WHAT IF Check report

This file was created 2012-01-19 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 pdb1znc.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

 514 SO4   ( 601-)  A  -
 515 SO4   ( 701-)  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: 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) :298.000

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

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 510 SER   ( 259-)  A      SG  -SG*   2.45   10.2
 510 SER   ( 259-)  A      SG  -SG*   2.45   10.2
  24 CYS   (  23-)  A      SG  -SG*   2.34    7.5
 207 CYS   ( 203-)  A      SG  -SG*   2.34    7.5
 207 CYS   ( 203-)  A      SG  -SG*   2.49   11.2
 207 CYS   ( 203-)  A      SG  -SG*   2.49   11.2

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.

 232 GLN   ( 227-)  A    4.42
 479 GLN   ( 227-)  B    4.31

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.

 422 THR   ( 174-)  B    -3.0
 175 THR   ( 174-)  A    -3.0
 279 PRO   (  13-)  B    -2.4
  17 PRO   (  13-)  A    -2.4
 197 ARG   ( 193-)  A    -2.0
 444 ARG   ( 193-)  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.

  22 GLY   (  21-)  A  Poor phi/psi
  26 LYS   (  25-)  A  Poor phi/psi
  30 SER   (  29-)  A  PRO omega poor
  57 GLN   (  55-)  A  Poor phi/psi
  67 SER   (  65-)  A  Poor phi/psi
  74 ASN   (  72-)  A  Poor phi/psi
 172 GLU   ( 171-)  A  Poor phi/psi
 205 PRO   ( 201-)  A  omega poor
 240 GLN   ( 237-)  A  Poor phi/psi
 246 ASP   ( 243-)  A  Poor phi/psi
 284 GLY   (  21-)  B  Poor phi/psi
 288 LYS   (  25-)  B  Poor phi/psi
 292 SER   (  29-)  B  PRO omega poor
 319 GLN   (  55-)  B  Poor phi/psi
 329 SER   (  65-)  B  Poor phi/psi
 336 ASN   (  72-)  B  Poor phi/psi
 419 GLU   ( 171-)  B  Poor phi/psi
 452 PRO   ( 201-)  B  omega poor
 487 GLN   ( 237-)  B  Poor phi/psi
 493 ASP   ( 243-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.628

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 TYR   (   7-)  A      0
  12 TYR   (  11-)  A      0
  13 PRO   (  11-)  A      0
  14 CYS   (  11-)  A      0
  19 LYS   (  15-)  A      0
  23 ASN   (  22-)  A      0
  24 CYS   (  23-)  A      0
  28 ARG   (  27-)  A      0
  29 GLN   (  28-)  A      0
  30 SER   (  29-)  A      0
  51 SER   (  50-)  A      0
  56 LYS   (  54-)  A      0
  57 GLN   (  55-)  A      0
  64 ASN   (  62-)  A      0
  66 HIS   (  64-)  A      0
  67 SER   (  65-)  A      0
  73 GLU   (  71-)  A      0
  74 ASN   (  72-)  A      0
  75 LYS   (  76-)  A      0
  84 PRO   (  85-)  A      0
  86 PRO   (  87-)  A      0
  90 LYS   (  91-)  A      0
  91 GLN   (  92-)  A      0
  95 HIS   (  96-)  A      0
  96 TRP   (  97-)  A      0
And so on for a total of 256 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 : 1.313

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.

 264 CYS   (   6-)  B      SG  <->  276 CYS   (  11-)  B      SG     0.94    2.51  INTRA BF
 264 CYS   (   6-)  B      SG  <->  276 CYS   (  11-)  B      CB     0.61    2.79  INTRA BF
 331 MET   (  67-)  B      SD  <->  353 GLN   (  92-)  B      NE2    0.43    2.87  INTRA BF
  69 MET   (  67-)  A      SD  <->   91 GLN   (  92-)  A      NE2    0.39    2.91  INTRA
 264 CYS   (   6-)  B      CB  <->  276 CYS   (  11-)  B      SG     0.17    3.23  INTRA BF
 292 SER   (  29-)  B      O   <->  496 ARG   ( 246-)  B      NH1    0.15    2.55  INTRA BL
  30 SER   (  29-)  A      O   <->  249 ARG   ( 246-)  A      NH1    0.12    2.58  INTRA BL
 331 MET   (  67-)  B      SD  <->  353 GLN   (  92-)  B      CD     0.11    3.29  INTRA BF
 451 THR   ( 200-)  B      O   <->  454 CYS   ( 203-)  B      N      0.09    2.61  INTRA
  69 MET   (  67-)  A      SD  <->   91 GLN   (  92-)  A      CD     0.09    3.31  INTRA
 264 CYS   (   6-)  B      N   <->  277 LEU   (  11-)  B      O      0.08    2.62  INTRA BF
  95 HIS   (  96-)  A      ND1 <->  247 ASN   ( 244-)  A      O      0.07    2.63  INTRA BL
 204 THR   ( 200-)  A      O   <->  207 CYS   ( 203-)  A      N      0.07    2.63  INTRA BL
   2 CYS   (   6-)  A      N   <->   15 LEU   (  11-)  A      O      0.07    2.63  INTRA
 357 HIS   (  96-)  B      ND1 <->  494 ASN   ( 244-)  B      O      0.06    2.64  INTRA BL
 315 TYR   (  51-)  B      O   <->  430 LEU   ( 182-)  B      N      0.04    2.66  INTRA BF
 390 VAL   ( 143-)  B      CG2 <->  391 LEU   ( 144-)  B      N      0.04    2.96  INTRA BL
 381 ILE   ( 120-)  B      CG2 <->  383 HIS   ( 122-)  B      CE1    0.03    3.17  INTRA
 130 ASN   ( 130-)  A      ND2 <->  132 LYS   ( 132-)  A      CB     0.03    3.07  INTRA
 368 HIS   ( 107-)  B      NE2 <->  445 TYR   ( 194-)  B      OH     0.03    2.67  INTRA BL
 267 VAL   (   9-)  B      CG1 <->  268 GLN   (  10-)  B      N      0.03    2.97  INTRA BF
 119 ILE   ( 120-)  A      CG2 <->  121 HIS   ( 122-)  A      CE1    0.03    3.17  INTRA BL
  53 TYR   (  51-)  A      O   <->  183 LEU   ( 182-)  A      N      0.02    2.68  INTRA BL
 130 ASN   ( 130-)  A      ND2 <->  132 LYS   ( 132-)  A      N      0.02    2.83  INTRA
 106 HIS   ( 107-)  A      NE2 <->  198 TYR   ( 194-)  A      OH     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.

 274 TYR   (  11-)  B      -7.66
  12 TYR   (  11-)  A      -7.65
 135 GLN   ( 135-)  A      -7.17
 464 ARG   ( 213-)  B      -6.10
 217 ARG   ( 213-)  A      -6.03
 253 GLN   ( 250-)  A      -6.01
 101 TYR   ( 102-)  A      -6.00
 500 GLN   ( 250-)  B      -5.98
 363 TYR   ( 102-)  B      -5.97
 440 ARG   ( 189-)  B      -5.56
 287 GLN   (  24-)  B      -5.54
  25 GLN   (  24-)  A      -5.53
 193 ARG   ( 189-)  A      -5.48
 273 ASN   (  11-)  B      -5.41
  11 ASN   (  11-)  A      -5.38
  44 LYS   (  43-)  A      -5.28
 306 LYS   (  43-)  B      -5.28
 167 ASN   ( 166-)  A      -5.27
 414 ASN   ( 166-)  B      -5.25
 503 GLN   ( 253-)  B      -5.19
 256 GLN   ( 253-)  A      -5.13
  75 LYS   (  76-)  A      -5.04
 124 GLU   ( 125-)  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.

  11 ASN   (  11-)  A        13 - PRO     11- ( A)         -5.68
 273 ASN   (  11-)  B       275 - PRO     11- ( B)         -5.70

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: 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.

  70 MET   (  68-)  A     -   73 GLU   (  71-)  A        -1.58

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

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.

 130 ASN   ( 130-)  A
 194 HIS   ( 190-)  A
 441 HIS   ( 190-)  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.

  28 ARG   (  27-)  A      NH2
  32 ILE   (  31-)  A      N
  54 ASP   (  52-)  A      N
  85 ALA   (  86-)  A      N
  97 SER   (  98-)  A      N
 101 TYR   ( 102-)  A      N
 138 GLU   ( 138-)  A      N
 175 THR   ( 174-)  A      OG1
 193 ARG   ( 189-)  A      N
 194 HIS   ( 190-)  A      N
 204 THR   ( 200-)  A      N
 208 ASP   ( 204-)  A      N
 224 ARG   ( 220-)  A      N
 231 SER   ( 227-)  A      OG
 239 GLU   ( 236-)  A      N
 241 THR   ( 238-)  A      N
 287 GLN   (  24-)  B      N
 294 ILE   (  31-)  B      N
 316 ASP   (  52-)  B      N
 319 GLN   (  55-)  B      NE2
 347 ALA   (  86-)  B      N
 359 SER   (  98-)  B      N
 363 TYR   ( 102-)  B      N
 387 GLU   ( 140-)  B      N
 440 ARG   ( 189-)  B      N
 441 HIS   ( 190-)  B      N
 451 THR   ( 200-)  B      N
 455 ASP   ( 204-)  B      N
 471 ARG   ( 220-)  B      N
 478 SER   ( 227-)  B      OG
 486 GLU   ( 236-)  B      N
 488 THR   ( 238-)  B      N
 492 LYS   ( 242-)  B      N
 495 VAL   ( 245-)  B      N
Only metal coordination for   95 HIS  (  96-) A      NE2
Only metal coordination for  118 HIS  ( 119-) A      ND1
Only metal coordination for  357 HIS  (  96-) B      NE2
Only metal coordination for  380 HIS  ( 119-) B      ND1

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.

  66 HIS   (  64-)  A      ND1
  73 GLU   (  71-)  A      OE2
 140 GLU   ( 140-)  A      OE1
 316 ASP   (  52-)  B      OD1
 328 HIS   (  64-)  B      ND1

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.

 208 ASP   ( 204-)  A   H-bonding suggests Asn; but Alt-Rotamer
 455 ASP   ( 204-)  B   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 :  -1.045
  2nd generation packing quality :  -1.894
  Ramachandran plot appearance   :  -2.413
  chi-1/chi-2 rotamer normality  :  -1.628
  Backbone conformation          :  -1.749

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.376 (tight)
  Bond angles                    :   0.640 (tight)
  Omega angle restraints         :   0.239 (tight)
  Side chain planarity           :   0.383 (tight)
  Improper dihedral distribution :   0.759
  B-factor distribution          :   0.643
  Inside/Outside distribution    :   1.000

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 :   0.0
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.376 (tight)
  Bond angles                    :   0.640 (tight)
  Omega angle restraints         :   0.239 (tight)
  Side chain planarity           :   0.383 (tight)
  Improper dihedral distribution :   0.759
  B-factor distribution          :   0.643
  Inside/Outside distribution    :   1.000
==============

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.