WHAT IF Check report

This file was created 2011-12-17 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 pdb2nul.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 132 VAL   ( 132-)  A  -   CG1
 132 VAL   ( 132-)  A  -   CG2

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'.

  19 LYS   (  19-)  A      CE
  19 LYS   (  19-)  A      NZ
  25 LYS   (  25-)  A      CD
  25 LYS   (  25-)  A      CE
  25 LYS   (  25-)  A      NZ
  32 ARG   (  32-)  A      NH1
  32 ARG   (  32-)  A      NH2
  33 GLU   (  33-)  A      CG
  33 GLU   (  33-)  A      CD
  33 GLU   (  33-)  A      OE1
  33 GLU   (  33-)  A      OE2
  43 ARG   (  43-)  A      NH1
  43 ARG   (  43-)  A      NH2
  60 LYS   (  60-)  A      NZ
  66 GLU   (  66-)  A      CG
  66 GLU   (  66-)  A      CD
  66 GLU   (  66-)  A      OE1
  66 GLU   (  66-)  A      OE2
  69 LYS   (  69-)  A      CE
  69 LYS   (  69-)  A      NZ
  77 LYS   (  77-)  A      CE
  77 LYS   (  77-)  A      NZ
  80 ARG   (  80-)  A      NH1
  80 ARG   (  80-)  A      NH2
  87 ARG   (  87-)  A      NH1
  87 ARG   (  87-)  A      NH2
  89 GLN   (  89-)  A      CG
  89 GLN   (  89-)  A      CD
  89 GLN   (  89-)  A      OE1
  89 GLN   (  89-)  A      NE2
 106 ASP   ( 106-)  A      CG
 106 ASP   ( 106-)  A      OD1
 106 ASP   ( 106-)  A      OD2
 116 GLN   ( 116-)  A      CG
 116 GLN   ( 116-)  A      CD
 116 GLN   ( 116-)  A      OE1
 116 GLN   ( 116-)  A      NE2
 135 LYS   ( 135-)  A      CE
 135 LYS   ( 135-)  A      NZ
 143 ARG   ( 143-)  A      NH1
 143 ARG   ( 143-)  A      NH2
 148 GLN   ( 148-)  A      CG
 148 GLN   ( 148-)  A      CD
 148 GLN   ( 148-)  A      OE1
 148 GLN   ( 148-)  A      NE2
 153 GLU   ( 153-)  A      CG
 153 GLU   ( 153-)  A      CD
 153 GLU   ( 153-)  A      OE1
 153 GLU   ( 153-)  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) :291.000

Note: B-factor plot

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

Chain identifier: A

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.

   2 VAL   (   2-)  A      CA   CB    1.61    4.2
  13 ILE   (  13-)  A      CA   CB    1.63    5.1
 132 VAL   ( 132-)  A      CA   CB    1.63    4.9

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

 |  0.996342 -0.000812 -0.000470|
 | -0.000812  1.000294 -0.000951|
 | -0.000470 -0.000951  0.996105|
Proposed new scale matrix

 |  0.022453  0.000018  0.000011|
 |  0.000012  0.014659  0.000014|
 |  0.000005  0.000009  0.009842|
With corresponding cell

    A    =  44.537  B   =  68.219  C    = 101.602
    Alpha=  90.109  Beta=  90.054  Gamma=  90.093

The CRYST1 cell dimensions

    A    =  44.700  B   =  68.200  C    = 102.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 39.791
(Under-)estimated Z-score: 4.649

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.

  13 ILE   (  13-)  A      N    CA   CB  103.27   -4.3
  41 PHE   (  41-)  A      N    CA   C    99.14   -4.3
  43 ARG   (  43-)  A      CB   CG   CD  105.60   -4.2
 157 ILE   ( 157-)  A      N    CA   C    97.14   -5.0

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.

 132 VAL   ( 132-)  A    5.48
 157 ILE   ( 157-)  A    5.12
  41 PHE   (  41-)  A    4.55
 156 ILE   ( 156-)  A    4.03

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.695

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

  92 HIS   (  92-)  A      CB   4.95
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.752

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.

  49 MET   (  49-)  A    -2.3
  48 PHE   (  48-)  A    -2.2
 103 VAL   ( 103-)  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.

  38 ASN   (  38-)  A  Poor phi/psi
  54 GLY   (  54-)  A  Poor phi/psi
  59 MET   (  59-)  A  Poor phi/psi
  78 ASN   (  78-)  A  Poor phi/psi
  95 THR   (  95-)  A  Poor phi/psi
 117 GLY   ( 117-)  A  Poor phi/psi
 149 ASP   ( 149-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.915

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!

   8 HIS   (   8-)  A      0
  16 PHE   (  16-)  A      0
  17 ASP   (  17-)  A      0
  33 GLU   (  33-)  A      0
  35 PHE   (  35-)  A      0
  37 ASN   (  37-)  A      0
  38 ASN   (  38-)  A      0
  40 ILE   (  40-)  A      0
  41 PHE   (  41-)  A      0
  42 HIS   (  42-)  A      0
  43 ARG   (  43-)  A      0
  46 ASN   (  46-)  A      0
  48 PHE   (  48-)  A      0
  49 MET   (  49-)  A      0
  51 GLN   (  51-)  A      0
  57 PRO   (  57-)  A      0
  59 MET   (  59-)  A      0
  65 LYS   (  65-)  A      0
  66 GLU   (  66-)  A      0
  72 ALA   (  72-)  A      0
  74 ASN   (  74-)  A      0
  78 ASN   (  78-)  A      0
  79 THR   (  79-)  A      0
  80 ARG   (  80-)  A      0
  86 ALA   (  86-)  A      0
And so on for a total of 80 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 : 2.412

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].

  57 PRO   (  57-)  A   103.1 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.

  70 ASN   (  70-)  A      N   <->   92 HIS   (  92-)  A      CD2    0.19    2.91  INTRA
  56 GLU   (  56-)  A      CD  <->   60 LYS   (  60-)  A      CE     0.13    3.07  INTRA
   5 HIS   (   5-)  A      NE2 <->  161 THR   ( 161-)  A      OG1    0.13    2.57  INTRA BL
  42 HIS   (  42-)  A      CE1 <->  164 HOH   ( 189 )  A      O      0.12    2.68  INTRA
  42 HIS   (  42-)  A      CD2 <->  164 HOH   ( 169 )  A      O      0.06    2.74  INTRA BL
  88 THR   (  88-)  A      N   <->   93 SER   (  93-)  A      OG     0.06    2.64  INTRA
 112 GLY   ( 112-)  A      O   <->  114 SER   ( 114-)  A      N      0.05    2.65  INTRA
  74 ASN   (  74-)  A      N   <->   75 GLY   (  75-)  A      N      0.04    2.56  INTRA B3
  26 ASN   (  26-)  A      ND2 <->   95 THR   (  95-)  A      O      0.03    2.67  INTRA
  63 ALA   (  63-)  A      N   <->  164 HOH   ( 198 )  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

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

  89 GLN   (  89-)  A   -3.24
 103 VAL   ( 103-)  A   -2.96
 116 GLN   ( 116-)  A   -2.88
 148 GLN   ( 148-)  A   -2.64
 153 GLU   ( 153-)  A   -2.61
  72 ALA   (  72-)  A   -2.50

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 164 HOH   ( 184 )  A      O     31.86  -20.25   -4.97
 164 HOH   ( 229 )  A      O     13.56  -32.79  -28.18

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.

  42 HIS   (  42-)  A
  51 GLN   (  51-)  A
  70 ASN   (  70-)  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.

  70 ASN   (  70-)  A      N
 112 GLY   ( 112-)  A      N

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.

  17 ASP   (  17-)  A   H-bonding suggests Asn

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:

  2nd generation packing quality :  -1.011
  Ramachandran plot appearance   :  -1.752
  chi-1/chi-2 rotamer normality  :  -0.915
  Backbone conformation          :  -0.966

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.873
  Bond angles                    :   0.970
  Omega angle restraints         :   0.439 (tight)
  Side chain planarity           :   0.705
  Improper dihedral distribution :   1.327
  B-factor distribution          :   0.758
  Inside/Outside distribution    :   0.957

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 : 2.10

Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.873
  Bond angles                    :   0.970
  Omega angle restraints         :   0.439 (tight)
  Side chain planarity           :   0.705
  Improper dihedral distribution :   1.327
  B-factor distribution          :   0.758
  Inside/Outside distribution    :   0.957

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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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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
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Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
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Matthews' Coefficient
      Solvent content of Protein Crystals
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Protein side chain planarity
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    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
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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
    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.