WHAT IF Check report

This file was created 2013-01-17 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 pdb4gbx.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: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: E

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'.

   3 GLN   (  14-)  C      CG
   3 GLN   (  14-)  C      CD
   3 GLN   (  14-)  C      OE1
   3 GLN   (  14-)  C      NE2
  45 LEU   (  56-)  C      CG
  45 LEU   (  56-)  C      CD1
  45 LEU   (  56-)  C      CD2
  53 GLN   (  64-)  C      CG
  53 GLN   (  64-)  C      CD
  53 GLN   (  64-)  C      OE1
  53 GLN   (  64-)  C      NE2
 134 PHE   ( 145-)  C      CG
 134 PHE   ( 145-)  C      CD1
 134 PHE   ( 145-)  C      CD2
 134 PHE   ( 145-)  C      CE1
 134 PHE   ( 145-)  C      CE2
 134 PHE   ( 145-)  C      CZ
 202 ASP   (  15-)  D      CG
 202 ASP   (  15-)  D      OD1
 202 ASP   (  15-)  D      OD2
 207 LYS   (  20-)  D      CG
 207 LYS   (  20-)  D      CD
 207 LYS   (  20-)  D      CE
 207 LYS   (  20-)  D      NZ
 261 ASN   (  74-)  D      CG
 261 ASN   (  74-)  D      OD1
 261 ASN   (  74-)  D      ND2
 631 LYS   (  65-)  B      CG
 631 LYS   (  65-)  B      CD
 631 LYS   (  65-)  B      CE
 631 LYS   (  65-)  B      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.

   1 ASP   (  12-)  C    High
   2 LEU   (  13-)  C    High
   3 GLN   (  14-)  C    High
   4 ASN   (  15-)  C    High
   5 HIS   (  16-)  C    High
   6 THR   (  17-)  C    High
  23 SER   (  34-)  C    High
  25 ALA   (  36-)  C    High
  27 ASP   (  38-)  C    High
  28 GLU   (  39-)  C    High
  31 LEU   (  42-)  C    High
  32 PHE   (  43-)  C    High
  33 PHE   (  44-)  C    High
  34 PHE   (  45-)  C    High
  35 ASP   (  46-)  C    High
  36 PHE   (  47-)  C    High
  37 SER   (  48-)  C    High
  38 GLN   (  49-)  C    High
  39 ASN   (  50-)  C    High
  40 THR   (  51-)  C    High
  41 ARG   (  52-)  C    High
  42 VAL   (  53-)  C    High
  44 ARG   (  55-)  C    High
  46 PRO   (  57-)  C    High
  47 GLU   (  58-)  C    High
And so on for a total of 170 lines.

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: 25

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: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: E

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.

 297 ARG   ( 110-)  D

Warning: Tyrosine convention problem

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

 152 TYR   ( 163-)  C
 310 TYR   ( 123-)  D
 457 TYR   (  79-)  A
 528 TYR   ( 150-)  A
 613 TYR   (  47-)  B
 649 TYR   (  83-)  B
 730 TYR   ( 171-)  B

Warning: Phenylalanine convention problem

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

   7 PHE   (  18-)  C
  33 PHE   (  44-)  C
  48 PHE   (  59-)  C
  95 PHE   ( 106-)  C
 138 PHE   ( 149-)  C
 163 PHE   ( 174-)  C
 235 PHE   (  48-)  D
 273 PHE   (  86-)  D
 294 PHE   ( 107-)  D
 309 PHE   ( 122-)  D
 404 PHE   (  26-)  A
 429 PHE   (  51-)  A
 432 PHE   (  54-)  A
 486 PHE   ( 108-)  A
 515 PHE   ( 137-)  A
 523 PHE   ( 145-)  A
 558 PHE   ( 180-)  A
 563 PHE   (  -3-)  B
 579 PHE   (  13-)  B
 655 PHE   (  89-)  B
 691 PHE   ( 132-)  B
 714 PHE   ( 155-)  B

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.

 172 ASP   ( 183-)  C
 218 ASP   (  31-)  D
 253 ASP   (  66-)  D
 403 ASP   (  25-)  A
 520 ASP   ( 142-)  A
 549 ASP   ( 171-)  A
 642 ASP   (  76-)  B

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.

  24 GLU   (  35-)  C
 101 GLU   ( 112-)  C
 170 GLU   ( 181-)  C
 195 GLU   (   8-)  D
 234 GLU   (  47-)  D
 364 GLU   ( 177-)  D
 449 GLU   (  71-)  A
 466 GLU   (  88-)  A
 479 GLU   ( 101-)  A
 536 GLU   ( 158-)  A

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.

 127 HIS   ( 138-)  C      CG   ND1  CE1 109.71    4.1
 621 ARG   (  55-)  B      CG   CD   NE  119.75    5.4

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.

  24 GLU   (  35-)  C
 101 GLU   ( 112-)  C
 170 GLU   ( 181-)  C
 172 ASP   ( 183-)  C
 195 GLU   (   8-)  D
 218 ASP   (  31-)  D
 234 GLU   (  47-)  D
 253 ASP   (  66-)  D
 297 ARG   ( 110-)  D
 364 GLU   ( 177-)  D
 403 ASP   (  25-)  A
 449 GLU   (  71-)  A
 466 GLU   (  88-)  A
 479 GLU   ( 101-)  A
 520 ASP   ( 142-)  A
 536 GLU   ( 158-)  A
 549 ASP   ( 171-)  A
 642 ASP   (  76-)  B

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 271 GLN   (  84-)  D    4.91

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.

 345 THR   ( 158-)  D    -3.2
  46 PRO   (  57-)  C    -3.1
 284 PRO   (  97-)  D    -2.9
 136 PRO   ( 147-)  C    -2.8
 531 PHE   ( 153-)  A    -2.8
 669 PRO   ( 103-)  B    -2.8
 346 LEU   ( 159-)  D    -2.7
 296 THR   ( 109-)  D    -2.5
 478 ARG   ( 100-)  A    -2.5
 155 PHE   ( 166-)  C    -2.5
 351 LEU   ( 164-)  D    -2.5
 683 PRO   ( 124-)  B    -2.4
  47 GLU   (  58-)  C    -2.4
 495 VAL   ( 117-)  A    -2.3
 532 LEU   ( 154-)  A    -2.3
  48 PHE   (  59-)  C    -2.2
 524 ARG   ( 146-)  A    -2.2
 512 GLU   ( 134-)  A    -2.2
 227 GLU   (  40-)  D    -2.2
 410 PHE   (  32-)  A    -2.2
 366 ILE   ( 179-)  D    -2.2
 358 THR   ( 171-)  D    -2.2
 282 ARG   (  95-)  D    -2.2
 314 VAL   ( 127-)  D    -2.2
 716 THR   ( 157-)  B    -2.1
 262 GLY   (  75-)  D    -2.1
 569 THR   (   3-)  B    -2.1
 566 PRO   (   0-)  B    -2.1
  28 GLU   (  39-)  C    -2.1
 254 THR   (  67-)  D    -2.1
   8 LEU   (  19-)  C    -2.1
 476 GLU   (  98-)  A    -2.1
 230 MET   (  43-)  D    -2.1
 673 LEU   ( 114-)  B    -2.0
 723 VAL   ( 164-)  B    -2.0
  22 LEU   (  33-)  C    -2.0
 735 GLU   ( 176-)  B    -2.0
  57 ASP   (  68-)  C    -2.0
 333 LYS   ( 146-)  D    -2.0
  10 THR   (  21-)  C    -2.0
  20 VAL   (  31-)  C    -2.0
  76 GLY   (  87-)  C    -2.0
 319 ARG   ( 132-)  D    -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.

  17 SER   (  28-)  C  PRO omega poor
  28 GLU   (  39-)  C  Poor phi/psi, omega poor
  44 ARG   (  55-)  C  Poor phi/psi
  46 PRO   (  57-)  C  omega poor
  47 GLU   (  58-)  C  omega poor
  48 PHE   (  59-)  C  omega poor
  52 ALA   (  63-)  C  Poor phi/psi
  53 GLN   (  64-)  C  omega poor
  57 ASP   (  68-)  C  omega poor
 114 ASN   ( 125-)  C  Poor phi/psi
 116 PHE   ( 127-)  C  PRO omega poor
 128 SER   ( 139-)  C  Poor phi/psi
 145 LEU   ( 156-)  C  Poor phi/psi
 169 HIS   ( 180-)  C  omega poor
 173 ARG   ( 184-)  C  Poor phi/psi
 184 ASN   ( 195-)  C  Poor phi/psi
 188 SER   ( 199-)  C  omega poor
 204 GLY   (  17-)  D  Poor phi/psi
 216 ASN   (  29-)  D  Poor phi/psi
 234 GLU   (  47-)  D  Poor phi/psi
 248 HIS   (  61-)  D  omega poor
 249 LEU   (  62-)  D  Poor phi/psi
 250 ASN   (  63-)  D  Poor phi/psi
 295 ASN   ( 108-)  D  Poor phi/psi
 310 TYR   ( 123-)  D  PRO omega poor
 341 TRP   ( 154-)  D  Poor phi/psi
 345 THR   ( 158-)  D  Poor phi/psi
 351 LEU   ( 164-)  D  omega poor
 393 ASN   (  15-)  A  PRO omega poor
 396 GLN   (  18-)  A  Poor phi/psi
 398 GLY   (  20-)  A  omega poor
 429 PHE   (  51-)  A  omega poor
 435 GLN   (  57-)  A  omega poor
 457 TYR   (  79-)  A  Poor phi/psi
 465 PRO   (  87-)  A  omega poor
 478 ARG   ( 100-)  A  Poor phi/psi
 489 LYS   ( 111-)  A  Poor phi/psi
 491 THR   ( 113-)  A  PRO omega poor
 493 PRO   ( 115-)  A  Poor phi/psi
 521 HIS   ( 143-)  A  Poor phi/psi
 540 ASP   ( 162-)  A  omega poor
 564 GLN   (  -2-)  B  Poor phi/psi
 599 ASN   (  33-)  B  Poor phi/psi
 682 TYR   ( 123-)  B  PRO omega poor
 693 ASN   ( 134-)  B  Poor phi/psi
 712 TRP   ( 153-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.147

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 : -4.147

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.

 654 SER   (  88-)  B    0.39

Warning: Unusual backbone conformations

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

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

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

  12 TYR   (  23-)  C      0
  13 CYS   (  24-)  C      0
  14 GLN   (  25-)  C      0
  15 ASP   (  26-)  C      0
  17 SER   (  28-)  C      0
  18 PRO   (  29-)  C      0
  19 SER   (  30-)  C      0
  26 TYR   (  37-)  C      0
  28 GLU   (  39-)  C      0
  30 GLN   (  41-)  C      0
  32 PHE   (  43-)  C      0
  33 PHE   (  44-)  C      0
  36 PHE   (  47-)  C      0
  44 ARG   (  55-)  C      0
  45 LEU   (  56-)  C      0
  46 PRO   (  57-)  C      0
  47 GLU   (  58-)  C      0
  48 PHE   (  59-)  C      0
  49 ALA   (  60-)  C      0
  50 ASP   (  61-)  C      0
  51 TRP   (  62-)  C      0
  52 ALA   (  63-)  C      0
  53 GLN   (  64-)  C      0
  55 GLN   (  66-)  C      0
  57 ASP   (  68-)  C      0
And so on for a total of 319 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].

  43 PRO   (  54-)  C   -65.5 envelop C-beta (-72 degrees)
  46 PRO   (  57-)  C   -18.0 half-chair C-alpha/N (-18 degrees)
 136 PRO   ( 147-)  C   -63.5 envelop C-beta (-72 degrees)
 157 PRO   ( 168-)  C   100.7 envelop C-beta (108 degrees)
 284 PRO   (  97-)  D   -65.6 envelop C-beta (-72 degrees)
 337 PRO   ( 150-)  D  -151.9 envelop C-delta (-144 degrees)
 371 PRO   ( 184-)  D   102.2 envelop C-beta (108 degrees)
 378 PRO   ( 191-)  D   111.0 envelop C-beta (108 degrees)
 683 PRO   ( 124-)  B    38.8 envelop C-delta (36 degrees)
 737 PRO   ( 178-)  B  -113.1 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

  15 ASP   (  26-)  C      OD2  <->   190 PHE   (   3-)  D      N    0.48    2.22  INTRA BL
 389 GLU   (  11-)  A      OE2  <->   440 ASN   (  62-)  A      ND2  0.45    2.25  INTRA BL
  44 ARG   (  55-)  C      NH2  <->   339 GLY   ( 152-)  D      O    0.39    2.31  INTRA BF
 286 VAL   (  99-)  D      O    <->   374 ARG   ( 187-)  D      NH1  0.37    2.33  INTRA BF
 212 CYS   (  25-)  D      CA   <->   222 CYS   (  35-)  D      SG   0.35    2.65  INTRA BF
 478 ARG   ( 100-)  A      NH1  <->   765 HOH   ( 308 )  A      O    0.32    2.38  INTRA BL
  87 ARG   (  98-)  C      NH1  <->   172 ASP   ( 183-)  C      OD2  0.31    2.39  INTRA BL
 236 GLY   (  49-)  D      O    <->   239 ASN   (  52-)  D      ND2  0.30    2.40  INTRA BF
 395 ASP   (  17-)  A      OD1  <->   572 ARG   (   6-)  B      NH1  0.29    2.41  INTRA BL
 568 ASP   (   2-)  B      OD2  <->   572 ARG   (   6-)  B      NH2  0.29    2.41  INTRA BL
   5 HIS   (  16-)  C      ND1  <->    26 TYR   (  37-)  C      OH   0.28    2.42  INTRA BF
 568 ASP   (   2-)  B      CG   <->   572 ARG   (   6-)  B      NH2  0.25    2.85  INTRA BL
 602 GLU   (  36-)  B      CD   <->   605 ARG   (  39-)  B      NH1  0.24    2.86  INTRA BL
 501 ARG   ( 123-)  A      NH2  <->   765 HOH   ( 311 )  A      O    0.24    2.46  INTRA BL
 276 SER   (  89-)  D      O    <->   280 ARG   (  93-)  D      N    0.24    2.46  INTRA BF
 311 PRO   ( 124-)  D      O    <->   365 HIS   ( 178-)  D      NE2  0.23    2.47  INTRA BF
 212 CYS   (  25-)  D      CB   <->   222 CYS   (  35-)  D      SG   0.23    2.27  INTRA BF
 266 CYS   (  79-)  D      O    <->   270 THR   (  83-)  D      N    0.22    2.48  INTRA BF
 408 GLU   (  30-)  A      OE2  <->   411 HIS   (  33-)  A      ND1  0.22    2.48  INTRA BL
 208 ASP   (  21-)  D      OD1  <->   209 PHE   (  22-)  D      N    0.21    2.39  INTRA BF
 395 ASP   (  17-)  A      CG   <->   572 ARG   (   6-)  B      NH1  0.21    2.89  INTRA BL
 255 LEU   (  68-)  D      O    <->   258 ARG   (  71-)  D      N    0.21    2.49  INTRA BF
 252 LYS   (  65-)  D      O    <->   256 MET   (  69-)  D      N    0.21    2.49  INTRA BF
 481 ASN   ( 103-)  A      OD1  <->   482 VAL   ( 104-)  A      N    0.20    2.40  INTRA BL
  87 ARG   (  98-)  C      NH2  <->   169 HIS   ( 180-)  C      ND1  0.20    2.80  INTRA BL
And so on for a total of 103 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 564 GLN   (  -2-)  B      -7.31
 235 PHE   (  48-)  D      -7.18
 563 PHE   (  -3-)  B      -6.48
 326 MET   ( 139-)  D      -6.45
 355 TYR   ( 168-)  D      -6.38
 294 PHE   ( 107-)  D      -6.08
  48 PHE   (  59-)  C      -5.93
 183 ARG   ( 194-)  C      -5.87
 282 ARG   (  95-)  D      -5.81
 132 GLU   ( 143-)  C      -5.72
 297 ARG   ( 110-)  D      -5.71
 698 LYS   ( 139-)  B      -5.59
 102 PHE   ( 113-)  C      -5.46
 260 ARG   (  73-)  D      -5.45
  74 GLN   (  85-)  C      -5.45
 396 GLN   (  18-)  A      -5.38
  44 ARG   (  55-)  C      -5.31
 234 GLU   (  47-)  D      -5.27
 269 HIS   (  82-)  D      -5.23
  54 GLU   (  65-)  C      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 562 LEU   (  -4-)  B       564 - GLN     -2- ( B)         -6.10

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: 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

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.

  53 GLN   (  64-)  C   -3.35
 134 PHE   ( 145-)  C   -2.66
 207 LYS   (  20-)  D   -2.59
  45 LEU   (  56-)  C   -2.54
 331 ALA   ( 144-)  D   -2.52

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: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 125 GLN   ( 136-)  C
 265 ASN   (  78-)  D
 338 ASN   ( 151-)  D
 344 GLN   ( 157-)  D
 647 HIS   (  81-)  B
 752 GLN   (  86-)  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.

   5 HIS   (  16-)  C      N
  23 SER   (  34-)  C      OG
  45 LEU   (  56-)  C      N
  48 PHE   (  59-)  C      N
  50 ASP   (  61-)  C      N
  51 TRP   (  62-)  C      N
  51 TRP   (  62-)  C      NE1
  52 ALA   (  63-)  C      N
  57 ASP   (  68-)  C      N
  61 ILE   (  72-)  C      N
  78 LYS   (  89-)  C      N
 114 ASN   ( 125-)  C      N
 116 PHE   ( 127-)  C      N
 152 TYR   ( 163-)  C      N
 158 GLU   ( 169-)  C      N
 160 SER   ( 171-)  C      N
 162 ILE   ( 173-)  C      N
 171 ILE   ( 182-)  C      N
 211 TYR   (  24-)  D      N
 218 ASP   (  31-)  D      N
 227 GLU   (  40-)  D      N
 231 ALA   (  44-)  D      N
 238 LEU   (  51-)  D      N
 239 ASN   (  52-)  D      N
 250 ASN   (  63-)  D      N
And so on for a total of 65 lines.

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.

 193 HIS   (   6-)  D      NE2
 313 GLU   ( 126-)  D      OE2
 348 HIS   ( 161-)  D      ND1
 389 GLU   (  11-)  A      OE1
 433 GLU   (  55-)  A      OE1
 444 ASP   (  66-)  A      OD1
 444 ASP   (  66-)  A      OD2
 576 GLN   (  10-)  B      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.

  69 GLU   (  80-)  C   H-bonding suggests Gln
 208 ASP   (  21-)  D   H-bonding suggests Asn
 357 ASP   ( 170-)  D   H-bonding suggests Asn
 399 GLU   (  21-)  A   H-bonding suggests Gln
 444 ASP   (  66-)  A   H-bonding suggests Asn
 728 GLU   ( 169-)  B   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 :  -0.961
  2nd generation packing quality :  -1.721
  Ramachandran plot appearance   :  -2.238
  chi-1/chi-2 rotamer normality  :  -4.147 (bad)
  Backbone conformation          :  -0.864

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.662 (tight)
  Omega angle restraints         :   1.161
  Side chain planarity           :   0.341 (tight)
  Improper dihedral distribution :   0.693
  B-factor distribution          :   0.445
  Inside/Outside distribution    :   1.061

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.662 (tight)
  Omega angle restraints         :   1.161
  Side chain planarity           :   0.341 (tight)
  Improper dihedral distribution :   0.693
  B-factor distribution          :   0.445
  Inside/Outside distribution    :   1.061
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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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
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      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,
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    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.