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 pdb3q29.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 C

All-atom RMS fit for the two chains : 2.666
CA-only RMS fit for the two chains : 2.523

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 C

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.

 766 MAL   (5044-)  A  -
 782 MAL   (5044-)  C  -

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: C

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'.

   1 LYS   (   2-)  A      CG
   1 LYS   (   2-)  A      CD
   1 LYS   (   2-)  A      CE
   1 LYS   (   2-)  A      NZ
  25 LYS   (  26-)  A      CG
  25 LYS   (  26-)  A      CD
  25 LYS   (  26-)  A      CE
  25 LYS   (  26-)  A      NZ
  26 LYS   (  27-)  A      CG
  26 LYS   (  27-)  A      CD
  26 LYS   (  27-)  A      CE
  26 LYS   (  27-)  A      NZ
  29 LYS   (  30-)  A      CG
  29 LYS   (  30-)  A      CD
  29 LYS   (  30-)  A      CE
  29 LYS   (  30-)  A      NZ
  34 LYS   (  35-)  A      CG
  34 LYS   (  35-)  A      CD
  34 LYS   (  35-)  A      CE
  34 LYS   (  35-)  A      NZ
  83 LYS   (  84-)  A      CG
  83 LYS   (  84-)  A      CD
  83 LYS   (  84-)  A      CE
  83 LYS   (  84-)  A      NZ
 288 GLU   ( 289-)  A      CG
And so on for a total of 66 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.

   2 ILE   (   3-)  A    High
   3 GLU   (   4-)  A    High
   4 GLU   (   5-)  A    High
   5 GLY   (   6-)  A    High
   6 LYS   (   7-)  A    High
  24 GLY   (  25-)  A    High
  28 GLU   (  29-)  A    High
  29 LYS   (  30-)  A    High
  30 ASP   (  31-)  A    High
  32 GLY   (  33-)  A    High
  38 GLU   (  39-)  A    High
  49 GLN   (  50-)  A    High
  55 ASP   (  56-)  A    High
  82 ASP   (  83-)  A    High
 172 GLU   ( 173-)  A    High
 239 LYS   ( 240-)  A    High
 278 GLU   ( 279-)  A    High
 291 GLU   ( 292-)  A    High
 295 LYS   ( 296-)  A    High
 308 GLU   ( 309-)  A    High
 309 GLU   ( 310-)  A    High
 310 GLU   ( 311-)  A    High
 311 LEU   ( 312-)  A    High
 312 ALA   ( 313-)  A    High
 313 LYS   ( 314-)  A    High
 321 MET   ( 322-)  A    High
 380 LYS   ( 381-)  A    High
 385 GLU   (   5-)  C    High
 406 LYS   (  26-)  C    High
 409 GLU   (  29-)  C    High
 410 LYS   (  30-)  C    High
 415 LYS   (  35-)  C    High
 427 LYS   (  47-)  C    High
 430 GLN   (  50-)  C    High
 436 ASP   (  56-)  C    High
 553 GLU   ( 173-)  C    High
 554 ASN   ( 174-)  C    High
 556 LYS   ( 176-)  C    High
 620 LYS   ( 240-)  C    High
 676 LYS   ( 296-)  C    High
 717 MET   ( 337-)  C    High
 735 ARG   ( 355-)  C    High
 743 LYS   ( 363-)  C    High
 746 GLN   ( 366-)  C    High
 764 GLU   ( 384-)  C    High
 765 GLY   ( 385-)  C    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: 1

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: C

Nomenclature related problems

Warning: Tyrosine convention problem

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

 106 TYR   ( 107-)  A
 307 TYR   ( 308-)  A
 341 TYR   ( 342-)  A
 548 TYR   ( 168-)  C
 722 TYR   ( 342-)  C

Warning: Phenylalanine convention problem

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

  67 PHE   (  68-)  A
  92 PHE   (  93-)  A
 374 PHE   ( 375-)  A
 448 PHE   (  68-)  C

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.

 287 ASP   ( 288-)  A
 439 ASP   (  59-)  C
 668 ASP   ( 288-)  C
 695 ASP   ( 315-)  C

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.

   4 GLU   (   5-)  A
 131 GLU   ( 132-)  A
 221 GLU   ( 222-)  A
 274 GLU   ( 275-)  A
 328 GLU   ( 329-)  A
 385 GLU   (   5-)  C
 512 GLU   ( 132-)  C
 602 GLU   ( 222-)  C
 655 GLU   ( 275-)  C
 669 GLU   ( 289-)  C
 689 GLU   ( 309-)  C
 691 GLU   ( 311-)  C

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.

   4 GLU   (   5-)  A
 131 GLU   ( 132-)  A
 221 GLU   ( 222-)  A
 274 GLU   ( 275-)  A
 287 ASP   ( 288-)  A
 328 GLU   ( 329-)  A
 385 GLU   (   5-)  C
 439 ASP   (  59-)  C
 512 GLU   ( 132-)  C
 602 GLU   ( 222-)  C
 655 GLU   ( 275-)  C
 668 ASP   ( 288-)  C
 669 GLU   ( 289-)  C
 689 GLU   ( 309-)  C
 691 GLU   ( 311-)  C
 695 ASP   ( 315-)  C

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.

 245 THR   ( 246-)  A    -2.4
 626 THR   ( 246-)  C    -2.4
 104 ILE   ( 105-)  A    -2.4
 694 LYS   ( 314-)  C    -2.2
 173 ASN   ( 174-)  A    -2.2
 485 ILE   ( 105-)  C    -2.2
 183 VAL   ( 184-)  A    -2.2
 460 ILE   (  80-)  C    -2.2
 583 LYS   ( 203-)  C    -2.1

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.

 105 ALA   ( 106-)  A  Poor phi/psi
 168 ALA   ( 169-)  A  Poor phi/psi
 173 ASN   ( 174-)  A  Poor phi/psi
 202 LYS   ( 203-)  A  Poor phi/psi
 239 LYS   ( 240-)  A  Poor phi/psi
 285 LEU   ( 286-)  A  Poor phi/psi
 527 ALA   ( 147-)  C  omega poor
 546 GLY   ( 166-)  C  Poor phi/psi
 549 ALA   ( 169-)  C  Poor phi/psi
 583 LYS   ( 203-)  C  Poor phi/psi
 620 LYS   ( 240-)  C  Poor phi/psi
 666 LEU   ( 286-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.075

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.

 592 SER   ( 212-)  C    0.36
 718 SER   ( 338-)  C    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!

   4 GLU   (   5-)  A      0
  17 TYR   (  18-)  A      0
  30 ASP   (  31-)  A      0
  41 ASP   (  42-)  A      0
  42 LYS   (  43-)  A      0
  53 THR   (  54-)  A      0
  55 ASP   (  56-)  A      0
  58 ASP   (  59-)  A      0
  62 TRP   (  63-)  A      0
  64 HIS   (  65-)  A      0
  75 LEU   (  76-)  A      0
  76 LEU   (  77-)  A      0
  80 THR   (  81-)  A      0
  81 PRO   (  82-)  A      0
  99 TYR   ( 100-)  A      0
 108 ILE   ( 109-)  A      0
 109 ALA   ( 110-)  A      0
 122 LEU   ( 123-)  A      0
 124 ASN   ( 125-)  A      0
 127 LYS   ( 128-)  A      0
 129 TRP   ( 130-)  A      0
 142 LYS   ( 143-)  A      0
 146 ALA   ( 147-)  A      0
 147 LEU   ( 148-)  A      0
 149 PHE   ( 150-)  A      0
And so on for a total of 250 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].

  91 PRO   (  92-)  A  -113.6 envelop C-gamma (-108 degrees)
 472 PRO   (  92-)  C  -113.9 envelop C-gamma (-108 degrees)
 488 PRO   ( 108-)  C   -22.0 half-chair C-alpha/N (-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.

 539 TRP   ( 159-)  C      N   <->  540 PRO   ( 160-)  C      CD     0.21    2.79  INTRA BL
 445 HIS   (  65-)  C      NE2 <->  711 MET   ( 331-)  C      O      0.19    2.51  INTRA BL
  64 HIS   (  65-)  A      ND1 <->  261 VAL   ( 262-)  A      N      0.19    2.81  INTRA BL
 649 ALA   ( 269-)  C      O   <->  654 LYS   ( 274-)  C      NZ     0.17    2.53  INTRA BF
 158 TRP   ( 159-)  A      N   <->  159 PRO   ( 160-)  A      CD     0.17    2.83  INTRA BL
 513 ILE   ( 133-)  C      N   <->  514 PRO   ( 134-)  C      CD     0.13    2.87  INTRA BL
 132 ILE   ( 133-)  A      N   <->  133 PRO   ( 134-)  A      CD     0.12    2.88  INTRA BL
 307 TYR   ( 308-)  A      O   <->  309 GLU   ( 310-)  A      N      0.12    2.58  INTRA BF
 631 PHE   ( 251-)  C      N   <->  634 GLN   ( 254-)  C      O      0.10    2.60  INTRA BL
  55 ASP   (  56-)  A      CG  <->   56 GLY   (  57-)  A      N      0.10    2.90  INTRA BF
  62 TRP   (  63-)  A      CD1 <->   66 ARG   (  67-)  A      CG     0.09    3.11  INTRA BL
 639 PHE   ( 259-)  C      CD2 <->  721 TRP   ( 341-)  C      CH2    0.09    3.11  INTRA BF
  47 PHE   (  48-)  A      N   <->   48 PRO   (  49-)  A      CD     0.09    2.91  INTRA BF
 600 LYS   ( 220-)  C      NZ  <->  784 HOH   ( 453 )  C      O      0.08    2.62  INTRA BL
 538 THR   ( 158-)  C      C   <->  540 PRO   ( 160-)  C      CD     0.08    3.12  INTRA BL
 307 TYR   ( 308-)  A      C   <->  309 GLU   ( 310-)  A      N      0.07    2.83  INTRA BF
 533 GLN   ( 153-)  C      O   <->  725 ARG   ( 345-)  C      NH1    0.06    2.64  INTRA BF
  95 ASP   (  96-)  A      OD1 <->   98 ARG   (  99-)  A      NH2    0.06    2.64  INTRA BF
 409 GLU   (  29-)  C      O   <->  413 GLY   (  33-)  C      N      0.06    2.64  INTRA BF
 492 GLU   ( 112-)  C      N   <->  641 GLY   ( 261-)  C      O      0.06    2.64  INTRA BL
  71 ALA   (  72-)  A      O   <->   74 GLY   (  75-)  A      N      0.06    2.64  INTRA BF
 270 SER   ( 271-)  A      O   <->  273 LYS   ( 274-)  A      NZ     0.05    2.65  INTRA BF
 546 GLY   ( 166-)  C      O   <->  566 ASN   ( 186-)  C      ND2    0.05    2.65  INTRA BF
 489 ILE   ( 109-)  C      N   <->  643 LEU   ( 263-)  C      O      0.05    2.65  INTRA BL
 714 ILE   ( 334-)  C      CG1 <->  717 MET   ( 337-)  C      CE     0.05    3.15  INTRA BF
And so on for a total of 56 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: C

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.

 354 ARG   ( 355-)  A      -6.06
 735 ARG   ( 355-)  C      -5.80
  72 GLN   (  73-)  A      -5.59
 706 GLN   ( 326-)  C      -5.58
 453 GLN   (  73-)  C      -5.50
 325 GLN   ( 326-)  A      -5.38
 124 ASN   ( 125-)  A      -5.26
 505 ASN   ( 125-)  C      -5.26
   3 GLU   (   4-)  A      -5.20
  66 ARG   (  67-)  A      -5.11
 282 ASN   ( 283-)  A      -5.05
 663 ASN   ( 283-)  C      -5.04

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.

 763 LYS   ( 383-)  C       765 - GLY    385- ( C)         -4.44

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: C

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: C

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 783 HOH   ( 441 )  A      O     21.20   27.46  -81.19
 784 HOH   ( 442 )  C      O     35.87  -50.09  -38.21
 784 HOH   ( 466 )  C      O     20.27  -12.56   -4.56

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.

 784 HOH   ( 449 )  C      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.

  72 GLN   (  73-)  A
 218 ASN   ( 219-)  A
 430 GLN   (  50-)  C
 481 ASN   ( 101-)  C
 599 ASN   ( 219-)  C

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.

   6 LYS   (   7-)  A      N
  43 LEU   (  44-)  A      N
  62 TRP   (  63-)  A      NE1
  76 LEU   (  77-)  A      N
 105 ALA   ( 106-)  A      N
 112 ALA   ( 113-)  A      N
 150 ASN   ( 151-)  A      ND2
 153 GLU   ( 154-)  A      N
 155 TYR   ( 156-)  A      N
 169 PHE   ( 170-)  A      N
 176 TYR   ( 177-)  A      N
 209 ASP   ( 210-)  A      N
 230 TRP   ( 231-)  A      N
 233 SER   ( 234-)  A      N
 304 LEU   ( 305-)  A      N
 333 ILE   ( 334-)  A      N
 387 LYS   (   7-)  C      N
 416 VAL   (  36-)  C      N
 443 TRP   (  63-)  C      NE1
 447 ARG   (  67-)  C      NE
 457 LEU   (  77-)  C      N
 486 ALA   ( 106-)  C      N
 493 ALA   ( 113-)  C      N
 534 GLU   ( 154-)  C      N
 536 TYR   ( 156-)  C      N
 538 THR   ( 158-)  C      OG1
 547 GLY   ( 167-)  C      N
 564 VAL   ( 184-)  C      N
 590 ASP   ( 210-)  C      N
 611 TRP   ( 231-)  C      N
 614 SER   ( 234-)  C      N
 669 GLU   ( 289-)  C      N
 685 LEU   ( 305-)  C      N
 714 ILE   ( 334-)  C      N
 716 GLN   ( 336-)  C      N
 772 GOL   (   1-)  A      O3

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.

  14 ASP   (  15-)  A      OD1
 565 ASP   ( 185-)  C      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 783 HOH   ( 410 )  A      O  0.94  K  4
 784 HOH   ( 437 )  C      O  1.05  K  4
 784 HOH   ( 488 )  C      O  0.87  K  4 ION-B H2O-B

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.

  30 ASP   (  31-)  A   H-bonding suggests Asn; but Alt-Rotamer
  55 ASP   (  56-)  A   H-bonding suggests Asn; but Alt-Rotamer
 439 ASP   (  59-)  C   H-bonding suggests Asn
 446 ASP   (  66-)  C   H-bonding suggests Asn; Ligand-contact
 468 ASP   (  88-)  C   H-bonding suggests Asn
 476 ASP   (  96-)  C   H-bonding suggests Asn; but Alt-Rotamer
 565 ASP   ( 185-)  C   H-bonding suggests Asn
 764 GLU   ( 384-)  C   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 :   0.070
  2nd generation packing quality :  -1.129
  Ramachandran plot appearance   :  -0.801
  chi-1/chi-2 rotamer normality  :  -1.075
  Backbone conformation          :  -0.061

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.215 (tight)
  Bond angles                    :   0.407 (tight)
  Omega angle restraints         :   0.810
  Side chain planarity           :   0.228 (tight)
  Improper dihedral distribution :   0.464
  B-factor distribution          :   1.089
  Inside/Outside distribution    :   0.911

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.215 (tight)
  Bond angles                    :   0.407 (tight)
  Omega angle restraints         :   0.810
  Side chain planarity           :   0.228 (tight)
  Improper dihedral distribution :   0.464
  B-factor distribution          :   1.089
  Inside/Outside distribution    :   0.911
==============

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

Bond lengths and angles, protein residues
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Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
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      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      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,
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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.