WHAT IF Check report

This file was created 2011-12-18 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 pdb1z4w.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 50198.176
Volume of the Unit Cell V= 3050654.0
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.064
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.340

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.

 455 DAN   ( 601-)  A  -
 456 NDG   (   1-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 449 NAG   (   2-)  A  -   O4  bound to  450 NAG   (   3-)  A  -   C1
 451 NAG   (   4-)  A  -   O4  bound to  452 NAG   (   5-)  A  -   C1

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Nomenclature related problems

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.

   3 ASP   ( 120-)  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.

 172 PRO   ( 289-)  A      N    CA   C   100.81   -4.4

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.

   3 ASP   ( 120-)  A

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.

 172 PRO   ( 289-)  A    4.90
  13 PHE   ( 130-)  A    4.14

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.

 440 PRO   ( 557-)  A    -2.9
 174 THR   ( 291-)  A    -2.7
 379 ILE   ( 496-)  A    -2.7
 374 THR   ( 491-)  A    -2.7
  47 ILE   ( 164-)  A    -2.6
 236 PHE   ( 353-)  A    -2.4
 294 PRO   ( 411-)  A    -2.4
 325 ARG   ( 442-)  A    -2.3
 345 VAL   ( 462-)  A    -2.3
  60 THR   ( 177-)  A    -2.3
 324 PRO   ( 441-)  A    -2.3
 169 THR   ( 286-)  A    -2.2
 343 THR   ( 460-)  A    -2.1
  92 PHE   ( 209-)  A    -2.1
 109 SER   ( 226-)  A    -2.1
 100 TYR   ( 217-)  A    -2.1
 204 ASN   ( 321-)  A    -2.1
 407 GLY   ( 524-)  A    -2.0
 432 LEU   ( 549-)  A    -2.0
 151 ASP   ( 268-)  A    -2.0
  61 HIS   ( 178-)  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.

  47 ILE   ( 164-)  A  Poor phi/psi
  70 ASP   ( 187-)  A  Poor phi/psi
 103 ASP   ( 220-)  A  Poor phi/psi
 151 ASP   ( 268-)  A  Poor phi/psi
 165 ASP   ( 282-)  A  Poor phi/psi
 174 THR   ( 291-)  A  Poor phi/psi
 204 ASN   ( 321-)  A  Poor phi/psi
 238 ASN   ( 355-)  A  Poor phi/psi
 291 SER   ( 408-)  A  Poor phi/psi
 307 ASN   ( 424-)  A  Poor phi/psi
 323 VAL   ( 440-)  A  Poor phi/psi
 380 ASN   ( 497-)  A  Poor phi/psi
 405 ALA   ( 522-)  A  Poor phi/psi
 418 VAL   ( 535-)  A  Poor phi/psi
 432 LEU   ( 549-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.112

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   ( 123-)  A      0
  10 ILE   ( 127-)  A      0
  11 ASN   ( 128-)  A      0
  12 GLN   ( 129-)  A      0
  14 TYR   ( 131-)  A      0
  23 LEU   ( 140-)  A      0
  31 MET   ( 148-)  A      0
  34 PHE   ( 151-)  A      0
  46 ARG   ( 163-)  A      0
  47 ILE   ( 164-)  A      0
  48 PRO   ( 165-)  A      0
  56 HIS   ( 173-)  A      0
  61 HIS   ( 178-)  A      0
  66 ASN   ( 183-)  A      0
  68 CYS   ( 185-)  A      0
  69 GLN   ( 186-)  A      0
  70 ASP   ( 187-)  A      0
  71 HIS   ( 188-)  A      0
  72 VAL   ( 189-)  A      0
  80 MET   ( 197-)  A      0
  84 GLU   ( 201-)  A      0
  90 PHE   ( 207-)  A      0
  91 PRO   ( 208-)  A      0
  96 LEU   ( 213-)  A      0
 102 SER   ( 219-)  A      0
And so on for a total of 211 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 : 1.449

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!

  43 GLY   ( 160-)  A   1.55   22

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.

  22 ASN   ( 139-)  A      ND2 <->  456 NDG   (   1-)  A      C1     1.24    1.46  INTRA BF
  22 ASN   ( 139-)  A      CG  <->  456 NDG   (   1-)  A      C1     0.78    2.42  INTRA BF
 325 ARG   ( 442-)  A      NH2 <->  331 CYS   ( 448-)  A      O      0.42    2.28  INTRA BF
 211 MET   ( 328-)  A      CE  <->  321 GLN   ( 438-)  A      NE2    0.29    2.81  INTRA BF
  53 THR   ( 170-)  A      CG2 <->   54 LYS   ( 171-)  A      N      0.28    2.72  INTRA BL
 202 GLN   ( 319-)  A      CG  <->  265 ASN   ( 382-)  A      ND2    0.24    2.86  INTRA
 374 THR   ( 491-)  A      CG2 <->  377 GLN   ( 494-)  A      O      0.22    2.58  INTRA BF
 419 MET   ( 536-)  A      CB  <->  444 GLN   ( 561-)  A      NE2    0.21    2.89  INTRA BF
 378 ARG   ( 495-)  A      NH2 <->  455 DAN   ( 601-)  A      O1B    0.21    2.49  INTRA BL
 414 ASP   ( 531-)  A      O   <->  418 VAL   ( 535-)  A      N      0.21    2.49  INTRA
 201 ASN   ( 318-)  A      O   <->  205 LYS   ( 322-)  A      NZ     0.20    2.50  INTRA BF
 216 CYS   ( 333-)  A      SG  <->  337 CYS   ( 454-)  A      SG     0.19    3.26  INTRA BF
 251 ARG   ( 368-)  A      NH1 <->  253 ASP   ( 370-)  A      CG     0.19    2.91  INTRA BF
 103 ASP   ( 220-)  A      OD1 <->  107 ARG   ( 224-)  A      NH2    0.18    2.52  INTRA
 268 VAL   ( 385-)  A      CG1 <->  287 GLN   ( 404-)  A      NE2    0.16    2.94  INTRA
 268 VAL   ( 385-)  A      CG1 <->  269 LEU   ( 386-)  A      N      0.16    2.84  INTRA
  70 ASP   ( 187-)  A      OD1 <->   73 SER   ( 190-)  A      N      0.16    2.54  INTRA BF
 141 GLU   ( 258-)  A      OE2 <->  143 ARG   ( 260-)  A      NE     0.15    2.55  INTRA BF
  37 THR   ( 154-)  A      CG2 <->   38 ALA   ( 155-)  A      N      0.13    2.87  INTRA BL
  14 TYR   ( 131-)  A      O   <->  413 ARG   ( 530-)  A      NH2    0.13    2.57  INTRA
  97 LYS   ( 214-)  A      NZ  <->  151 ASP   ( 268-)  A      OD1    0.12    2.58  INTRA
  22 ASN   ( 139-)  A      O   <->  448 SER   ( 565-)  A      N      0.12    2.58  INTRA BF
 304 THR   ( 421-)  A      O   <->  311 SER   ( 428-)  A      N      0.11    2.59  INTRA BF
 395 GLN   ( 512-)  A      OE1 <->  443 ARG   ( 560-)  A      NH1    0.11    2.59  INTRA
 379 ILE   ( 496-)  A      CG2 <->  380 ASN   ( 497-)  A      CG     0.11    3.09  INTRA
And so on for a total of 62 lines.

Packing, accessibility and threading

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.

  69 GLN   ( 186-)  A      -6.75
  65 LEU   ( 182-)  A      -6.16
 432 LEU   ( 549-)  A      -5.91
 325 ARG   ( 442-)  A      -5.72
 397 PHE   ( 514-)  A      -5.64
 181 LEU   ( 298-)  A      -5.39
 164 LEU   ( 281-)  A      -5.26
  30 ASN   ( 147-)  A      -5.21
 251 ARG   ( 368-)  A      -5.03
 396 GLN   ( 513-)  A      -5.01

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.

   7 ILE   ( 124-)  A   -2.68

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.

   8 ASN   ( 125-)  A
 256 ASN   ( 373-)  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.

  23 LEU   ( 140-)  A      N
  30 ASN   ( 147-)  A      ND2
  34 PHE   ( 151-)  A      N
  40 THR   ( 157-)  A      N
  46 ARG   ( 163-)  A      NH2
  56 HIS   ( 173-)  A      N
  90 PHE   ( 207-)  A      N
  98 THR   ( 215-)  A      N
 106 ASN   ( 223-)  A      ND2
 128 GLN   ( 245-)  A      N
 163 VAL   ( 280-)  A      N
 170 LEU   ( 287-)  A      N
 195 GLY   ( 312-)  A      N
 237 GLY   ( 354-)  A      N
 251 ARG   ( 368-)  A      NH1
 254 LEU   ( 371-)  A      N
 258 CYS   ( 375-)  A      N
 293 TRP   ( 410-)  A      N
 293 TRP   ( 410-)  A      NE1
 295 MET   ( 412-)  A      N
 309 GLN   ( 426-)  A      N
 325 ARG   ( 442-)  A      NH2
 339 GLY   ( 456-)  A      N
 345 VAL   ( 462-)  A      N
 346 TYR   ( 463-)  A      N
 358 THR   ( 475-)  A      N
 366 THR   ( 483-)  A      N
 377 GLN   ( 494-)  A      N
 411 CYS   ( 528-)  A      N
 432 LEU   ( 549-)  A      N
 443 ARG   ( 560-)  A      NE
 443 ARG   ( 560-)  A      NH2

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.

 171 ASN   ( 288-)  A      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.

  70 ASP   ( 187-)  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:

  1st generation packing quality :  -0.361
  2nd generation packing quality :  -1.221
  Ramachandran plot appearance   :  -1.921
  chi-1/chi-2 rotamer normality  :  -2.112
  Backbone conformation          :  -0.275

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.307 (tight)
  Bond angles                    :   0.646 (tight)
  Omega angle restraints         :   0.263 (tight)
  Side chain planarity           :   0.265 (tight)
  Improper dihedral distribution :   0.649
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.031

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.307 (tight)
  Bond angles                    :   0.646 (tight)
  Omega angle restraints         :   0.263 (tight)
  Side chain planarity           :   0.265 (tight)
  Improper dihedral distribution :   0.649
  B-factor distribution          :   0.396
  Inside/Outside distribution    :   1.031
==============

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

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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
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Puckering parameters
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      A general definition of ring puckering coordinates
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Quality Control
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      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.