WHAT IF Check report

This file was created 2011-12-21 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 pdb1bag.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.

 434 BGC   ( 430-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 427 GLC   ( 427-)  A  -   O4  bound to  426 GLC   ( 426-)  A  -   C1
 428 GLC   ( 428-)  A  -   O4  bound to  427 GLC   ( 427-)  A  -   C1
 429 GLC   ( 429-)  A  -   O4  bound to  428 GLC   ( 428-)  A  -   C1

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Crystal temperature (K) :288.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 10.57

Geometric checks

Error: Tau angle problems

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

 272 ALA   ( 272-)  A    6.02
 260 LYS   ( 260-)  A    4.75
 138 GLN   ( 138-)  A    4.49

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.

 242 ARG   ( 242-)  A    -2.6
 387 THR   ( 387-)  A    -2.5
 355 PRO   ( 355-)  A    -2.3
 264 TRP   ( 264-)  A    -2.2
  50 GLN   (  50-)  A    -2.1
 198 THR   ( 198-)  A    -2.1
 316 PHE   ( 316-)  A    -2.1
 413 THR   ( 413-)  A    -2.1
 302 LEU   ( 302-)  A    -2.1
 422 LEU   ( 422-)  A    -2.0
 126 GLN   ( 126-)  A    -2.0
 306 ARG   ( 306-)  A    -2.0
 406 ASN   ( 406-)  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.

  16 ASN   (  16-)  A  Poor phi/psi
 119 ASN   ( 119-)  A  Poor phi/psi
 142 LEU   ( 142-)  A  Poor phi/psi
 186 ASP   ( 186-)  A  Poor phi/psi
 212 ASP   ( 212-)  A  Poor phi/psi
 242 ARG   ( 242-)  A  Poor phi/psi
 250 SER   ( 250-)  A  Poor phi/psi
 276 GLU   ( 276-)  A  Poor phi/psi
 298 GLY   ( 298-)  A  Poor phi/psi
 312 ASN   ( 312-)  A  Poor phi/psi
 356 ASN   ( 356-)  A  Poor phi/psi
 423 TYR   ( 423-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.906

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!

   6 ILE   (   6-)  A      0
   8 SER   (   8-)  A      0
  14 ALA   (  14-)  A      0
  15 TRP   (  15-)  A      0
  16 ASN   (  16-)  A      0
  17 TRP   (  17-)  A      0
  25 ASN   (  25-)  A      0
  26 MET   (  26-)  A      0
  46 LYS   (  46-)  A      0
  50 GLN   (  50-)  A      0
  53 LYS   (  53-)  A      0
  58 TRP   (  58-)  A      0
  59 TYR   (  59-)  A      0
  60 TRP   (  60-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 ILE   (  69-)  A      0
  74 LEU   (  74-)  A      0
  90 TYR   (  90-)  A      0
 100 ILE   ( 100-)  A      0
 101 ASN   ( 101-)  A      0
 110 ILE   ( 110-)  A      0
 118 PRO   ( 118-)  A      0
And so on for a total of 180 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 : 1.324

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.

 248 ASN   ( 248-)  A      ND2 <->  435 HOH   ( 515 )  A      O      0.28    2.42  INTRA
   1 LEU   (   1-)  A      N   <->  435 HOH   ( 488 )  A      O      0.27    2.43  INTRA
 179 LYS   ( 179-)  A      NZ  <->  434 BGC   ( 430-)  A      O3     0.24    2.46  INTRA
 251 HIS   ( 251-)  A      ND1 <->  435 HOH   ( 547 )  A      O      0.18    2.52  INTRA
  16 ASN   (  16-)  A      O   <->  323 GLY   ( 323-)  A      N      0.17    2.53  INTRA BL
 296 ARG   ( 296-)  A      NH1 <->  350 GLU   ( 350-)  A      OE2    0.15    2.55  INTRA BL
 348 GLN   ( 348-)  A      CD  <->  369 HIS   ( 369-)  A      CD2    0.14    3.06  INTRA
 394 TYR   ( 394-)  A      CE2 <->  405 VAL   ( 405-)  A      CG2    0.12    3.08  INTRA
 348 GLN   ( 348-)  A      NE2 <->  369 HIS   ( 369-)  A      CD2    0.12    2.98  INTRA
 122 HIS   ( 122-)  A      N   <->  146 ASP   ( 146-)  A      O      0.11    2.59  INTRA BL
 273 ASN   ( 273-)  A      ND2 <->  435 HOH   ( 476 )  A      O      0.09    2.61  INTRA BL
  37 ILE   (  37-)  A      O   <->   95 ILE   (  95-)  A      N      0.09    2.61  INTRA BL
  38 GLN   (  38-)  A      NE2 <->  206 TYR   ( 206-)  A      OH     0.09    2.61  INTRA BL
 194 TRP   ( 194-)  A      O   <->  198 THR   ( 198-)  A      CB     0.08    2.72  INTRA
 260 LYS   ( 260-)  A      N   <->  261 LEU   ( 261-)  A      N      0.07    2.53  INTRA BL
 295 SER   ( 295-)  A      N   <->  296 ARG   ( 296-)  A      N      0.06    2.54  INTRA BL
 122 HIS   ( 122-)  A      N   <->  123 GLY   ( 123-)  A      N      0.06    2.54  INTRA BL
 154 VAL   ( 154-)  A      CG2 <->  155 GLN   ( 155-)  A      N      0.06    2.94  INTRA BL
 272 ALA   ( 272-)  A      O   <->  315 ARG   ( 315-)  A      NH1    0.04    2.66  INTRA BL
  26 MET   (  26-)  A      SD  <->   87 ALA   (  87-)  A      CA     0.04    3.36  INTRA BL
 250 SER   ( 250-)  A      O   <->  296 ARG   ( 296-)  A      NH2    0.04    2.66  INTRA
 338 VAL   ( 338-)  A      O   <->  342 HIS   ( 342-)  A      N      0.03    2.67  INTRA BL
 393 ARG   ( 393-)  A      NH2 <->  402 SER   ( 402-)  A      OG     0.03    2.67  INTRA BF
 245 GLY   ( 245-)  A      O   <->  248 ASN   ( 248-)  A      ND2    0.03    2.67  INTRA
 193 PHE   ( 193-)  A      CE2 <->  197 ILE   ( 197-)  A      CD1    0.03    3.17  INTRA
 368 SER   ( 368-)  A      N   <->  369 HIS   ( 369-)  A      N      0.02    2.58  INTRA B3
 264 TRP   ( 264-)  A      N   <->  435 HOH   ( 460 )  A      O      0.02    2.68  INTRA BL
 127 ILE   ( 127-)  A      N   <->  140 SER   ( 140-)  A      O      0.02    2.68  INTRA
 133 ARG   ( 133-)  A      NH2 <->  186 ASP   ( 186-)  A      OD2    0.02    2.68  INTRA
  13 HIS   (  13-)  A      N   <->  303 PHE   ( 303-)  A      O      0.02    2.68  INTRA BL
 220 TYR   ( 220-)  A      O   <->  223 TYR   ( 223-)  A      N      0.02    2.68  INTRA
 179 LYS   ( 179-)  A      NZ  <->  212 ASP   ( 212-)  A      OD2    0.02    2.68  INTRA BL
 385 THR   ( 385-)  A      O   <->  410 LEU   ( 410-)  A      N      0.02    2.68  INTRA
  71 ASN   (  71-)  A      N   <->   75 GLY   (  75-)  A      O      0.02    2.68  INTRA BL
 265 VAL   ( 265-)  A      N   <->  266 GLU   ( 266-)  A      N      0.01    2.59  INTRA BL
 185 ASP   ( 185-)  A      CG  <->  216 ARG   ( 216-)  A      NH2    0.01    3.09  INTRA
 325 ARG   ( 325-)  A      NH1 <->  326 GLY   ( 326-)  A      O      0.01    2.59  INTRA
  45 VAL   (  45-)  A      N   <->  435 HOH   ( 487 )  A      O      0.01    2.69  INTRA BL
 120 TRP   ( 120-)  A      O   <->  148 ASN   ( 148-)  A      N      0.01    2.69  INTRA
 388 LYS   ( 388-)  A      N   <->  389 LEU   ( 389-)  A      N      0.01    2.59  INTRA B3
 371 VAL   ( 371-)  A      N   <->  422 LEU   ( 422-)  A      O      0.01    2.69  INTRA

Packing, accessibility and threading

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.

 319 LYS   ( 319-)  A      -6.45
  50 GLN   (  50-)  A      -5.76
  49 ASN   (  49-)  A      -5.34
 241 ASN   ( 241-)  A      -5.31
 167 ASN   ( 167-)  A      -5.30
 356 ASN   ( 356-)  A      -5.20
 138 GLN   ( 138-)  A      -5.14

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.

  49 ASN   (  49-)  A        51 - GLY     51- ( A)         -5.08

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.

 125 THR   ( 125-)  A   -3.09
 142 LEU   ( 142-)  A   -2.89
 304 PHE   ( 304-)  A   -2.62
 127 ILE   ( 127-)  A   -2.51

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.

 124 ASN   ( 124-)  A     -  127 ILE   ( 127-)  A        -1.81

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.

 435 HOH   ( 450 )  A      O     -5.23    7.85   21.80
 435 HOH   ( 480 )  A      O     -0.44   11.71   19.74
 435 HOH   ( 483 )  A      O     -7.42   47.40   28.82
 435 HOH   ( 548 )  A      O      1.76   12.10   25.20

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.

 435 HOH   ( 510 )  A      O
 435 HOH   ( 542 )  A      O
Strange metal coordination for HIS 180

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.

  38 GLN   (  38-)  A
  68 GLN   (  68-)  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.

   2 THR   (   2-)  A      N
   5 SER   (   5-)  A      N
  10 THR   (  10-)  A      OG1
  16 ASN   (  16-)  A      ND2
  35 THR   (  35-)  A      OG1
  40 SER   (  40-)  A      OG
  42 ILE   (  42-)  A      N
  43 ASN   (  43-)  A      ND2
  59 TYR   (  59-)  A      N
  66 SER   (  66-)  A      OG
  97 ASP   (  97-)  A      N
 102 HIS   ( 102-)  A      N
 121 THR   ( 121-)  A      OG1
 129 ASN   ( 129-)  A      N
 135 ASP   ( 135-)  A      N
 142 LEU   ( 142-)  A      N
 174 ARG   ( 174-)  A      NH1
 179 LYS   ( 179-)  A      N
 179 LYS   ( 179-)  A      NZ
 189 TYR   ( 189-)  A      N
 200 THR   ( 200-)  A      OG1
 216 ARG   ( 216-)  A      NE
 216 ARG   ( 216-)  A      NH2
 227 THR   ( 227-)  A      OG1
 250 SER   ( 250-)  A      N
 251 HIS   ( 251-)  A      N
 253 ALA   ( 253-)  A      N
 295 SER   ( 295-)  A      N
 296 ARG   ( 296-)  A      NH2
 316 PHE   ( 316-)  A      N
 325 ARG   ( 325-)  A      NH1
 326 GLY   ( 326-)  A      N
 343 ASN   ( 343-)  A      ND2
 387 THR   ( 387-)  A      OG1
 389 LEU   ( 389-)  A      N
 397 LYS   ( 397-)  A      NZ
 399 GLY   ( 399-)  A      N
Only metal coordination for  101 ASN  ( 101-) A      OD1

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.

  97 ASP   (  97-)  A      OD1
 168 ASP   ( 168-)  A      OD2
 342 HIS   ( 342-)  A      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 431  CA   ( 431-)  A     0.72   0.96 Scores about as good as NA
 432  CA   ( 432-)  A     0.75   0.98 Scores about as good as NA
 433  CA   ( 433-)  A     0.71   0.94 Scores about as good as NA

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.

 351 GLU   ( 351-)  A   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 :  -0.508
  2nd generation packing quality :  -1.500
  Ramachandran plot appearance   :  -2.533
  chi-1/chi-2 rotamer normality  :  -2.906
  Backbone conformation          :  -1.066

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.658 (tight)
  Omega angle restraints         :   0.241 (tight)
  Side chain planarity           :   0.510 (tight)
  Improper dihedral distribution :   0.837
  Inside/Outside distribution    :   0.955

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.658 (tight)
  Omega angle restraints         :   0.241 (tight)
  Side chain planarity           :   0.510 (tight)
  Improper dihedral distribution :   0.837
  Inside/Outside distribution    :   0.955
==============

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.