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 pdb1xq0.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 261 4TR   ( 270-)  A  -         Fragmented

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.

  37 LYS   (  39-)  A  -   CE
  37 LYS   (  39-)  A  -   NZ
  43 LYS   (  45-)  A  -   CE
  43 LYS   (  45-)  A  -   NZ
  51 GLN   (  53-)  A  -   CG
  51 GLN   (  53-)  A  -   CD
  51 GLN   (  53-)  A  -   OE1
  51 GLN   (  53-)  A  -   NE2
  78 LYS   (  80-)  A  -   NZ
 109 LYS   ( 111-)  A  -   CE
 109 LYS   ( 111-)  A  -   NZ
 124 LYS   ( 127-)  A  -   CE
 124 LYS   ( 127-)  A  -   NZ
 130 LYS   ( 133-)  A  -   CE
 130 LYS   ( 133-)  A  -   NZ
 156 LYS   ( 159-)  A  -   CE
 156 LYS   ( 159-)  A  -   NZ
 165 LYS   ( 168-)  A  -   CE
 165 LYS   ( 168-)  A  -   NZ
 210 LYS   ( 213-)  A  -   CE
 210 LYS   ( 213-)  A  -   NZ
 222 LYS   ( 225-)  A  -   CE
 222 LYS   ( 225-)  A  -   NZ
 225 LYS   ( 228-)  A  -   CD
 225 LYS   ( 228-)  A  -   CE
 225 LYS   ( 228-)  A  -   NZ
 252 GLN   ( 255-)  A  -   CD
 252 GLN   ( 255-)  A  -   OE1
 252 GLN   ( 255-)  A  -   NE2

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: 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) :298.000

Note: B-factor plot

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

Chain identifier: A

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.

  39 ASP   (  41-)  A
 240 ASP   ( 243-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 115 GLU   ( 117-)  A
 235 GLU   ( 238-)  A
 236 GLU   ( 239-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.246
RMS-deviation in bond distances: 0.006

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.644
RMS-deviation in bond angles: 1.382

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.

  39 ASP   (  41-)  A
 115 GLU   ( 117-)  A
 235 GLU   ( 238-)  A
 236 GLU   ( 239-)  A
 240 ASP   ( 243-)  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.

 204 VAL   ( 207-)  A    4.02

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.

  81 PRO   (  83-)  A    -2.6
 173 PHE   ( 176-)  A    -2.4
  90 GLN   (  92-)  A    -2.3
 160 VAL   ( 163-)  A    -2.1
  98 LEU   ( 100-)  A    -2.1
 148 GLY   ( 151-)  A    -2.0
 104 GLU   ( 106-)  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.

   2 HIS   (   4-)  A  Poor phi/psi
  27 SER   (  29-)  A  PRO omega poor
  63 ALA   (  65-)  A  Poor phi/psi
  73 ASP   (  75-)  A  Poor phi/psi
  74 LYS   (  76-)  A  Poor phi/psi
 109 LYS   ( 111-)  A  Poor phi/psi
 175 ASN   ( 178-)  A  Poor phi/psi
 198 PRO   ( 201-)  A  PRO omega poor
 200 LEU   ( 203-)  A  Poor phi/psi
 240 ASP   ( 243-)  A  Poor phi/psi
 249 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.081

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!

   3 TRP   (   5-)  A      0
   5 TYR   (   7-)  A      0
   8 HIS   (  10-)  A      0
  17 ASP   (  19-)  A      0
  18 PHE   (  20-)  A      0
  22 LYS   (  24-)  A      0
  25 ARG   (  27-)  A      0
  26 GLN   (  28-)  A      0
  27 SER   (  29-)  A      0
  48 SER   (  50-)  A      0
  52 ALA   (  54-)  A      0
  56 ARG   (  58-)  A      0
  60 ASN   (  62-)  A      0
  62 HIS   (  64-)  A      0
  63 ALA   (  65-)  A      0
  64 PHE   (  66-)  A      0
  70 ASP   (  72-)  A      0
  71 SER   (  73-)  A      0
  72 GLN   (  74-)  A      0
  73 ASP   (  75-)  A      0
  74 LYS   (  76-)  A      0
  75 ALA   (  77-)  A      0
  78 LYS   (  80-)  A      0
  81 PRO   (  83-)  A      0
  83 ASP   (  85-)  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 : 1.491

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.

  13 HIS   (  15-)  A      ND1 <->   16 LYS   (  18-)  A      NZ     0.19    2.81  INTRA BL
  65 ASN   (  67-)  A      ND2 <->  262 HOH   ( 441 )  A      O      0.18    2.52  INTRA
  76 VAL   (  78-)  A      CG2 <->   78 LYS   (  80-)  A      NZ     0.10    3.00  INTRA
 196 THR   ( 199-)  A      OG1 <->  261 4TR   ( 270-)  A      N1     0.09    2.61  INTRA BL
   1 HIS   (   3-)  A      N   <->  262 HOH   ( 310 )  A      O      0.09    2.61  INTRA BF
 249 LYS   ( 252-)  A      NZ  <->  262 HOH   ( 389 )  A      O      0.08    2.62  INTRA
 105 HIS   ( 107-)  A      NE2 <->  191 TYR   ( 194-)  A      OH     0.07    2.63  INTRA BL
 177 ASP   ( 180-)  A      OD2 <->  179 ARG   ( 182-)  A      NH2    0.07    2.63  INTRA
  92 HIS   (  94-)  A      ND1 <->  262 HOH   ( 441 )  A      O      0.06    2.64  INTRA
 165 LYS   ( 168-)  A      NZ  <->  225 LYS   ( 228-)  A      O      0.06    2.64  INTRA BL
  74 LYS   (  76-)  A      CB  <->   75 ALA   (  77-)  A      N      0.06    2.64  INTRA BF
 195 LEU   ( 198-)  A      CD2 <->  261 4TR   ( 270-)  A     BR      0.04    3.16  INTRA
  26 GLN   (  28-)  A      NE2 <->  243 ARG   ( 246-)  A      NH1    0.04    2.81  INTRA BL
  25 ARG   (  27-)  A      C   <->  251 ARG   ( 254-)  A      NH1    0.04    3.06  INTRA BL
 165 LYS   ( 168-)  A      CE  <->  227 ASN   ( 230-)  A      ND2    0.04    3.06  INTRA
 249 LYS   ( 252-)  A      CB  <->  250 ASN   ( 253-)  A      N      0.03    2.67  INTRA B3
  72 GLN   (  74-)  A      C   <->   74 LYS   (  76-)  A      N      0.02    2.88  INTRA BF
  49 TYR   (  51-)  A      OH  <->  120 HIS   ( 122-)  A      NE2    0.02    2.68  INTRA BL
  72 GLN   (  74-)  A      O   <->   74 LYS   (  76-)  A      N      0.02    2.68  INTRA BF
  65 ASN   (  67-)  A      ND2 <->  262 HOH   ( 298 )  A      O      0.02    2.68  INTRA
   2 HIS   (   4-)  A      CD2 <->    3 TRP   (   5-)  A      N      0.02    2.98  INTRA BF
  63 ALA   (  65-)  A      CA  <->  238 MET   ( 241-)  A      SD     0.01    3.39  INTRA BL
 115 GLU   ( 117-)  A      OE2 <->  117 HIS   ( 119-)  A      NE2    0.01    2.69  INTRA BL
   1 HIS   (   3-)  A      N   <->    2 HIS   (   4-)  A      N      0.01    2.59  INTRA BF

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.

   8 HIS   (  10-)  A      -5.95
   2 HIS   (   4-)  A      -5.43
 133 GLN   ( 136-)  A      -5.02

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: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 247 PRO   ( 250-)  A     -  250 ASN   ( 253-)  A        -1.85

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: 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.

   1 HIS   (   3-)  A
   2 HIS   (   4-)  A
  26 GLN   (  28-)  A
  65 ASN   (  67-)  A
  72 GLN   (  74-)  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.

  29 VAL   (  31-)  A      N
  98 LEU   ( 100-)  A      N
 127 ASP   ( 130-)  A      N
 162 ASP   ( 165-)  A      N
 165 LYS   ( 168-)  A      N
 197 THR   ( 200-)  A      N
 201 LEU   ( 204-)  A      N
 230 GLY   ( 233-)  A      N
 242 TRP   ( 245-)  A      N
 257 PHE   ( 260-)  A      N
Only metal coordination for   62 HIS  (  64-) A      NE2
Only metal coordination for   92 HIS  (  94-) A      NE2
Only metal coordination for   94 HIS  (  96-) A      NE2
Only metal coordination for  117 HIS  ( 119-) A      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 259  ZN   ( 262-)  A   -.-  -.-  Too few ligands (1)
 260  ZN   ( 263-)  A   -.-  -.-  Too few ligands (2)

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 262 HOH   ( 275 )  A      O  0.99  K  4

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.

 159 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.491
  2nd generation packing quality :   0.016
  Ramachandran plot appearance   :  -1.486
  chi-1/chi-2 rotamer normality  :   0.081
  Backbone conformation          :  -0.911

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.246 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.271 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.580
  B-factor distribution          :   0.760
  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 : 1.76


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.246 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.271 (tight)
  Side chain planarity           :   0.219 (tight)
  Improper dihedral distribution :   0.580
  B-factor distribution          :   0.760
  Inside/Outside distribution    :   0.957
==============

WHAT IF
    G.Vriend,
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    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,
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      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.