WHAT IF Check report

This file was created 2012-01-12 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 pdb1rk4.ent

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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.

 144 ARG   ( 165-)  A      CG   CD    1.37   -5.2
 320 ASN   ( 128-)  B      CA   C     1.61    4.0

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997434  0.000381 -0.001356|
 |  0.000381  0.999440  0.000171|
 | -0.001356  0.000171  0.998155|
Proposed new scale matrix

 |  0.016748 -0.000006  0.000023|
 | -0.000006  0.014461 -0.000002|
 |  0.000013 -0.000002  0.009319|
With corresponding cell

    A    =  59.709  B   =  69.151  C    = 107.306
    Alpha=  89.980  Beta=  90.156  Gamma=  89.956

The CRYST1 cell dimensions

    A    =  59.861  B   =  69.189  C    = 107.506
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 46.652
(Under-)estimated Z-score: 5.034

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.

  33 THR   (  54-)  A      CG2  CB   OG1 100.86   -4.2
 266 HIS   (  74-)  B      CG   ND1  CE1 109.91    4.3
 284 ARG   (  92-)  B      CG   CD   NE  118.11    4.5

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.

  97 ILE   ( 118-)  A    -2.5
 310 ILE   ( 118-)  B    -2.5
 317 LEU   ( 125-)  B    -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.

  52 VAL   (  73-)  A  omega poor
  67 LEU   (  88-)  A  omega poor
  69 PRO   (  90-)  A  PRO omega poor
 174 ARG   ( 195-)  A  Poor phi/psi
 212 TYR   ( 233-)  A  omega poor
 218 PHE   (  26-)  B  omega poor
 282 PRO   (  90-)  B  PRO omega poor
 chi-1/chi-2 correlation Z-score : -1.113

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 396 SER   ( 211-)  B    0.35

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 CYS   (  24-)  A      0
   5 PHE   (  26-)  A      0
  16 LYS   (  37-)  A      0
  22 VAL   (  43-)  A      0
  38 CYS   (  59-)  A      0
  42 GLN   (  63-)  A      0
  43 LEU   (  64-)  A      0
  45 PHE   (  66-)  A      0
  53 HIS   (  74-)  A      0
  67 LEU   (  88-)  A      0
  68 CYS   (  89-)  A      0
  69 PRO   (  90-)  A      0
  71 ARG   (  92-)  A      0
  72 TYR   (  93-)  A      0
  75 LEU   (  96-)  A      0
  85 ALA   ( 106-)  A      0
  87 LEU   ( 108-)  A      0
 105 ASN   ( 126-)  A      0
 127 LEU   ( 148-)  A      0
 136 ALA   ( 157-)  A      0
 137 GLU   ( 158-)  A      0
 138 ASP   ( 159-)  A      0
 139 GLU   ( 160-)  A      0
 143 GLN   ( 164-)  A      0
 145 LYS   ( 166-)  A      0
And so on for a total of 125 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  44 PRO   (  65-)  A    0.11 LOW
 161 PRO   ( 182-)  A    0.47 HIGH
 257 PRO   (  65-)  B    0.19 LOW
 293 PRO   ( 101-)  B    0.17 LOW
 409 PRO   ( 224-)  B    0.12 LOW

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].

 179 PRO   ( 200-)  A   102.8 envelop C-beta (108 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.

 243 ARG   (  51-)  B      NH2 <->  421 HOH   ( 407 )  B      O      0.40    2.30  INTRA
 287 LYS   (  95-)  B      NZ  <->  289 ALA   (  97-)  B      O      0.29    2.41  INTRA
  61 GLU   (  82-)  A      OE1 <->  420 HOH   ( 393 )  A      O      0.19    2.21  INTRA
 105 ASN   ( 126-)  A      ND2 <->  420 HOH   ( 306 )  A      O      0.17    2.53  INTRA
 350 ARG   ( 165-)  B      O   <->  393 ARG   ( 208-)  B      NH2    0.13    2.57  INTRA
 193 TYR   ( 214-)  A      CD1 <->  198 PHE   ( 219-)  A      CE2    0.13    3.07  INTRA
 164 HIS   ( 185-)  A      CE1 <->  420 HOH   ( 360 )  A      O      0.13    2.67  INTRA
 370 HIS   ( 185-)  B      CE1 <->  421 HOH   ( 244 )  B      O      0.11    2.69  INTRA BL
 167 GLN   ( 188-)  A      OE1 <->  193 TYR   ( 214-)  A      OH     0.10    2.30  INTRA
  32 GLU   (  53-)  A      OE2 <->  420 HOH   ( 397 )  A      O      0.10    2.30  INTRA
 349 GLN   ( 164-)  B      C   <->  393 ARG   ( 208-)  B      NH2    0.08    3.02  INTRA
  16 LYS   (  37-)  A      NZ  <->   67 LEU   (  88-)  A      O      0.08    2.62  INTRA BL
 370 HIS   ( 185-)  B      CE1 <->  408 CYS   ( 223-)  B      SG     0.07    3.33  INTRA
 196 GLU   ( 217-)  A      OE1 <->  420 HOH   ( 274 )  A      O      0.05    2.35  INTRA
 193 TYR   ( 214-)  A      CE1 <->  198 PHE   ( 219-)  A      CE2    0.05    3.15  INTRA
  26 ASP   (  47-)  A      OD2 <->  281 CYS   (  89-)  B      SG     0.04    2.96  INTRA
 151 GLU   ( 172-)  A      OE1 <->  420 HOH   ( 280 )  A      O      0.04    2.36  INTRA
 229 LYS   (  37-)  B      NZ  <->  280 LEU   (  88-)  B      O      0.04    2.66  INTRA BL
 160 LEU   ( 181-)  A      N   <->  161 PRO   ( 182-)  A      CD     0.01    2.99  INTRA BL
 300 LEU   ( 108-)  B      O   <->  421 HOH   ( 266 )  B      O      0.01    2.39  INTRA
 232 THR   (  40-)  B      C   <->  233 PHE   (  41-)  B      CD1    0.01    3.09  INTRA
 299 GLY   ( 107-)  B      N   <->  421 HOH   ( 346 )  B      O      0.01    2.69  INTRA BL
 173 TYR   ( 194-)  A      OH  <->  213 GLU   ( 234-)  A      CG     0.01    2.79  INTRA BF

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.

  71 ARG   (  92-)  A      -6.42
 284 ARG   (  92-)  B      -6.17
  78 LEU   (  99-)  A      -6.10
 291 LEU   (  99-)  B      -5.99
 380 ARG   ( 195-)  B      -5.27
 174 ARG   ( 195-)  A      -5.22
  42 GLN   (  63-)  A      -5.17
 255 GLN   (  63-)  B      -5.16

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.

 343 GLU   ( 151-)  B       345 - ASP    153- ( B)         -4.77

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.

 131 VAL   ( 152-)  A   -3.06

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.

 314 ASN   ( 122-)  B     -  317 LEU   ( 125-)  B        -1.48

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.

 105 ASN   ( 126-)  A
 164 HIS   ( 185-)  A
 167 GLN   ( 188-)  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.

  20 PHE   (  41-)  A      N
 106 ASP   ( 127-)  A      N
 107 ASN   ( 128-)  A      N
 153 THR   ( 174-)  A      OG1
 155 ALA   ( 176-)  A      N
 206 GLU   ( 227-)  A      N
 220 GLN   (  28-)  B      NE2
 233 PHE   (  41-)  B      N
 236 THR   (  44-)  B      N
 255 GLN   (  63-)  B      NE2
 309 TYR   ( 117-)  B      OH
 359 THR   ( 174-)  B      OG1
 383 THR   ( 198-)  B      N
 397 ASN   ( 212-)  B      ND2

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.

 412 GLU   ( 227-)  B      OE1

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.

 420 HOH   ( 310 )  A      O  0.96  K  5
 421 HOH   ( 344 )  B      O  1.12  K  5
 421 HOH   ( 345 )  B      O  0.96  K  4

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.

 209 GLU   ( 230-)  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 :  -0.421
  2nd generation packing quality :  -1.622
  Ramachandran plot appearance   :   0.379
  chi-1/chi-2 rotamer normality  :  -1.113
  Backbone conformation          :  -0.153

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.796
  Bond angles                    :   0.851
  Omega angle restraints         :   1.008
  Side chain planarity           :   1.196
  Improper dihedral distribution :   1.041
  B-factor distribution          :   0.628
  Inside/Outside distribution    :   1.011

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 : 1.79


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.796
  Bond angles                    :   0.851
  Omega angle restraints         :   1.008
  Side chain planarity           :   1.196
  Improper dihedral distribution :   1.041
  B-factor distribution          :   0.628
  Inside/Outside distribution    :   1.011
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Matthews' Coefficient
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Protein side chain planarity
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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Ion Checks
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      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?
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Checking checks
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      Who checks the checkers
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