WHAT IF Check report

This file was created 2011-12-21 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 pdb14gs.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 391 MES   ( 210-)  A  -
 392 MES   ( 210-)  B  -

Administrative problems that can generate validation failures

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone 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. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  35 TYR   (  49-)  A  -   N
  35 TYR   (  49-)  A  -   CA
  35 TYR   (  49-)  A  -   C
  35 TYR   (  49-)  A  -   O
 229 TYR   (  49-)  B  -   N
 229 TYR   (  49-)  B  -   CA
 229 TYR   (  49-)  B  -   C
 229 TYR   (  49-)  B  -   O

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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  34 VAL   (  35-)  A    High
 227 THR   (  34-)  B    High
 228 VAL   (  35-)  B    High

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) :288.000

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 : 1.591 over 2717 bonds
Average difference in B over a bond : 3.95
RMS difference in B over a bond : 5.29

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Geometric checks

Warning: Unusual bond 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.

 250 HIS   (  71-)  B      CG   ND1  CE1 109.63    4.0

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.

  43 GLY   (  58-)  A    4.19
 237 GLY   (  58-)  B    4.08

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.

 366 PRO   ( 187-)  B    -3.1
 172 PRO   ( 187-)  A    -3.1
 258 TYR   (  79-)  B    -2.9
  64 TYR   (  79-)  A    -2.9
   6 TYR   (   7-)  A    -2.8
 200 TYR   (   7-)  B    -2.8
 224 GLU   (  31-)  B    -2.4
  30 GLU   (  31-)  A    -2.4
 205 GLY   (  12-)  B    -2.3
  11 GLY   (  12-)  A    -2.3
 255 LEU   (  76-)  B    -2.2
  61 LEU   (  76-)  A    -2.2
 320 THR   ( 141-)  B    -2.2
 126 THR   ( 141-)  A    -2.2
   8 PRO   (   9-)  A    -2.1
 202 PRO   (   9-)  B    -2.1
 322 ILE   ( 143-)  B    -2.0
 128 ILE   ( 143-)  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.

   8 PRO   (   9-)  A  Poor phi/psi
  11 GLY   (  12-)  A  Poor phi/psi
  37 LEU   (  52-)  A  PRO omega poor
  49 GLN   (  64-)  A  Poor phi/psi
  94 THR   ( 109-)  A  Poor phi/psi
 126 THR   ( 141-)  A  Poor phi/psi
 172 PRO   ( 187-)  A  Poor phi/psi
 202 PRO   (   9-)  B  Poor phi/psi
 205 GLY   (  12-)  B  Poor phi/psi
 231 LEU   (  52-)  B  PRO omega poor
 243 GLN   (  64-)  B  Poor phi/psi
 288 THR   ( 109-)  B  Poor phi/psi
 320 THR   ( 141-)  B  Poor phi/psi
 366 PRO   ( 187-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.842

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.

 162 SER   ( 177-)  A    0.37
 356 SER   ( 177-)  B    0.37

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!

   6 TYR   (   7-)  A      0
   7 PHE   (   8-)  A      0
   8 PRO   (   9-)  A      0
  10 ARG   (  11-)  A      0
  12 ARG   (  13-)  A      0
  13 CYS   (  14-)  A      0
  23 GLN   (  24-)  A      0
  33 THR   (  34-)  A      0
  34 VAL   (  35-)  A      0
  35 TYR   (  49-)  A      0
  36 GLN   (  51-)  A      0
  37 LEU   (  52-)  A      0
  38 PRO   (  53-)  A      0
  42 ASP   (  57-)  A      0
  44 ASP   (  59-)  A      0
  48 TYR   (  63-)  A      0
  49 GLN   (  64-)  A      0
  61 LEU   (  76-)  A      0
  63 LEU   (  78-)  A      0
  64 TYR   (  79-)  A      0
  66 LYS   (  81-)  A      0
  93 TYR   ( 108-)  A      0
  94 THR   ( 109-)  A      0
  95 ASN   ( 110-)  A      0
 122 GLN   ( 137-)  A      0
And so on for a total of 111 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 : 1.010

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.

 126 THR   ( 141-)  A      O   <->  167 ARG   ( 182-)  A      NH1    0.20    2.50  INTRA BF
 320 THR   ( 141-)  B      O   <->  361 ARG   ( 182-)  B      NH1    0.19    2.51  INTRA
   6 TYR   (   7-)  A      CD2 <->   13 CYS   (  14-)  A      SG     0.19    3.21  INTRA
 200 TYR   (   7-)  B      CD2 <->  207 CYS   (  14-)  B      SG     0.16    3.24  INTRA
   6 TYR   (   7-)  A      CG  <->   13 CYS   (  14-)  A      SG     0.15    3.25  INTRA
  60 THR   (  75-)  A      CG2 <->  262 GLN   (  83-)  B      NE2    0.14    2.96  INTRA BL
 112 LYS   ( 127-)  A      N   <->  113 PRO   ( 128-)  A      CD     0.13    2.87  INTRA
 200 TYR   (   7-)  B      CG  <->  207 CYS   (  14-)  B      SG     0.12    3.28  INTRA
 306 LYS   ( 127-)  B      N   <->  307 PRO   ( 128-)  B      CD     0.12    2.88  INTRA BL
  56 HIS   (  71-)  A      ND1 <->  393 HOH   ( 213 )  A      O      0.09    2.61  INTRA BL
 279 ARG   ( 100-)  B      NH2 <->  333 ASN   ( 154-)  B      ND2    0.06    2.79  INTRA BL
  85 ARG   ( 100-)  A      NH2 <->  139 ASN   ( 154-)  A      ND2    0.05    2.80  INTRA BL
  13 CYS   (  14-)  A      SG  <->   38 PRO   (  53-)  A      CB     0.03    3.37  INTRA
 207 CYS   (  14-)  B      SG  <->  232 PRO   (  53-)  B      CB     0.02    3.38  INTRA BF
  75 ASP   (  90-)  A      OD2 <->  253 ARG   (  74-)  B      NH2    0.02    2.68  INTRA BL
  15 ALA   (  16-)  A      N   <->  393 HOH   ( 211 )  A      O      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

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.

 319 LYS   ( 140-)  B      -5.76
 125 LYS   ( 140-)  A      -5.75
 122 GLN   ( 137-)  A      -5.65
 316 GLN   ( 137-)  B      -5.64
 260 LYS   (  81-)  B      -5.58
  66 LYS   (  81-)  A      -5.56

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: 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.

  23 GLN   (  24-)  A
 121 ASN   ( 136-)  A
 132 GLN   ( 147-)  A
 217 GLN   (  24-)  B
 315 ASN   ( 136-)  B
 326 GLN   ( 147-)  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.

   7 PHE   (   8-)  A      N
   9 VAL   (  10-)  A      N
  27 TRP   (  28-)  A      N
  35 TYR   (  49-)  A      OH
  37 LEU   (  52-)  A      N
  65 GLY   (  80-)  A      N
  78 ASN   (  93-)  A      ND2
 102 ASP   ( 117-)  A      N
 126 THR   ( 141-)  A      N
 126 THR   ( 141-)  A      OG1
 132 GLN   ( 147-)  A      N
 167 ARG   ( 182-)  A      NH1
 182 GLU   ( 197-)  A      N
 201 PHE   (   8-)  B      N
 203 VAL   (  10-)  B      N
 209 ALA   (  16-)  B      N
 229 TYR   (  49-)  B      OH
 231 LEU   (  52-)  B      N
 242 TYR   (  63-)  B      N
 253 ARG   (  74-)  B      NE
 253 ARG   (  74-)  B      NH2
 259 GLY   (  80-)  B      N
 272 ASN   (  93-)  B      ND2
 296 ASP   ( 117-)  B      N
 320 THR   ( 141-)  B      N
 321 PHE   ( 142-)  B      N
 323 VAL   ( 144-)  B      N
 326 GLN   ( 147-)  B      N
 361 ARG   ( 182-)  B      NH1
 376 GLU   ( 197-)  B      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.

  78 ASN   (  93-)  A      OD1
 250 HIS   (  71-)  B      ND1
 272 ASN   (  93-)  B      OD1
 336 ASP   ( 157-)  B      OD1

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.

  83 ASP   (  98-)  A   H-bonding suggests Asn
 101 ASP   ( 116-)  A   H-bonding suggests Asn
 137 ASP   ( 152-)  A   H-bonding suggests Asn
 156 ASP   ( 171-)  A   H-bonding suggests Asn
 277 ASP   (  98-)  B   H-bonding suggests Asn
 295 ASP   ( 116-)  B   H-bonding suggests Asn
 331 ASP   ( 152-)  B   H-bonding suggests Asn
 350 ASP   ( 171-)  B   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:

  1st generation packing quality :  -0.478
  2nd generation packing quality :  -0.762
  Ramachandran plot appearance   :  -2.087
  chi-1/chi-2 rotamer normality  :  -2.842
  Backbone conformation          :   0.185

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.302 (tight)
  Bond angles                    :   0.576 (tight)
  Omega angle restraints         :   0.184 (tight)
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.816
  B-factor distribution          :   1.591 (loose)
  Inside/Outside distribution    :   0.960

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.302 (tight)
  Bond angles                    :   0.576 (tight)
  Omega angle restraints         :   0.184 (tight)
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.816
  B-factor distribution          :   1.591 (loose)
  Inside/Outside distribution    :   0.960
==============

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.