WHAT IF Check report

This file was created 2011-12-16 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 pdb1i6o.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.856
CA-only RMS fit for the two chains : 0.407

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and 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) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  97 TYR   (  99-)  A
 311 TYR   (  99-)  B

Warning: Phenylalanine convention problem

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

 126 PHE   ( 128-)  A
 238 PHE   (  26-)  B
 340 PHE   ( 128-)  B

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.

   1 ASP   (   3-)  A
 142 ASP   ( 144-)  A
 402 ASP   ( 190-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  18 GLU   (  20-)  A
 414 GLU   ( 202-)  B

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.

  59 PHE   (  61-)  A      N    CA   C    97.44   -4.9
 273 PHE   (  61-)  B      N    CA   C    99.22   -4.3

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.

   1 ASP   (   3-)  A
  18 GLU   (  20-)  A
 142 ASP   ( 144-)  A
 402 ASP   ( 190-)  B
 414 GLU   ( 202-)  B

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.

  59 PHE   (  61-)  A    5.30
  60 VAL   (  62-)  A    4.88
 273 PHE   (  61-)  B    4.52
 274 VAL   (  62-)  B    4.50

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.

 395 ILE   ( 183-)  B    -2.6
 181 ILE   ( 183-)  A    -2.4
 114 ILE   ( 116-)  A    -2.3
  66 ASN   (  68-)  A    -2.2
 257 SER   (  45-)  B    -2.2
 328 ILE   ( 116-)  B    -2.2
 353 ARG   ( 141-)  B    -2.2
  43 SER   (  45-)  A    -2.1
 280 ASN   (  68-)  B    -2.1
 404 ASP   ( 192-)  B    -2.1
 176 GLY   ( 178-)  A    -2.0
 390 GLY   ( 178-)  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.

  65 ALA   (  67-)  A  Poor phi/psi
  87 GLU   (  89-)  A  Poor phi/psi
 108 ASN   ( 110-)  A  Poor phi/psi
 183 ASP   ( 185-)  A  Poor phi/psi
 212 LEU   ( 214-)  A  Poor phi/psi
 244 ALA   (  32-)  B  Poor phi/psi
 279 ALA   (  67-)  B  Poor phi/psi
 301 GLU   (  89-)  B  Poor phi/psi
 397 ASP   ( 185-)  B  Poor phi/psi
 404 ASP   ( 192-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.761

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.

 164 SER   ( 166-)  A    0.36

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!

  15 MSE   (  17-)  A      0
  29 GLN   (  31-)  A      0
  30 ALA   (  32-)  A      0
  42 ASP   (  44-)  A      0
  43 SER   (  45-)  A      0
  55 PRO   (  57-)  A      0
  57 GLU   (  59-)  A      0
  63 ASN   (  65-)  A      0
  64 VAL   (  66-)  A      0
  65 ALA   (  67-)  A      0
  66 ASN   (  68-)  A      0
  67 LEU   (  69-)  A      0
  69 ILE   (  71-)  A      0
  70 HIS   (  72-)  A      0
  71 THR   (  73-)  A      0
  84 ASP   (  86-)  A      0
  87 GLU   (  89-)  A      0
  97 TYR   (  99-)  A      0
  99 CYS   ( 101-)  A      0
 108 ASN   ( 110-)  A      0
 110 GLU   ( 112-)  A      0
 113 LEU   ( 115-)  A      0
 134 GLU   ( 136-)  A      0
 135 MSE   ( 137-)  A      0
 150 MSE   ( 152-)  A      0
And so on for a total of 142 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 : 1.224

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 211 LYS   ( 213-)  A   1.79   12

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.

  84 ASP   (  86-)  A      OD1 <->  168 ARG   ( 170-)  A      NH2    0.22    2.48  INTRA BF
 150 MSE   ( 152-)  A      CE  <->  206 GLY   ( 208-)  A      C      0.22    2.98  INTRA BL
 229 MSE   (  17-)  B      O   <->  233 GLU   (  21-)  B      N      0.21    2.49  INTRA BF
 248 ARG   (  36-)  B      NH2 <->  300 LEU   (  88-)  B      O      0.20    2.50  INTRA BF
  28 ALA   (  30-)  A      O   <->   30 ALA   (  32-)  A      N      0.20    2.50  INTRA BF
 353 ARG   ( 141-)  B      NH2 <->  356 ASP   ( 144-)  B      OD2    0.19    2.51  INTRA BF
  34 ARG   (  36-)  A      NH2 <->   86 LEU   (  88-)  A      O      0.18    2.52  INTRA BF
 139 ARG   ( 141-)  A      NH1 <->  142 ASP   ( 144-)  A      OD2    0.18    2.52  INTRA BF
 254 CYS   (  42-)  B      SG  <->  255 SER   (  43-)  B      N      0.18    3.02  INTRA BL
 268 GLU   (  56-)  B      N   <->  271 GLU   (  59-)  B      OE1    0.16    2.54  INTRA BF
 368 TYR   ( 156-)  B      CZ  <->  372 HIS   ( 160-)  B      NE2    0.15    2.95  INTRA BF
 168 ARG   ( 170-)  A      NH2 <->  170 GLN   ( 172-)  A      OE1    0.15    2.55  INTRA BF
 276 ARG   (  64-)  B      NH2 <->  431 HOH   ( 311 )  B      O      0.15    2.55  INTRA BL
  90 HIS   (  92-)  A      ND1 <->  175 HIS   ( 177-)  A      NE2    0.14    2.86  INTRA BL
 158 HIS   ( 160-)  A      NE2 <->  200 GLU   ( 202-)  A      OE2    0.13    2.57  INTRA BL
 382 ARG   ( 170-)  B      NH2 <->  384 GLN   ( 172-)  B      OE1    0.13    2.57  INTRA BF
 317 GLN   ( 105-)  B      NE2 <->  321 GLU   ( 109-)  B      OE2    0.13    2.57  INTRA BF
  40 CYS   (  42-)  A      SG  <->   41 SER   (  43-)  A      N      0.13    3.07  INTRA BL
 353 ARG   ( 141-)  B      NH2 <->  356 ASP   ( 144-)  B      CG     0.13    2.97  INTRA BF
 405 VAL   ( 193-)  B      N   <->  406 THR   ( 194-)  B      N      0.13    2.47  INTRA BF
 353 ARG   ( 141-)  B      NH2 <->  356 ASP   ( 144-)  B      CB     0.13    2.97  INTRA BF
 364 MSE   ( 152-)  B      CE  <->  420 GLY   ( 208-)  B      C      0.13    3.07  INTRA BF
 284 HIS   (  72-)  B      ND1 <->  431 HOH   ( 328 )  B      O      0.12    2.58  INTRA BL
 279 ALA   (  67-)  B      C   <->  280 ASN   (  68-)  B      CG     0.12    2.98  INTRA BL
 243 GLN   (  31-)  B      OE1 <->  245 GLN   (  33-)  B      NE2    0.11    2.59  INTRA BF
And so on for a total of 69 lines.

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.

  31 GLN   (  33-)  A      -6.49
 245 GLN   (  33-)  B      -6.24
  44 ARG   (  46-)  A      -6.06
 258 ARG   (  46-)  B      -5.90
 110 GLU   ( 112-)  A      -5.70
 372 HIS   ( 160-)  B      -5.64
 324 GLU   ( 112-)  B      -5.58
 158 HIS   ( 160-)  A      -5.47
 182 HIS   ( 184-)  A      -5.44
 396 HIS   ( 184-)  B      -5.35
 382 ARG   ( 170-)  B      -5.11
 321 GLU   ( 109-)  B      -5.11
 107 GLU   ( 109-)  A      -5.06
 348 GLU   ( 136-)  B      -5.05
  19 GLU   (  21-)  A      -5.04

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

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: 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.

 430 HOH   ( 330 )  A      O
 431 HOH   ( 303 )  B      O
 431 HOH   ( 321 )  B      O
 431 HOH   ( 326 )  B      O
 431 HOH   ( 334 )  B      O
Metal-coordinating Histidine residue  96 fixed to   1
Metal-coordinating Histidine residue 310 fixed to   1

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.

 423 ASN   ( 211-)  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.

   3 ASP   (   5-)  A      N
  24 PHE   (  26-)  A      N
  44 ARG   (  46-)  A      N
  58 LEU   (  60-)  A      N
 138 GLU   ( 140-)  A      N
 139 ARG   ( 141-)  A      NE
 142 ASP   ( 144-)  A      N
 161 ILE   ( 163-)  A      N
 249 PHE   (  37-)  B      N
 352 GLU   ( 140-)  B      N
 375 ILE   ( 163-)  B      N
 396 HIS   ( 184-)  B      N
 399 LEU   ( 187-)  B      N
 410 ARG   ( 198-)  B      N
Only metal coordination for   96 HIS  (  98-) A      NE2
Only metal coordination for  310 HIS  (  98-) B      NE2

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.

  74 ASN   (  76-)  A      OD1
 352 GLU   ( 140-)  B      OE2

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.

 123 ASP   ( 125-)  A   H-bonding suggests Asn
 232 GLU   (  20-)  B   H-bonding suggests Gln
 337 ASP   ( 125-)  B   H-bonding suggests Asn
 348 GLU   ( 136-)  B   H-bonding suggests Gln
 404 ASP   ( 192-)  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 :  -0.089
  2nd generation packing quality :  -1.728
  Ramachandran plot appearance   :  -1.046
  chi-1/chi-2 rotamer normality  :  -0.761
  Backbone conformation          :   0.090

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.280 (tight)
  Bond angles                    :   0.609 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.260 (tight)
  Improper dihedral distribution :   0.556
  B-factor distribution          :   0.476
  Inside/Outside distribution    :   0.965

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.280 (tight)
  Bond angles                    :   0.609 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.260 (tight)
  Improper dihedral distribution :   0.556
  B-factor distribution          :   0.476
  Inside/Outside distribution    :   0.965
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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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,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

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?
    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.