      SD     0.18    3.22  INTRA BL
  44 GLU   (  47-)  A      OE2 <->  426 ARG   (  50-)  D      NH2    0.18    2.52  INTRA BF
 189 GLN   (  10-)  B      NE2 <->  759 HOH   ( 204 )  B      O      0.17    2.53  INTRA BL
  27 GLU   (  30-)  A      OE2 <->   30 HIS   (  33-)  A      ND1    0.17    2.53  INTRA BL
  45 PHE   (  48-)  A      CD1 <->  268 PHE   (  89-)  B      CD2    0.17    3.03  INTRA BF
  73 ARG   (  76-)  A      NH1 <->  232 LEU   (  53-)  B      O      0.17    2.53  INTRA BL
 475 LEU   (  99-)  D      CD1 <->  556 PHE   ( 180-)  D      CZ     0.16    3.04  INTRA BF
  55 GLY   (  58-)  A      C   <->  367 MET   ( 109-)  C      SD     0.16    3.24  INTRA BL
 374 GLN   ( 116-)  C      N   <->  760 HOH   (  38 )  C      O      0.15    2.55  INTRA BL
 174 HIS   ( 177-)  A      CD2 <->  175 TRP   ( 178-)  A      N      0.15    2.85  INTRA BF
 207 GLU   (  28-)  B      OE1 <->  226 TYR   (  47-)  B      OH     0.14    2.26  INTRA BL
  44 GLU   (  47-)  A      CD  <->  426 ARG   (  50-)  D      NH2    0.14    2.96  INTRA BF
   8 GLU   (  11-)  A      OE1 <->   63 ASP   (  66-)  A      OD2    0.14    2.26  INTRA BL
 519 HIS   ( 143-)  D      ND1 <->  570 LYS   (  12-)  E      NZ     0.13    2.87  INTRA BL
 761 HOH   ( 223 )  D      O   <->  761 HOH   ( 239 )  D      O      0.13    2.07  INTRA BF
  47 ARG   (  50-)  A      NH1 <->  423 GLU   (  47-)  D      OE2    0.13    2.57  INTRA BF
 562 ARG   (   4-)  E      O   <->  564 ARG   (   6-)  E      NH1    0.13    2.57  INTRA BL
And so on for a total of 102 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.

 741 ARG   ( 189-)  E      -6.33
 362 ARG   ( 189-)  B      -6.29
 691 LYS   ( 139-)  E      -5.82
 312 LYS   ( 139-)  B      -5.72
 755 LEU   ( 118-)  F      -5.65
 376 LEU   ( 118-)  C      -5.64
 339 ARG   ( 166-)  B      -5.63
 718 ARG   ( 166-)  E      -5.59
  15 GLN   (  18-)  A      -5.49
 394 GLN   (  18-)  D      -5.22
 281 TYR   ( 102-)  B      -5.05
 273 ARG   (  94-)  B      -5.02

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.

  97 ARG   ( 100-)  A   -2.66
 476 ARG   ( 100-)  D   -2.59

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.

 758 HOH   ( 229 )  A      O
 759 HOH   ( 231 )  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.

 115 ASN   ( 118-)  A
 146 HIS   ( 149-)  A
 249 GLN   (  70-)  B
 329 GLN   ( 156-)  B
 494 ASN   ( 118-)  D
 525 HIS   ( 149-)  D
 628 GLN   (  70-)  E
 708 GLN   ( 156-)  E
 726 GLN   ( 174-)  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
 110 THR   ( 113-)  A      OG1
 118 TRP   ( 121-)  A      NE1
 143 ARG   ( 146-)  A      NH2
 164 HIS   ( 167-)  A      N
 179 MET   (   0-)  B      N
 180 GLY   (   1-)  B      N
 208 ARG   (  29-)  B      NE
 225 GLU   (  46-)  B      N
 254 VAL   (  75-)  B      N
 323 ASN   ( 150-)  B      ND2
 339 ARG   ( 166-)  B      N
 344 TYR   ( 171-)  B      OH
 345 THR   ( 172-)  B      OG1
 398 PHE   (  22-)  D      N
 421 LEU   (  45-)  D      N
 489 THR   ( 113-)  D      OG1
 497 TRP   ( 121-)  D      NE1
 558 MET   (   0-)  E      N
 559 GLY   (   1-)  E      N
 564 ARG   (   6-)  E      NH2
 587 ARG   (  29-)  E      NE
 604 GLU   (  46-)  E      N
 633 VAL   (  75-)  E      N
 682 ARG   ( 130-)  E      NH1
 702 ASN   ( 150-)  E      ND2
 716 VAL   ( 164-)  E      N
 718 ARG   ( 166-)  E      N
 754 ALA   ( 117-)  F      N
 757 MET   ( 120-)  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
  63 ASP   (  66-)  A      OD2
 215 GLU   (  36-)  B      OE2
 342 GLU   ( 169-)  B      OE1
 387 GLU   (  11-)  D      OE1
 442 ASP   (  66-)  D      OD2
 594 GLU   (  36-)  E      OE2

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.

  63 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
 159 ASP   ( 162-)  A   H-bonding suggests Asn
 442 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
 538 ASP   ( 162-)  D   H-bonding suggests Asn
 690 GLU   ( 138-)  E   H-bonding suggests Gln

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 :  -0.014
  2nd generation packing quality :  -1.245
  Ramachandran plot appearance   :  -0.838
  chi-1/chi-2 rotamer normality  :  -2.912
  Backbone conformation          :   0.339

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.600 (tight)
  Omega angle restraints         :   1.013
  Side chain planarity           :   0.427 (tight)
  Improper dihedral distribution :   0.617
  B-factor distribution          :   1.497
  Inside/Outside distribution    :   1.038

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 : 2.72


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.600 (tight)
  Omega angle restraints         :   1.013
  Side chain planarity           :   0.427 (tight)
  Improper dihedral distribution :   0.617
  B-factor distribution          :   1.497
  Inside/Outside distribution    :   1.038
==============

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.