WHAT IF Check report

This file was created 2014-03-19 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 pdb4g50.ent

Checks that need to be done early-on in validation

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.

 384 861   ( 201-)  A  -
 391 861   ( 201-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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'.

  39 GLU   ( -39-)  A      CG
  39 GLU   ( -39-)  A      CD
  39 GLU   ( -39-)  A      OE1
  39 GLU   ( -39-)  A      OE2
  41 ASP   ( -37-)  A      CG
  41 ASP   ( -37-)  A      OD1
  41 ASP   ( -37-)  A      OD2
  85 GLU   (   7-)  A      CG
  85 GLU   (   7-)  A      CD
  85 GLU   (   7-)  A      OE1
  85 GLU   (   7-)  A      OE2
 102 ARG   (  24-)  A      CG
 102 ARG   (  24-)  A      CD
 102 ARG   (  24-)  A      NE
 102 ARG   (  24-)  A      CZ
 102 ARG   (  24-)  A      NH1
 102 ARG   (  24-)  A      NH2
 120 LYS   (  42-)  A      CG
 120 LYS   (  42-)  A      CD
 120 LYS   (  42-)  A      CE
 120 LYS   (  42-)  A      NZ
 127 ARG   (  49-)  A      CG
 127 ARG   (  49-)  A      CD
 127 ARG   (  49-)  A      NE
 127 ARG   (  49-)  A      CZ
And so on for a total of 73 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: 4

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

 241 ARG   ( -27-)  B
 348 ARG   (  80-)  B

Warning: Tyrosine convention problem

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

  90 TYR   (  12-)  A
 111 TYR   (  33-)  A
 280 TYR   (  12-)  B

Warning: Phenylalanine convention problem

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

  16 PHE   ( -62-)  A
  17 PHE   ( -61-)  A
  45 PHE   ( -33-)  A
 131 PHE   (  53-)  A
 184 PHE   ( 106-)  A
 235 PHE   ( -33-)  B
 374 PHE   ( 106-)  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.

  30 GLU   ( -48-)  A
  59 GLU   ( -19-)  A
  74 GLU   (  -4-)  A
 249 GLU   ( -19-)  B
 290 GLU   (  22-)  B

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.

  30 GLU   ( -48-)  A
  59 GLU   ( -19-)  A
  74 GLU   (  -4-)  A
 241 ARG   ( -27-)  B
 249 GLU   ( -19-)  B
 290 GLU   (  22-)  B
 348 ARG   (  80-)  B

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.

 252 ASP   ( -16-)  B    -2.2
 367 PRO   (  99-)  B    -2.2
 318 ASN   (  50-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  13 SER   ( -65-)  A  omega poor
  66 ASN   ( -12-)  A  Poor phi/psi
  72 HIS   (  -6-)  A  omega poor
 109 VAL   (  31-)  A  omega poor
 111 TYR   (  33-)  A  omega poor
 160 THR   (  82-)  A  omega poor
 179 ASN   ( 101-)  A  Poor phi/psi
 184 PHE   ( 106-)  A  omega poor
 193 HIS   ( -75-)  B  omega poor
 203 SER   ( -65-)  B  omega poor
 252 ASP   ( -16-)  B  Poor phi/psi
 256 ASN   ( -12-)  B  Poor phi/psi
 265 GLN   (  -3-)  B  omega poor
 299 VAL   (  31-)  B  omega poor
 304 TRP   (  36-)  B  omega poor
 317 ARG   (  49-)  B  omega poor
 318 ASN   (  50-)  B  Poor phi/psi
 350 THR   (  82-)  B  omega poor
 360 ARG   (  92-)  B  omega poor
 362 ALA   (  94-)  B  omega poor
 369 ASN   ( 101-)  B  Poor phi/psi
 374 PHE   ( 106-)  B  omega poor
 chi-1/chi-2 correlation Z-score : 1.095

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!

  10 ASP   ( -68-)  A      0
  12 SER   ( -66-)  A      0
  13 SER   ( -65-)  A      0
  25 LEU   ( -53-)  A      0
  36 GLN   ( -42-)  A      0
  43 LEU   ( -35-)  A      0
  63 MET   ( -15-)  A      0
  65 ASP   ( -13-)  A      0
  66 ASN   ( -12-)  A      0
  75 GLN   (  -3-)  A      0
  86 SER   (   8-)  A      0
  93 LEU   (  15-)  A      0
  94 THR   (  16-)  A      0
  99 ALA   (  21-)  A      0
 103 ALA   (  25-)  A      0
 110 HIS   (  32-)  A      0
 121 PHE   (  43-)  A      0
 123 SER   (  45-)  A      0
 127 ARG   (  49-)  A      0
 135 LEU   (  57-)  A      0
 139 MET   (  61-)  A      0
 140 VAL   (  62-)  A      0
 149 GLN   (  71-)  A      0
 151 MET   (  73-)  A      0
 153 VAL   (  75-)  A      0
And so on for a total of 123 lines.

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!

 361 GLY   (  93-)  B   1.61   11

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].

  58 PRO   ( -20-)  A    99.0 envelop C-beta (108 degrees)
 163 PRO   (  85-)  A  -112.3 envelop C-gamma (-108 degrees)
 177 PRO   (  99-)  A   -65.9 envelop C-beta (-72 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.

  29 MET   ( -49-)  A      CE  <->   52 ILE   ( -26-)  A      CG2    0.44    2.76  INTRA
 152 LYS   (  74-)  A      NZ  <->  392 HOH   ( 335 )  A      O      0.25    2.45  INTRA
 219 MET   ( -49-)  B      CE  <->  230 MET   ( -38-)  B      CE     0.18    3.02  INTRA
  35 ARG   ( -43-)  A      NH2 <->  392 HOH   ( 392 )  A      O      0.14    2.56  INTRA
  10 ASP   ( -68-)  A      OD1 <->   13 SER   ( -65-)  A      N      0.14    2.56  INTRA
 348 ARG   (  80-)  B      NE  <->  393 HOH   ( 425 )  B      O      0.11    2.59  INTRA
  95 GLU   (  17-)  A      CD  <->  392 HOH   ( 335 )  A      O      0.11    2.69  INTRA
 119 GLN   (  41-)  A    A NE2 <->  392 HOH   ( 466 )  A      O      0.10    2.60  INTRA
  26 ARG   ( -52-)  A      NE  <->  392 HOH   ( 448 )  A      O      0.09    2.61  INTRA
 110 HIS   (  32-)  A      ND1 <->  124 SER   (  46-)  A      OG     0.09    2.61  INTRA BL
  59 GLU   ( -19-)  A      OE1 <->  392 HOH   ( 387 )  A      O      0.09    2.31  INTRA
 189 LEU   ( 111-)  A      O   <->  392 HOH   ( 461 )  A      O      0.08    2.32  INTRA
 158 ARG   (  80-)  A    A NH1 <->  392 HOH   ( 432 )  A      O      0.08    2.62  INTRA
  75 GLN   (  -3-)  A      N   <->  392 HOH   ( 343 )  A      O      0.06    2.64  INTRA
  55 ASP   ( -23-)  A    A OD1 <->  392 HOH   ( 454 )  A      O      0.05    2.35  INTRA
 254 GLU   ( -14-)  B      N   <->  257 ASP   ( -11-)  B      OD2    0.05    2.65  INTRA
  29 MET   ( -49-)  A      CE  <->   52 ILE   ( -26-)  A      CB     0.05    3.15  INTRA
 220 GLU   ( -48-)  B      OE2 <->  393 HOH   ( 409 )  B      O      0.04    2.36  INTRA
 192 THR   ( -76-)  B      O   <->  393 HOH   ( 365 )  B      O      0.03    2.37  INTRA BF
  95 GLU   (  17-)  A      N   <->  392 HOH   ( 457 )  A      O      0.02    2.68  INTRA
  32 PHE   ( -46-)  A      CE1 <->   36 GLN   ( -42-)  A      NE2    0.02    3.08  INTRA
 223 ALA   ( -45-)  B      O   <->  228 LYS   ( -40-)  B      N      0.01    2.69  INTRA
  26 ARG   ( -52-)  A      NH1 <->  392 HOH   ( 390 )  A      O      0.01    2.69  INTRA
 104 GLY   (  26-)  A      N   <->  135 LEU   (  57-)  A      O      0.01    2.69  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 139 MET   (  61-)  A      -7.76
 360 ARG   (  92-)  B      -6.53
 317 ARG   (  49-)  B      -6.28
 170 ARG   (  92-)  A      -6.25
 329 MET   (  61-)  B      -5.89
 275 GLU   (   7-)  B      -5.81
  75 GLN   (  -3-)  A      -5.68
 354 GLN   (  86-)  B      -5.63
 164 GLN   (  86-)  A      -5.62
 225 ARG   ( -43-)  B      -5.50
  35 ARG   ( -43-)  A      -5.25
 226 GLN   ( -42-)  B      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

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.

 127 ARG   (  49-)  A   -2.72
 228 LYS   ( -40-)  B   -2.71
 211 LYS   ( -57-)  B   -2.71

Warning: Abnormal packing Z-score for sequential residues

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

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

 352 PRO   (  84-)  B     -  355 LEU   (  87-)  B        -1.25

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 393 HOH   ( 395 )  B      O     29.93  -15.63   15.72

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.

 195 ASN   ( -73-)  B
 256 ASN   ( -12-)  B

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.

  23 THR   ( -55-)  A      OG1
  27 ARG   ( -51-)  A      NH2
  35 ARG   ( -43-)  A      NH1
 141 ILE   (  63-)  A      N
 144 TRP   (  66-)  A      NE1
 167 TYR   (  89-)  A      OH
 217 ARG   ( -51-)  B      NE
 217 ARG   ( -51-)  B      NH1
 225 ARG   ( -43-)  B      NH2
 330 VAL   (  62-)  B      N
 334 TRP   (  66-)  B      NE1
 339 GLN   (  71-)  B      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.

 275 GLU   (   7-)  B      OE2

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.

 392 HOH   ( 346 )  A      O  1.12  K  4
 393 HOH   ( 417 )  B      O  0.92  K  4 Ion-B
 393 HOH   ( 422 )  B      O  0.90  K  4 ION-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.

  10 ASP   ( -68-)  A   H-bonding suggests Asn; 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 :  -0.031
  2nd generation packing quality :  -1.211
  Ramachandran plot appearance   :   1.076
  chi-1/chi-2 rotamer normality  :   1.095
  Backbone conformation          :   1.558

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.737
  Bond angles                    :   0.745
  Omega angle restraints         :   1.175
  Side chain planarity           :   0.892
  Improper dihedral distribution :   0.815
  B-factor distribution          :   0.500
  Inside/Outside distribution    :   0.987

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 : 1.75


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :   0.8
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.737
  Bond angles                    :   0.745
  Omega angle restraints         :   1.175
  Side chain planarity           :   0.892
  Improper dihedral distribution :   0.815
  B-factor distribution          :   0.500
  Inside/Outside distribution    :   0.987
==============

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.