WHAT IF Check report

This file was created 2012-01-04 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 pdb1n1y.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 629 SIA   ( 700-)  A  -

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

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'.

  26 SER   (  26-)  A      OG
 126 GLN   ( 126-)  A      CG
 126 GLN   ( 126-)  A      CD
 126 GLN   ( 126-)  A      OE1
 126 GLN   ( 126-)  A      NE2
 128 ARG   ( 128-)  A      CG
 128 ARG   ( 128-)  A      CD
 128 ARG   ( 128-)  A      NE
 128 ARG   ( 128-)  A      CZ
 128 ARG   ( 128-)  A      NH1
 128 ARG   ( 128-)  A      NH2
 159 LYS   ( 159-)  A      CG
 159 LYS   ( 159-)  A      CD
 159 LYS   ( 159-)  A      CE
 159 LYS   ( 159-)  A      NZ
 170 GLU   ( 170-)  A      CG
 170 GLU   ( 170-)  A      CD
 170 GLU   ( 170-)  A      OE1
 170 GLU   ( 170-)  A      OE2
 394 ASN   ( 394-)  A      CG
 394 ASN   ( 394-)  A      OD1
 394 ASN   ( 394-)  A      ND2
 538 GLU   ( 544-)  A      CG
 538 GLU   ( 544-)  A      CD
 538 GLU   ( 544-)  A      OE1
 538 GLU   ( 544-)  A      OE2
 542 LYS   ( 548-)  A      CG
 542 LYS   ( 548-)  A      CD
 542 LYS   ( 548-)  A      CE
 542 LYS   ( 548-)  A      NZ
 628 ASP   ( 634-)  A      CG
 628 ASP   ( 634-)  A      OD1
 628 ASP   ( 634-)  A      OD2

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

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.

  39 ARG   (  39-)  A
  91 ARG   (  91-)  A
 254 ARG   ( 254-)  A
 255 ARG   ( 255-)  A
 387 ARG   ( 387-)  A
 435 ARG   ( 441-)  A
 472 ARG   ( 478-)  A
 552 ARG   ( 558-)  A

Warning: Tyrosine convention problem

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

  58 TYR   (  58-)  A
  73 TYR   (  73-)  A
 111 TYR   ( 111-)  A
 196 TYR   ( 196-)  A
 357 TYR   ( 357-)  A
 473 TYR   ( 479-)  A
 516 TYR   ( 522-)  A
 526 TYR   ( 532-)  A
 543 TYR   ( 549-)  A
 583 TYR   ( 589-)  A

Warning: Phenylalanine convention problem

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

  14 PHE   (  14-)  A
  38 PHE   (  38-)  A
 171 PHE   ( 171-)  A
 208 PHE   ( 208-)  A
 230 PHE   ( 230-)  A
 332 PHE   ( 332-)  A
 420 PHE   ( 426-)  A
 453 PHE   ( 459-)  A
 475 PHE   ( 481-)  A
 582 PHE   ( 588-)  A

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.

  63 ASP   (  63-)  A
  77 ASP   (  77-)  A
 172 ASP   ( 172-)  A
 216 ASP   ( 216-)  A
 217 ASP   ( 217-)  A
 251 ASP   ( 251-)  A
 262 ASP   ( 262-)  A
 319 ASP   ( 319-)  A
 327 ASP   ( 327-)  A
 354 ASP   ( 354-)  A
 508 ASP   ( 514-)  A

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.

  12 GLU   (  12-)  A
  32 GLU   (  32-)  A
 259 GLU   ( 259-)  A
 299 GLU   ( 299-)  A
 342 GLU   ( 342-)  A
 361 GLU   ( 361-)  A
 431 GLU   ( 437-)  A
 504 GLU   ( 510-)  A

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.

  12 GLU   (  12-)  A
  32 GLU   (  32-)  A
  39 ARG   (  39-)  A
  63 ASP   (  63-)  A
  77 ASP   (  77-)  A
  91 ARG   (  91-)  A
 172 ASP   ( 172-)  A
 216 ASP   ( 216-)  A
 217 ASP   ( 217-)  A
 251 ASP   ( 251-)  A
 254 ARG   ( 254-)  A
 255 ARG   ( 255-)  A
 259 GLU   ( 259-)  A
 262 ASP   ( 262-)  A
 299 GLU   ( 299-)  A
 319 ASP   ( 319-)  A
 327 ASP   ( 327-)  A
 342 GLU   ( 342-)  A
 354 ASP   ( 354-)  A
 361 GLU   ( 361-)  A
 387 ARG   ( 387-)  A
 431 GLU   ( 437-)  A
 435 ARG   ( 441-)  A
 472 ARG   ( 478-)  A
 504 GLU   ( 510-)  A
 508 ASP   ( 514-)  A
 552 ARG   ( 558-)  A

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.

 273 THR   ( 273-)  A    -3.2
 293 PHE   ( 293-)  A    -2.9
 135 PRO   ( 135-)  A    -2.9
 276 HIS   ( 276-)  A    -2.8
  40 ILE   (  40-)  A    -2.7
 534 THR   ( 540-)  A    -2.6
  60 THR   (  60-)  A    -2.6
 238 LEU   ( 238-)  A    -2.5
 279 THR   ( 279-)  A    -2.5
 588 ARG   ( 594-)  A    -2.5
 299 GLU   ( 299-)  A    -2.4
 359 LEU   ( 359-)  A    -2.3
 253 ASN   ( 253-)  A    -2.3
 494 GLY   ( 500-)  A    -2.2
 420 PHE   ( 426-)  A    -2.2
  93 SER   (  93-)  A    -2.2
 229 LYS   ( 229-)  A    -2.2
 586 GLY   ( 592-)  A    -2.2
 263 MET   ( 263-)  A    -2.2
 167 PHE   ( 167-)  A    -2.1
 243 LYS   ( 243-)  A    -2.1
 422 SER   ( 428-)  A    -2.1
 222 LYS   ( 222-)  A    -2.0
 296 VAL   ( 296-)  A    -2.0
 428 SER   ( 434-)  A    -2.0
 150 LYS   ( 150-)  A    -2.0
  65 SER   (  65-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  91 ARG   (  91-)  A  Poor phi/psi
 100 ASP   ( 100-)  A  Poor phi/psi
 119 LYS   ( 119-)  A  Poor phi/psi
 129 ASP   ( 129-)  A  Poor phi/psi
 145 SER   ( 145-)  A  Poor phi/psi
 146 ALA   ( 146-)  A  Poor phi/psi
 147 ALA   ( 147-)  A  Poor phi/psi
 172 ASP   ( 172-)  A  Poor phi/psi
 183 VAL   ( 183-)  A  Poor phi/psi
 234 GLU   ( 234-)  A  Poor phi/psi
 273 THR   ( 273-)  A  Poor phi/psi
 276 HIS   ( 276-)  A  Poor phi/psi
 281 SER   ( 281-)  A  Poor phi/psi
 284 SER   ( 284-)  A  Poor phi/psi
 308 HIS   ( 308-)  A  Poor phi/psi
 311 ASN   ( 311-)  A  Poor phi/psi
 315 ARG   ( 315-)  A  Poor phi/psi
 320 ARG   ( 320-)  A  Poor phi/psi
 328 ASN   ( 328-)  A  Poor phi/psi
 344 SER   ( 344-)  A  Poor phi/psi
 365 ASN   ( 365-)  A  Poor phi/psi
 366 ASP   ( 366-)  A  Poor phi/psi
 422 SER   ( 428-)  A  Poor phi/psi
 435 ARG   ( 441-)  A  Poor phi/psi
 449 ASN   ( 455-)  A  Poor phi/psi
 464 VAL   ( 470-)  A  Poor phi/psi
 499 LEU   ( 505-)  A  Poor phi/psi
 520 ARG   ( 526-)  A  Poor phi/psi
 540 HIS   ( 546-)  A  Poor phi/psi
 552 ARG   ( 558-)  A  Poor phi/psi
 559 ASP   ( 565-)  A  Poor phi/psi
 588 ARG   ( 594-)  A  Poor phi/psi
 593 PRO   ( 599-)  A  Poor phi/psi
 602 ASN   ( 608-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.034

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.034

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.

 384 SER   ( 384-)  A    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!

   3 SER   (   3-)  A      0
   4 LEU   (   4-)  A      0
   6 PRO   (   6-)  A      0
   8 SER   (   8-)  A      0
   9 SER   (   9-)  A      0
  10 ARG   (  10-)  A      0
  13 LEU   (  13-)  A      0
  16 ARG   (  16-)  A      0
  17 LYS   (  17-)  A      0
  18 ASN   (  18-)  A      0
  19 SER   (  19-)  A      0
  36 HIS   (  36-)  A      0
  39 ARG   (  39-)  A      0
  40 ILE   (  40-)  A      0
  41 PRO   (  41-)  A      0
  59 GLU   (  59-)  A      0
  60 THR   (  60-)  A      0
  62 PHE   (  62-)  A      0
  65 SER   (  65-)  A      0
  66 PHE   (  66-)  A      0
  75 VAL   (  75-)  A      0
  77 ASP   (  77-)  A      0
  80 THR   (  80-)  A      0
  90 SER   (  90-)  A      0
  91 ARG   (  91-)  A      0
And so on for a total of 288 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.588

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 250 VAL   ( 250-)  A   1.58   10

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].

  41 PRO   (  41-)  A    17.8 half-chair N/C-delta (18 degrees)
 135 PRO   ( 135-)  A    25.5 half-chair N/C-delta (18 degrees)
 497 PRO   ( 503-)  A    52.3 half-chair C-delta/C-gamma (54 degrees)
 530 PRO   ( 536-)  A  -119.3 half-chair C-delta/C-gamma (-126 degrees)
 562 PRO   ( 568-)  A    47.1 half-chair C-delta/C-gamma (54 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.

 210 LYS   ( 210-)  A      NZ  <->  224 ALA   ( 224-)  A      O      0.41    2.29  INTRA
 485 THR   ( 491-)  A      OG1 <->  622 GLN   ( 628-)  A      NE2    0.40    2.30  INTRA
 588 ARG   ( 594-)  A      NH2 <->  591 GLY   ( 597-)  A      O      0.39    2.31  INTRA BL
 363 ASN   ( 363-)  A      ND2 <->  364 THR   ( 364-)  A      N      0.31    2.44  INTRA
 189 ALA   ( 189-)  A      O   <->  192 GLY   ( 192-)  A      N      0.28    2.42  INTRA BL
 515 SER   ( 521-)  A      O   <->  523 ARG   ( 529-)  A      N      0.26    2.44  INTRA
 308 HIS   ( 308-)  A      ND1 <->  309 PRO   ( 309-)  A      CD     0.24    2.86  INTRA BL
 180 VAL   ( 180-)  A      CG1 <->  181 GLY   ( 181-)  A      N      0.24    2.76  INTRA
 441 VAL   ( 447-)  A      CG1 <->  442 ALA   ( 448-)  A      N      0.23    2.77  INTRA BL
 288 ASP   ( 288-)  A      CG  <->  289 CYS   ( 289-)  A      N      0.23    2.77  INTRA BL
 171 PHE   ( 171-)  A      O   <->  172 ASP   ( 172-)  A      C      0.22    2.38  INTRA BF
 339 ILE   ( 339-)  A      N   <->  342 GLU   ( 342-)  A      OE2    0.21    2.49  INTRA BL
 292 SER   ( 292-)  A      OG  <->  307 THR   ( 307-)  A      OG1    0.20    2.20  INTRA BL
 288 ASP   ( 288-)  A      OD1 <->  289 CYS   ( 289-)  A      N      0.20    2.40  INTRA BL
 289 CYS   ( 289-)  A      SG  <->  290 GLN   ( 290-)  A      N      0.19    3.01  INTRA BL
 171 PHE   ( 171-)  A      O   <->  174 ILE   ( 174-)  A      N      0.18    2.52  INTRA BF
 327 ASP   ( 327-)  A      OD1 <->  330 ARG   ( 330-)  A      N      0.18    2.52  INTRA BL
 609 ARG   ( 615-)  A      NH1 <->  610 LEU   ( 616-)  A      O      0.16    2.44  INTRA BL
 343 ASN   ( 343-)  A      O   <->  363 ASN   ( 363-)  A      N      0.16    2.54  INTRA
 356 LEU   ( 356-)  A      CD2 <->  375 LEU   ( 375-)  A      CD1    0.15    3.05  INTRA
  57 ARG   (  57-)  A      NH1 <->   61 SER   (  61-)  A      O      0.14    2.56  INTRA
 280 ASN   ( 280-)  A      ND2 <->  281 SER   ( 281-)  A      OG     0.14    2.56  INTRA BL
  72 LYS   (  72-)  A      NZ  <->   83 THR   (  83-)  A      OG1    0.14    2.56  INTRA BF
 103 VAL   ( 103-)  A      O   <->  186 ALA   ( 186-)  A      N      0.13    2.57  INTRA
 164 LYS   ( 164-)  A      N   <->  165 PRO   ( 165-)  A      CD     0.13    2.87  INTRA BF
And so on for a total of 69 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

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.

 572 ARG   ( 578-)  A      -8.49
 446 ARG   ( 452-)  A      -6.66
 588 ARG   ( 594-)  A      -6.42
 203 MET   ( 203-)  A      -6.24
 590 LYS   ( 596-)  A      -6.16
 493 LYS   ( 499-)  A      -6.07
 121 ARG   ( 121-)  A      -6.00
 466 ARG   ( 472-)  A      -5.61
 467 GLN   ( 473-)  A      -5.42
 526 TYR   ( 532-)  A      -5.38
 403 VAL   ( 403-)  A      -5.19
 540 HIS   ( 546-)  A      -5.02

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.

 403 VAL   ( 403-)  A       406 - ALA    406- ( A)         -4.42
 588 ARG   ( 594-)  A       590 - LYS    596- ( A)         -5.75

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

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.

 128 ARG   ( 128-)  A   -2.60

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

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.

  64 ASN   (  64-)  A
  89 ASN   (  89-)  A
 127 HIS   ( 127-)  A
 199 GLN   ( 199-)  A
 253 ASN   ( 253-)  A
 280 ASN   ( 280-)  A
 363 ASN   ( 363-)  A
 602 ASN   ( 608-)  A
 622 GLN   ( 628-)  A

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.

  10 ARG   (  10-)  A      NH1
  57 ARG   (  57-)  A      NH2
  59 GLU   (  59-)  A      N
  89 ASN   (  89-)  A      ND2
 101 ALA   ( 101-)  A      N
 150 LYS   ( 150-)  A      N
 152 THR   ( 152-)  A      N
 179 PHE   ( 179-)  A      N
 181 GLY   ( 181-)  A      N
 211 ILE   ( 211-)  A      N
 247 ASN   ( 247-)  A      ND2
 248 ASN   ( 248-)  A      ND2
 249 ARG   ( 249-)  A      NH1
 249 ARG   ( 249-)  A      NH2
 256 LEU   ( 256-)  A      N
 258 TYR   ( 258-)  A      OH
 278 TRP   ( 278-)  A      NE1
 281 SER   ( 281-)  A      N
 289 CYS   ( 289-)  A      N
 292 SER   ( 292-)  A      OG
 316 TRP   ( 316-)  A      N
 318 ARG   ( 318-)  A      NE
 318 ARG   ( 318-)  A      NH2
 320 ARG   ( 320-)  A      N
 338 SER   ( 338-)  A      OG
 399 ILE   ( 399-)  A      N
 467 GLN   ( 473-)  A      NE2
 473 TYR   ( 479-)  A      N
 537 TRP   ( 543-)  A      NE1
 571 VAL   ( 577-)  A      N
 575 THR   ( 581-)  A      N
 590 LYS   ( 596-)  A      N
 596 SER   ( 602-)  A      N
 608 ARG   ( 614-)  A      N
 623 ASP   ( 629-)  A      N
 625 ILE   ( 631-)  A      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.

 100 ASP   ( 100-)  A      OD1
 127 HIS   ( 127-)  A      NE2
 178 GLU   ( 178-)  A      OE1
 288 ASP   ( 288-)  A      OD1
 360 HIS   ( 360-)  A      NE2
 449 ASN   ( 455-)  A      OD1
 544 HIS   ( 550-)  A      NE2

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 :  -1.219
  2nd generation packing quality :  -1.308
  Ramachandran plot appearance   :  -1.728
  chi-1/chi-2 rotamer normality  :  -3.034 (poor)
  Backbone conformation          :  -0.197

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.176 (tight)
  Bond angles                    :   0.568 (tight)
  Omega angle restraints         :   0.471 (tight)
  Side chain planarity           :   0.150 (tight)
  Improper dihedral distribution :   0.523
  B-factor distribution          :   0.347
  Inside/Outside distribution    :   0.989

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.176 (tight)
  Bond angles                    :   0.568 (tight)
  Omega angle restraints         :   0.471 (tight)
  Side chain planarity           :   0.150 (tight)
  Improper dihedral distribution :   0.523
  B-factor distribution          :   0.347
  Inside/Outside distribution    :   0.989
==============

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.