WHAT IF Check report

This file was created 2012-01-19 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1zsa.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.

   1 HIS   (   4-)  A  -   CG
   1 HIS   (   4-)  A  -   ND1
   1 HIS   (   4-)  A  -   CD2
   1 HIS   (   4-)  A  -   CE1
   1 HIS   (   4-)  A  -   NE2
 257 LYS   ( 261-)  A  -   CB
 257 LYS   ( 261-)  A  -   CG
 257 LYS   ( 261-)  A  -   CD
 257 LYS   ( 261-)  A  -   CE
 257 LYS   ( 261-)  A  -   NZ

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: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  61 HIS   (  64-)  A    0.62

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.19

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.505 over 1853 bonds
Average difference in B over a bond : 2.93
RMS difference in B over a bond : 3.81

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 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.

  64 ASN   (  67-)  A      C    CA   CB  102.48   -4.0
 204 THR   ( 208-)  A      N    CA   C    95.20   -5.7
 257 LYS   ( 261-)  A      N    CA   C    98.87   -4.4

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.

 204 THR   ( 208-)  A    6.01
 257 LYS   ( 261-)  A    4.79
 124 TYR   ( 128-)  A    4.26

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 : 1.678

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.

  39 PRO   (  42-)  A    -2.6
  47 SER   (  50-)  A    -2.3
 163 ILE   ( 167-)  A    -2.2
 147 GLY   ( 151-)  A    -2.1
  89 GLN   (  92-)  A    -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.

  26 SER   (  29-)  A  PRO omega poor
  61 HIS   (  64-)  A  Poor phi/psi
 108 LYS   ( 111-)  A  Poor phi/psi
 197 PRO   ( 201-)  A  PRO omega poor
 239 ASP   ( 243-)  A  Poor phi/psi
 248 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.753

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!

   4 TYR   (   7-)  A      0
   7 HIS   (  10-)  A      0
  16 ASP   (  19-)  A      0
  17 PHE   (  20-)  A      0
  21 LYS   (  24-)  A      0
  24 ARG   (  27-)  A      0
  26 SER   (  29-)  A      0
  47 SER   (  50-)  A      0
  49 ASP   (  52-)  A      0
  51 ALA   (  54-)  A      0
  54 LEU   (  57-)  A      0
  59 ASN   (  62-)  A      0
  61 HIS   (  64-)  A      0
  69 ASP   (  72-)  A      0
  70 SER   (  73-)  A      0
  72 ASP   (  75-)  A      0
  73 LYS   (  76-)  A      0
  77 LYS   (  80-)  A      0
  80 PRO   (  83-)  A      0
  82 ASP   (  85-)  A      0
  89 GLN   (  92-)  A      0
 100 GLN   ( 103-)  A      0
 104 HIS   ( 107-)  A      0
 108 LYS   ( 111-)  A      0
 112 ALA   ( 115-)  A      0
And so on for a total of 113 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 : 1.830

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]

 151 PRO   ( 155-)  A    0.47 HIGH
 197 PRO   ( 201-)  A    0.47 HIGH

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.

   5 GLY   (   8-)  A      O   <->    9 GLY   (  12-)  A      N      0.24    2.46  INTRA
 164 LYS   ( 168-)  A      NZ  <->  258 HOH   ( 323 )  A      O      0.24    2.46  INTRA BF
 126 ASP   ( 130-)  A      OD2 <->  129 LYS   ( 133-)  A      NZ     0.19    2.51  INTRA
  12 HIS   (  15-)  A      ND1 <->   15 LYS   (  18-)  A      NZ     0.19    2.81  INTRA
 157 VAL   ( 161-)  A      CG1 <->  221 LYS   ( 225-)  A      CD     0.16    3.04  INTRA
  45 SER   (  48-)  A      N   <->   77 LYS   (  80-)  A      O      0.13    2.57  INTRA
 104 HIS   ( 107-)  A      ND1 <->  114 GLN   ( 117-)  A      NE2    0.13    2.87  INTRA BL
 121 ASN   ( 124-)  A      N   <->  136 GLY   ( 140-)  A      O      0.12    2.58  INTRA
  93 HIS   (  96-)  A      NE2 <->  258 HOH   ( 327 )  A      O      0.11    2.59  INTRA BL
  24 ARG   (  27-)  A      NH2 <->  203 VAL   ( 207-)  A      O      0.10    2.60  INTRA BL
 154 GLN   ( 158-)  A      NE2 <->  157 VAL   ( 161-)  A      CG1    0.08    3.02  INTRA BL
  54 LEU   (  57-)  A      O   <->  172 PHE   ( 176-)  A      N      0.06    2.64  INTRA
  71 GLN   (  74-)  A      O   <->   73 LYS   (  76-)  A      N      0.06    2.64  INTRA
 196 THR   ( 200-)  A      O   <->  199 LEU   ( 203-)  A      N      0.06    2.64  INTRA
 114 GLN   ( 117-)  A      NE2 <->  116 HIS   ( 119-)  A      NE2    0.06    2.94  INTRA BL
 203 VAL   ( 207-)  A      CG1 <->  204 THR   ( 208-)  A      N      0.06    2.94  INTRA BL
 150 LYS   ( 154-)  A      O   <->  218 GLN   ( 222-)  A      NE2    0.05    2.65  INTRA BL
  94 TRP   (  97-)  A      NE1 <->  237 MET   ( 241-)  A      O      0.05    2.65  INTRA BL
  26 SER   (  29-)  A      O   <->  242 ARG   ( 246-)  A      NH1    0.05    2.65  INTRA BL
   8 ASN   (  11-)  A      N   <->    9 GLY   (  12-)  A      N      0.04    2.56  INTRA B3
 216 SER   ( 220-)  A      O   <->  220 LEU   ( 224-)  A      N      0.04    2.66  INTRA
  29 ASP   (  32-)  A      OD1 <->  108 LYS   ( 111-)  A      N      0.04    2.66  INTRA
 228 ASN   ( 232-)  A      OD1 <->  235 GLU   ( 239-)  A      N      0.03    2.67  INTRA
 123 LYS   ( 127-)  A      N   <->  124 TYR   ( 128-)  A      N      0.03    2.57  INTRA BL
  91 HIS   (  94-)  A      NE2 <->  258 HOH   ( 327 )  A      O      0.03    2.67  INTRA BL
  69 ASP   (  72-)  A      OD2 <->  120 TRP   ( 123-)  A      NE1    0.02    2.68  INTRA BL
  58 ASN   (  61-)  A      OD1 <->   60 GLY   (  63-)  A      N      0.02    2.68  INTRA BL
   2 TRP   (   5-)  A      CE3 <->   13 TRP   (  16-)  A      CZ2    0.02    3.18  INTRA BL
  36 LYS   (  39-)  A      CB  <->  251 GLN   ( 255-)  A      NE2    0.02    3.08  INTRA
  27 PRO   (  30-)  A      O   <->  245 GLN   ( 249-)  A      N      0.02    2.68  INTRA BL
  17 PHE   (  20-)  A      CA  <->   18 PRO   (  21-)  A      CD     0.02    2.78  INTRA BL
  54 LEU   (  57-)  A      N   <->   66 GLU   (  69-)  A      O      0.01    2.69  INTRA
  70 SER   (  73-)  A      N   <->   71 GLN   (  74-)  A      N      0.01    2.59  INTRA B3
  89 GLN   (  92-)  A      O   <->  118 VAL   ( 121-)  A      N      0.01    2.69  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

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.

   7 HIS   (  10-)  A      -5.98
  97 LEU   ( 100-)  A      -5.39

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.

 258 HOH   ( 333 )  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.

 100 GLN   ( 103-)  A
 251 GLN   ( 255-)  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.

  28 VAL   (  31-)  A      N
  41 LEU   (  44-)  A      N
  50 GLN   (  53-)  A      N
  71 GLN   (  74-)  A      N
  79 GLY   (  82-)  A      N
  97 LEU   ( 100-)  A      N
 101 GLY   ( 104-)  A      N
 114 GLN   ( 117-)  A      NE2
 160 LEU   ( 164-)  A      N
 165 THR   ( 169-)  A      OG1
 178 ARG   ( 182-)  A      N
 178 ARG   ( 182-)  A      NE
 190 TYR   ( 194-)  A      OH
 196 THR   ( 200-)  A      N
 200 LEU   ( 204-)  A      N
 223 ARG   ( 227-)  A      NH2
 226 ASN   ( 230-)  A      ND2
 228 ASN   ( 232-)  A      N
 229 GLY   ( 233-)  A      N
 256 PHE   ( 260-)  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.

 116 HIS   ( 119-)  A      NE2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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 :  -0.434
  2nd generation packing quality :  -0.020
  Ramachandran plot appearance   :  -2.702
  chi-1/chi-2 rotamer normality  :  -2.753
  Backbone conformation          :  -0.997

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.577 (tight)
  Bond angles                    :   0.849
  Omega angle restraints         :   0.333 (tight)
  Side chain planarity           :   0.626 (tight)
  Improper dihedral distribution :   1.140
  B-factor distribution          :   1.505 (loose)
  Inside/Outside distribution    :   0.950

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 :   0.5
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.577 (tight)
  Bond angles                    :   0.849
  Omega angle restraints         :   0.333 (tight)
  Side chain planarity           :   0.626 (tight)
  Improper dihedral distribution :   1.140
  B-factor distribution          :   1.505 (loose)
  Inside/Outside distribution    :   0.950
==============

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.