WHAT IF Check report

This file was created 2012-01-30 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 pdb3o5x.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.

 256 JZG   (   1-)  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'.

 255 ARG   ( 527-)  A      CG
 255 ARG   ( 527-)  A      CD
 255 ARG   ( 527-)  A      NE
 255 ARG   ( 527-)  A      CZ
 255 ARG   ( 527-)  A      NH1
 255 ARG   ( 527-)  A      NH2

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  50 MET   ( 311-)  A    0.50
 116 VAL   ( 388-)  A    0.50
 165 ASP   ( 437-)  A    0.50
 204 ILE   ( 476-)  A    0.50
 232 MET   ( 504-)  A    0.50
 234 GLN   ( 506-)  A    0.50

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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.

  28 ARG   ( 289-)  A
 141 ARG   ( 413-)  A

Warning: Tyrosine convention problem

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

  55 TYR   ( 327-)  A
 146 TYR   ( 418-)  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.

 159 ASP   ( 431-)  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.

 251 GLU   ( 523-)  A

Geometric checks

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  62 LEU   ( 334-)  A      N    CA   C    98.99   -4.4

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  28 ARG   ( 289-)  A
 141 ARG   ( 413-)  A
 159 ASP   ( 431-)  A
 251 GLU   ( 523-)  A

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.

  62 LEU   ( 334-)  A    4.98

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.

 122 HIS   ( 394-)  A    -2.2
 141 ARG   ( 413-)  A    -2.2
 105 LEU   ( 377-)  A    -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.

  77 ASN   ( 349-)  A  Poor phi/psi
  90 ARG   ( 362-)  A  Poor phi/psi
  95 CYS   ( 367-)  A  Poor phi/psi
 103 TYR   ( 375-)  A  Poor phi/psi
 122 HIS   ( 394-)  A  Poor phi/psi
 137 GLY   ( 409-)  A  Poor phi/psi
 187 CYS   ( 459-)  A  Poor phi/psi
 233 VAL   ( 505-)  A  Poor phi/psi
 254 GLN   ( 526-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.028

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!

  17 ARG   ( 278-)  A      0
  18 TYR   ( 279-)  A      0
  32 HIS   ( 293-)  A      0
  33 ASP   ( 294-)  A      0
  35 ASP   ( 296-)  A      0
  39 PRO   ( 300-)  A      0
  40 VAL   ( 301-)  A      0
  41 SER   ( 302-)  A      0
  42 ASP   ( 303-)  A      0
  44 ILE   ( 305-)  A      0
  45 ASN   ( 306-)  A      0
  50 MET   ( 311-)  A      0
  51 PRO   ( 312-)  A      0
  52 LYS   ( 324-)  A      0
  53 LYS   ( 325-)  A      0
  76 GLU   ( 348-)  A      0
  77 ASN   ( 349-)  A      0
  78 SER   ( 350-)  A      0
  80 VAL   ( 352-)  A      0
  87 GLU   ( 359-)  A      0
  89 GLU   ( 361-)  A      0
  90 ARG   ( 362-)  A      0
  94 LYS   ( 366-)  A      0
  95 CYS   ( 367-)  A      0
  97 LYS   ( 369-)  A      0
And so on for a total of 92 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 : 1.240

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.

  83 MET   ( 355-)  A      CE  <->  145 GLN   ( 417-)  A      NE2    0.37    2.73  INTRA BL
 253 LEU   ( 525-)  A      O   <->  255 ARG   ( 527-)  A      N      0.27    2.43  INTRA BF
 253 LEU   ( 525-)  A      C   <->  255 ARG   ( 527-)  A      N      0.26    2.64  INTRA BF
 139 THR   ( 411-)  A      O   <->  141 ARG   ( 413-)  A      NE     0.24    2.46  INTRA BF
 238 GLN   ( 510-)  A      NE2 <->  256 JZG   (   1-)  A      O2     0.21    2.49  INTRA BL
 187 CYS   ( 459-)  A      SG  <->  190 GLY   ( 462-)  A      N      0.20    3.10  INTRA BL
  53 LYS   ( 325-)  A      NZ  <->  201 ASP   ( 473-)  A      OD2    0.18    2.52  INTRA
  47 ASN   ( 308-)  A      OD1 <->  229 ARG   ( 501-)  A      NH1    0.18    2.52  INTRA BL
 193 ARG   ( 465-)  A      NH2 <->  256 JZG   (   1-)  A      O3     0.16    2.54  INTRA BL
 108 TYR   ( 380-)  A      N   <->  111 MET   ( 383-)  A      O      0.10    2.60  INTRA
  61 CYS   ( 333-)  A      SG  <->   69 PHE   ( 341-)  A      CB     0.09    3.31  INTRA BL
 127 ARG   ( 399-)  A      NH2 <->  149 ARG   ( 421-)  A      NH2    0.08    2.77  INTRA BF
  17 ARG   ( 278-)  A      NH1 <->   60 GLY   ( 332-)  A      O      0.08    2.62  INTRA BL
  82 VAL   ( 354-)  A      N   <->  184 VAL   ( 456-)  A      O      0.08    2.62  INTRA BL
  85 THR   ( 357-)  A      O   <->  147 HIS   ( 419-)  A      NE2    0.08    2.62  INTRA BL
  61 CYS   ( 333-)  A      SG  <->   69 PHE   ( 341-)  A      CG     0.07    3.33  INTRA BL
  44 ILE   ( 305-)  A      O   <->   46 ALA   ( 307-)  A      N      0.07    2.63  INTRA BL
  83 MET   ( 355-)  A      CE  <->  147 HIS   ( 419-)  A      ND1    0.06    3.04  INTRA BL
 222 ILE   ( 494-)  A      CD1 <->  239 TYR   ( 511-)  A      CE1    0.06    3.14  INTRA
 129 LEU   ( 401-)  A      O   <->  143 VAL   ( 415-)  A      N      0.06    2.64  INTRA BL
 187 CYS   ( 459-)  A      SG  <->  190 GLY   ( 462-)  A      CA     0.06    3.34  INTRA BL
  86 LYS   ( 358-)  A      NZ  <->  257 HOH   (  73 )  A      O      0.05    2.65  INTRA
  49 ILE   ( 310-)  A      N   <->   55 TYR   ( 327-)  A      O      0.04    2.66  INTRA BL
 163 VAL   ( 435-)  A      O   <->  167 LEU   ( 439-)  A      N      0.04    2.66  INTRA BL
  83 MET   ( 355-)  A      CE  <->  147 HIS   ( 419-)  A      CG     0.04    3.16  INTRA BL
  97 LYS   ( 369-)  A      NZ  <->   99 TRP   ( 371-)  A      O      0.04    2.66  INTRA BL
 151 TRP   ( 423-)  A      CD1 <->  193 ARG   ( 465-)  A      CZ     0.04    3.16  INTRA BL
  18 TYR   ( 279-)  A      OH  <->  188 SER   ( 460-)  A      OG     0.03    2.37  INTRA
  79 ARG   ( 351-)  A      O   <->  144 TRP   ( 416-)  A      N      0.03    2.67  INTRA BL
 133 LYS   ( 405-)  A      CD  <->  136 GLN   ( 408-)  A      NE2    0.02    3.08  INTRA BF
  81 ILE   ( 353-)  A      O   <->  146 TYR   ( 418-)  A      N      0.02    2.68  INTRA BL
  12 ASN   ( 273-)  A      OD1 <->   15 LYS   ( 276-)  A      NZ     0.02    2.68  INTRA
 205 ASP   ( 477-)  A      OD1 <->  208 ARG   ( 480-)  A      NH1    0.01    2.69  INTRA
 151 TRP   ( 423-)  A      CZ3 <->  197 PHE   ( 469-)  A      CE1    0.01    3.19  INTRA BL
 159 ASP   ( 431-)  A      OD1 <->  161 GLY   ( 433-)  A      N      0.01    2.69  INTRA
 125 THR   ( 397-)  A      OG1 <->  149 ARG   ( 421-)  A      NH1    0.01    2.69  INTRA BF
  35 ASP   ( 296-)  A      OD1 <->   37 ASN   ( 298-)  A      N      0.01    2.69  INTRA
  98 TYR   ( 370-)  A      OH  <->  186 HIS   ( 458-)  A      NE2    0.01    2.69  INTRA BL
 227 SER   ( 499-)  A      N   <->  228 GLN   ( 500-)  A      N      0.01    2.59  INTRA BL
 121 ALA   ( 393-)  A      CB  <->  124 TYR   ( 396-)  A      CZ     0.01    3.19  INTRA

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.

 178 MET   ( 450-)  A      -6.70
  90 ARG   ( 362-)  A      -6.66
 154 HIS   ( 426-)  A      -6.21
  50 MET   ( 311-)  A      -6.04
  32 HIS   ( 293-)  A      -5.64
 234 GLN   ( 506-)  A      -5.44
 136 GLN   ( 408-)  A      -5.24
   8 GLN   ( 269-)  A      -5.15
 254 GLN   ( 526-)  A      -5.01

Warning: Abnormal packing environment for sequential residues

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

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

 208 ARG   ( 480-)  A       210 - LYS    482- ( A)         -4.54

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.

 154 HIS   ( 426-)  A   -2.90
 255 ARG   ( 527-)  A   -2.56
 209 GLU   ( 481-)  A   -2.50

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: 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.

 257 HOH   (  70 )  A      O
 257 HOH   ( 129 )  A      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.

 171 HIS   ( 443-)  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.

  85 THR   ( 357-)  A      N
  98 TYR   ( 370-)  A      N
  99 TRP   ( 371-)  A      N
 122 HIS   ( 394-)  A      ND1
 145 GLN   ( 417-)  A      NE2
 189 ALA   ( 461-)  A      N
 193 ARG   ( 465-)  A      N
 193 ARG   ( 465-)  A      NE

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.

 165 ASP   ( 437-)  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 :   0.115
  2nd generation packing quality :  -0.849
  Ramachandran plot appearance   :  -0.263
  chi-1/chi-2 rotamer normality  :  -1.028
  Backbone conformation          :   0.130

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.277 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   0.225 (tight)
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.499
  Inside/Outside distribution    :   1.023

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 : 2.00

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.277 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   0.225 (tight)
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.499
  Inside/Outside distribution    :   1.023

      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
    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).

    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
      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
    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.