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 pdb1j42.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

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'.

  39 LYS   (  41-)  A      CG
  39 LYS   (  41-)  A      CD
  39 LYS   (  41-)  A      CE
  39 LYS   (  41-)  A      NZ
  57 GLU   (  59-)  A      CG
  57 GLU   (  59-)  A      CD
  57 GLU   (  59-)  A      OE1
  57 GLU   (  59-)  A      OE2
  88 GLU   (  90-)  A      CG
  88 GLU   (  90-)  A      CD
  88 GLU   (  90-)  A      OE1
  88 GLU   (  90-)  A      OE2
  92 GLU   (  94-)  A      CG
  92 GLU   (  94-)  A      CD
  92 GLU   (  94-)  A      OE1
  92 GLU   (  94-)  A      OE2
  96 ARG   (  98-)  A      CG
  96 ARG   (  98-)  A      CD
  96 ARG   (  98-)  A      NE
  96 ARG   (  98-)  A      CZ
  96 ARG   (  98-)  A      NH1
  96 ARG   (  98-)  A      NH2
 174 GLU   ( 176-)  A      CG
 174 GLU   ( 176-)  A      CD
 174 GLU   ( 176-)  A      OE1
 174 GLU   ( 176-)  A      OE2

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

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.056

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

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.

 143 ARG   ( 145-)  A

Warning: Tyrosine convention problem

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

 137 TYR   ( 139-)  A

Warning: Phenylalanine convention problem

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

 160 PHE   ( 162-)  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.

  53 ASP   (  55-)  A
  66 ASP   (  68-)  A
 129 ASP   ( 131-)  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.

  13 GLU   (  15-)  A
  14 GLU   (  16-)  A
  16 GLU   (  18-)  A
 141 GLU   ( 143-)  A
 168 GLU   ( 170-)  A

Geometric checks

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.

  13 GLU   (  15-)  A
  14 GLU   (  16-)  A
  16 GLU   (  18-)  A
  53 ASP   (  55-)  A
  66 ASP   (  68-)  A
 129 ASP   ( 131-)  A
 141 GLU   ( 143-)  A
 143 ARG   ( 145-)  A
 168 GLU   ( 170-)  A

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.

  74 ASN   (  76-)  A    -2.6
 104 CYS   ( 106-)  A    -2.5
 123 THR   ( 125-)  A    -2.5
 121 VAL   ( 123-)  A    -2.3
 125 PRO   ( 127-)  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.

  47 ASP   (  49-)  A  Poor phi/psi
  62 GLU   (  64-)  A  Poor phi/psi
  63 GLY   (  65-)  A  Poor phi/psi
  97 LYS   (  99-)  A  Poor phi/psi
 104 CYS   ( 106-)  A  Poor phi/psi
 157 GLY   ( 159-)  A  Poor phi/psi
 184 VAL   ( 186-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.306

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!

  10 LYS   (  12-)  A      0
  37 ALA   (  39-)  A      0
  39 LYS   (  41-)  A      0
  47 ASP   (  49-)  A      0
  62 GLU   (  64-)  A      0
  64 PRO   (  66-)  A      0
  66 ASP   (  68-)  A      0
  96 ARG   (  98-)  A      0
 103 ILE   ( 105-)  A      0
 104 CYS   ( 106-)  A      0
 105 ALA   ( 107-)  A      0
 107 PRO   ( 109-)  A      0
 117 CYS   ( 119-)  A      0
 136 HIS   ( 138-)  A      0
 137 TYR   ( 139-)  A      0
 142 ASN   ( 144-)  A      0
 143 ARG   ( 145-)  A      0
 147 ASP   ( 149-)  A      0
 149 LEU   ( 151-)  A      0
 154 ARG   ( 156-)  A      0
 171 ASN   ( 173-)  A      0
  44 CYS   (  46-)  A      1
  46 ARG   (  48-)  A      1
  53 ASP   (  55-)  A      1
  54 ALA   (  56-)  A      1
  97 LYS   (  99-)  A      1
 114 GLU   ( 116-)  A      1
 115 ILE   ( 117-)  A      1
 120 LYS   ( 122-)  A      1
 121 VAL   ( 123-)  A      1
 124 HIS   ( 126-)  A      1
 132 MET   ( 134-)  A      1
 133 ASN   ( 135-)  A      1
 156 PRO   ( 158-)  A      1
 158 THR   ( 160-)  A      1
 182 PRO   ( 184-)  A      1
 183 LEU   ( 185-)  A      1
  12 ALA   (  14-)  A      2
  36 LEU   (  38-)  A      2
  51 CYS   (  53-)  A      2
  65 TYR   (  67-)  A      2
  74 ASN   (  76-)  A      2
 108 THR   ( 110-)  A      2
 119 SER   ( 121-)  A      2
 141 GLU   ( 143-)  A      2
 170 LEU   ( 172-)  A      2

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 : 1.154

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!

  38 GLY   (  40-)  A   1.56   14

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.

  87 LYS   (  89-)  A      NZ  <->  113 HIS   ( 115-)  A      ND1    0.35    2.65  INTRA
   8 LEU   (  10-)  A      CD1 <->   42 VAL   (  44-)  A      CG1    0.25    2.95  INTRA
  14 GLU   (  16-)  A      CG  <->   48 VAL   (  50-)  A      CG2    0.21    2.99  INTRA
   4 ALA   (   6-)  A      N   <->   29 ILE   (  31-)  A      CD1    0.20    2.90  INTRA
 110 LEU   ( 112-)  A      O   <->  115 ILE   ( 117-)  A      N      0.18    2.52  INTRA
 143 ARG   ( 145-)  A      NH1 <->  161 GLU   ( 163-)  A      OE2    0.17    2.53  INTRA
   3 ARG   (   5-)  A      N   <->   66 ASP   (  68-)  A      OD2    0.17    2.53  INTRA
 167 VAL   ( 169-)  A      O   <->  171 ASN   ( 173-)  A      N      0.16    2.54  INTRA
  14 GLU   (  16-)  A      CG  <->   48 VAL   (  50-)  A      CG1    0.15    3.05  INTRA
  87 LYS   (  89-)  A      CB  <->  113 HIS   ( 115-)  A      ND1    0.13    2.97  INTRA
  48 VAL   (  50-)  A      CG2 <->   50 ILE   (  52-)  A      CD1    0.12    3.08  INTRA
 124 HIS   ( 126-)  A      CD2 <->  126 LEU   ( 128-)  A      N      0.12    2.98  INTRA
  61 LYS   (  63-)  A      O   <->   63 GLY   (  65-)  A      N      0.12    2.58  INTRA
 107 PRO   ( 109-)  A      C   <->  109 ALA   ( 111-)  A      N      0.12    2.78  INTRA
   8 LEU   (  10-)  A      CD1 <->   42 VAL   (  44-)  A      CB     0.11    3.09  INTRA
 158 THR   ( 160-)  A      N   <->  159 SER   ( 161-)  A      N      0.11    2.49  INTRA B3
  43 GLN   (  45-)  A      N   <->  186 HOH   ( 193 )  A      O      0.10    2.60  INTRA
  70 LEU   (  72-)  A      N   <->  101 ALA   ( 103-)  A      O      0.09    2.61  INTRA
 120 LYS   ( 122-)  A      N   <->  147 ASP   ( 149-)  A      OD2    0.09    2.61  INTRA
  14 GLU   (  16-)  A      OE2 <->   46 ARG   (  48-)  A      N      0.08    2.62  INTRA
 120 LYS   ( 122-)  A      C   <->  121 VAL   ( 123-)  A      CG1    0.07    3.03  INTRA
 168 GLU   ( 170-)  A      O   <->  172 GLY   ( 174-)  A      N      0.06    2.64  INTRA
  87 LYS   (  89-)  A      CG  <->  113 HIS   ( 115-)  A      ND1    0.06    3.04  INTRA
   4 ALA   (   6-)  A      CB  <->   29 ILE   (  31-)  A      CD1    0.05    3.15  INTRA
  95 ASN   (  97-)  A      C   <->   97 LYS   (  99-)  A      N      0.05    2.85  INTRA
 155 GLY   ( 157-)  A      N   <->  158 THR   ( 160-)  A      OG1    0.05    2.65  INTRA
  26 ARG   (  28-)  A      NH1 <->  186 HOH   ( 197 )  A      O      0.05    2.65  INTRA
 158 THR   ( 160-)  A      O   <->  162 PHE   ( 164-)  A      N      0.04    2.66  INTRA
  42 VAL   (  44-)  A      N   <->   50 ILE   (  52-)  A      O      0.04    2.66  INTRA
  56 LEU   (  58-)  A      O   <->   60 LYS   (  62-)  A      N      0.04    2.66  INTRA
 143 ARG   ( 145-)  A      NH1 <->  161 GLU   ( 163-)  A      CD     0.04    3.06  INTRA
  53 ASP   (  55-)  A      N   <->   54 ALA   (  56-)  A      N      0.04    2.56  INTRA B3
  14 GLU   (  16-)  A      CD  <->   44 CYS   (  46-)  A      CB     0.03    3.17  INTRA
 124 HIS   ( 126-)  A      O   <->  127 ALA   ( 129-)  A      N      0.03    2.67  INTRA
 161 GLU   ( 163-)  A      OE2 <->  186 HOH   ( 226 )  A      O      0.03    2.37  INTRA
 104 CYS   ( 106-)  A      CB  <->  105 ALA   ( 107-)  A      N      0.02    2.68  INTRA B3
  92 GLU   (  94-)  A      O   <->   96 ARG   (  98-)  A      N      0.02    2.68  INTRA
 121 VAL   ( 123-)  A      O   <->  140 SER   ( 142-)  A      N      0.01    2.69  INTRA
 159 SER   ( 161-)  A      O   <->  163 ALA   ( 165-)  A      N      0.01    2.69  INTRA
 122 THR   ( 124-)  A      C   <->  123 THR   ( 125-)  A      CG2    0.01    3.09  INTRA
   3 ARG   (   5-)  A      C   <->   29 ILE   (  31-)  A      CD1    0.01    3.19  INTRA
 123 THR   ( 125-)  A      O   <->  154 ARG   ( 156-)  A      NE     0.01    2.69  INTRA
 145 GLU   ( 147-)  A      N   <->  152 THR   ( 154-)  A      O      0.01    2.69  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.

  26 ARG   (  28-)  A      -5.36
 171 ASN   ( 173-)  A      -5.11

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: 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.

 186 HOH   ( 203 )  A      O
 186 HOH   ( 204 )  A      O
 186 HOH   ( 210 )  A      O
 186 HOH   ( 218 )  A      O
 186 HOH   ( 219 )  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.

  43 GLN   (  45-)  A
 124 HIS   ( 126-)  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.

  40 ASP   (  42-)  A      N
  46 ARG   (  48-)  A      NE
  73 GLY   (  75-)  A      N
  76 GLY   (  78-)  A      N
 137 TYR   ( 139-)  A      N
 175 VAL   ( 177-)  A      N

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.

  16 GLU   (  18-)  A      OE2
  22 ASP   (  24-)  A      OD2

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 :  -0.073
  2nd generation packing quality :  -0.290
  Ramachandran plot appearance   :  -1.568
  chi-1/chi-2 rotamer normality  :  -2.306
  Backbone conformation          :   0.994

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.348 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   0.210 (tight)
  Side chain planarity           :   0.238 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   0.974

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.348 (tight)
  Bond angles                    :   0.621 (tight)
  Omega angle restraints         :   0.210 (tight)
  Side chain planarity           :   0.238 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   0.974
==============

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.