WHAT IF Check report

This file was created 2012-01-25 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 pdb2f4e.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.518
CA-only RMS fit for the two chains : 1.139

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   6 LYS   (  39-)  A      CG
   6 LYS   (  39-)  A      CD
   6 LYS   (  39-)  A      CE
   6 LYS   (  39-)  A      NZ
 137 LYS   (  39-)  B      CG
 137 LYS   (  39-)  B      CD
 137 LYS   (  39-)  B      CE
 137 LYS   (  39-)  B      NZ

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

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 lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 132 GLY   (  34-)  B      N    CA    1.52    4.4

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.

  47 ASN   (  80-)  A      N    CA   C   122.41    4.0
 119 GLU   ( 152-)  A      N    CA   C    98.81   -4.4
 140 SER   (  42-)  B     -C    N    CA  114.17   -4.2
 140 SER   (  42-)  B      N    CA   C   130.20    6.8
 181 HIS   (  83-)  B      CG   ND1  CE1 109.82    4.2

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.

 140 SER   (  42-)  B    7.09
 119 GLU   ( 152-)  A    4.58
 250 GLU   ( 152-)  B    4.01

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.

 165 TYR   (  67-)  B    -2.9
  34 TYR   (  67-)  A    -2.8
 170 LEU   (  72-)  B    -2.7
 141 GLU   (  43-)  B    -2.6
  39 LEU   (  72-)  A    -2.6
 140 SER   (  42-)  B    -2.5
 108 PRO   ( 141-)  A    -2.4
  49 GLN   (  82-)  A    -2.4
 178 ASN   (  80-)  B    -2.3
 136 PRO   (  38-)  B    -2.3
 155 LYS   (  57-)  B    -2.2
  53 GLU   (  86-)  A    -2.2
 247 LEU   ( 149-)  B    -2.1
 190 GLN   (  92-)  B    -2.1
 193 ILE   (  95-)  B    -2.1
 184 GLU   (  86-)  B    -2.0
 181 HIS   (  83-)  B    -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 ASN   (  35-)  A  Poor phi/psi
  34 TYR   (  67-)  A  Poor phi/psi
  48 SER   (  81-)  A  Poor phi/psi
  49 GLN   (  82-)  A  Poor phi/psi
  98 ALA   ( 131-)  A  Poor phi/psi
 107 PHE   ( 140-)  A  PRO omega poor
 139 ASP   (  41-)  B  Poor phi/psi
 140 SER   (  42-)  B  Poor phi/psi
 141 GLU   (  43-)  B  Poor phi/psi
 165 TYR   (  67-)  B  Poor phi/psi
 180 GLN   (  82-)  B  Poor phi/psi
 229 ALA   ( 131-)  B  Poor phi/psi
 238 PHE   ( 140-)  B  Poor phi/psi, PRO omega poor
 chi-1/chi-2 correlation Z-score : -2.481

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   8 ASP   (  41-)  A      0
   9 SER   (  42-)  A      0
  10 GLU   (  43-)  A      0
  17 LYS   (  50-)  A      0
  18 VAL   (  51-)  A      0
  27 HIS   (  60-)  A      0
  33 LYS   (  66-)  A      0
  34 TYR   (  67-)  A      0
  40 HIS   (  73-)  A      0
  47 ASN   (  80-)  A      0
  48 SER   (  81-)  A      0
  49 GLN   (  82-)  A      0
  51 LYS   (  84-)  A      0
  52 PHE   (  85-)  A      0
  53 GLU   (  86-)  A      0
  60 GLN   (  93-)  A      0
  66 LEU   (  99-)  A      0
  85 SER   ( 118-)  A      0
  97 LEU   ( 130-)  A      0
  98 ALA   ( 131-)  A      0
  99 TYR   ( 132-)  A      0
 101 LYS   ( 134-)  A      0
 104 ASN   ( 137-)  A      0
 105 PHE   ( 138-)  A      0
 106 SER   ( 139-)  A      0
And so on for a total of 117 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 : 1.431

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 239 PRO   ( 141-)  B   -56.4 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  46 LYS   (  79-)  A      NZ  <->   92 HIS   ( 125-)  A      ND1    0.47    2.53  INTRA
   9 SER   (  42-)  A      O   <->   21 GLN   (  54-)  A      NE2    0.37    2.33  INTRA BF
 140 SER   (  42-)  B      CB  <->  141 GLU   (  43-)  B      N      0.25    2.45  INTRA BF
 219 ARG   ( 121-)  B      NE  <->  252 GLU   ( 154-)  B      OE1    0.16    2.54  INTRA BF
 235 ASN   ( 137-)  B      N   <->  241 VAL   ( 143-)  B      O      0.14    2.56  INTRA BL
 187 TRP   (  89-)  B      O   <->  190 GLN   (  92-)  B      N      0.14    2.56  INTRA BL
 168 CYS   (  70-)  B      N   <->  195 LEU   (  97-)  B      O      0.12    2.58  INTRA BL
  51 LYS   (  84-)  A      NZ  <->   54 ASP   (  87-)  A      OD2    0.10    2.60  INTRA BL
  48 SER   (  81-)  A      N   <->   49 GLN   (  82-)  A      N      0.10    2.50  INTRA BF
 181 HIS   (  83-)  B      CE1 <->  183 PHE   (  85-)  B      CB     0.10    3.10  INTRA BF
  38 PHE   (  71-)  A      O   <->  123 ILE   ( 156-)  A      N      0.10    2.60  INTRA BL
 211 VAL   ( 113-)  B      O   <->  214 MET   ( 116-)  B      N      0.10    2.60  INTRA BL
 235 ASN   ( 137-)  B      ND2 <->  239 PRO   ( 141-)  B      O      0.10    2.60  INTRA BL
 189 GLU   (  91-)  B      C   <->  190 GLN   (  92-)  B      CG     0.09    3.01  INTRA BF
 217 GLY   ( 119-)  B      N   <->  253 VAL   ( 155-)  B      O      0.08    2.62  INTRA BL
 185 ASP   (  87-)  B      OD1 <->  188 HIS   (  90-)  B      N      0.07    2.63  INTRA BF
 251 VAL   ( 153-)  B      CG1 <->  252 GLU   ( 154-)  B      N      0.07    2.93  INTRA BL
  20 LYS   (  53-)  A      CG  <->   21 GLN   (  54-)  A      N      0.06    2.94  INTRA BL
 143 GLU   (  45-)  B      N   <->  151 LYS   (  53-)  B      O      0.06    2.64  INTRA BF
  92 HIS   ( 125-)  A      CB  <->  244 MET   ( 146-)  B      SD     0.05    3.35  INTRA
  15 ASP   (  48-)  A      CG  <->   16 GLU   (  49-)  A      N      0.05    2.95  INTRA BF
  63 GLU   (  96-)  A      OE2 <->  259 HOH   ( 198 )  A      O      0.05    2.35  INTRA BF
 135 PRO   (  37-)  B      CG  <->  180 GLN   (  82-)  B      NE2    0.05    3.05  INTRA BF
 204 LEU   ( 106-)  B      N   <->  205 ALA   ( 107-)  B      N      0.04    2.56  INTRA BL
   1 GLY   (  34-)  A      N   <->   42 ARG   (  75-)  A      NH2    0.03    2.82  INTRA BF
 211 VAL   ( 113-)  B      C   <->  213 SER   ( 115-)  B      N      0.03    2.87  INTRA BL
 172 TYR   (  74-)  B      N   <->  186 THR   (  88-)  B      OG1    0.03    2.67  INTRA BL
  20 LYS   (  53-)  A      NZ  <->   82 SER   ( 115-)  A      OG     0.03    2.67  INTRA BL
 176 THR   (  78-)  B      O   <->  180 GLN   (  82-)  B      N      0.03    2.67  INTRA BF
  93 VAL   ( 126-)  A      C   <->  244 MET   ( 146-)  B      CE     0.03    3.17  INTRA BF
  98 ALA   ( 131-)  A      CB  <->   99 TYR   ( 132-)  A      N      0.03    2.67  INTRA BL
  91 VAL   ( 124-)  A      N   <->  118 TYR   ( 151-)  A      O      0.03    2.67  INTRA BL
 118 TYR   ( 151-)  A      OH  <->  259 HOH   ( 182 )  A      O      0.03    2.37  INTRA BL
 229 ALA   ( 131-)  B      CB  <->  230 TYR   ( 132-)  B      N      0.03    2.67  INTRA BL
 152 GLN   (  54-)  B      OE1 <->  223 HIS   ( 125-)  B      NE2    0.02    2.68  INTRA BL
   2 ASN   (  35-)  A      N   <->    3 VAL   (  36-)  A      N      0.02    2.58  INTRA BF
 120 VAL   ( 153-)  A      CG2 <->  121 GLU   ( 154-)  A      N      0.02    2.98  INTRA BL
 207 LEU   ( 109-)  B      O   <->  211 VAL   ( 113-)  B      N      0.02    2.68  INTRA BL
 151 LYS   (  53-)  B      CG  <->  152 GLN   (  54-)  B      N      0.02    2.98  INTRA BL
 211 VAL   ( 113-)  B      O   <->  213 SER   ( 115-)  B      N      0.01    2.69  INTRA BL
   7 VAL   (  40-)  A      O   <->   21 GLN   (  54-)  A      NE2    0.01    2.69  INTRA BF
 146 ASP   (  48-)  B      CG  <->  147 GLU   (  49-)  B      N      0.01    2.99  INTRA BF
 171 HIS   (  73-)  B      ND1 <->  186 THR   (  88-)  B      OG1    0.01    2.69  INTRA BL
 104 ASN   ( 137-)  A      N   <->  110 VAL   ( 143-)  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.

 107 PHE   ( 140-)  A      -7.50
 238 PHE   ( 140-)  B      -7.37
 105 PHE   ( 138-)  A      -6.25
 130 GLU   ( 163-)  A      -6.10
 101 LYS   ( 134-)  A      -5.70
 134 VAL   (  36-)  B      -5.13
   3 VAL   (  36-)  A      -5.06
 129 LYS   ( 162-)  A      -5.05
 165 TYR   (  67-)  B      -5.01

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 129 LYS   ( 162-)  A       131 - GLY    164- ( A)         -5.17

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

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.

 229 ALA   ( 131-)  B   -2.68

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.

  50 HIS   (  83-)  A
 133 ASN   (  35-)  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.

  49 GLN   (  82-)  A      NE2
 140 SER   (  42-)  B      N
 147 GLU   (  49-)  B      N
 182 LYS   (  84-)  B      N
 187 TRP   (  89-)  B      NE1
 200 GLU   ( 102-)  B      N
 216 SER   ( 118-)  B      N

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  53 GLU   (  86-)  A   H-bonding suggests Gln
 130 GLU   ( 163-)  A   H-bonding suggests Gln

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 :  -0.755
  2nd generation packing quality :  -1.654
  Ramachandran plot appearance   :  -2.661
  chi-1/chi-2 rotamer normality  :  -2.481
  Backbone conformation          :  -0.760

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.381 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   0.260 (tight)
  Side chain planarity           :   0.285 (tight)
  Improper dihedral distribution :   0.666
  B-factor distribution          :   0.502
  Inside/Outside distribution    :   1.116

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 : 2.32


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.381 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   0.260 (tight)
  Side chain planarity           :   0.285 (tight)
  Improper dihedral distribution :   0.666
  B-factor distribution          :   0.502
  Inside/Outside distribution    :   1.116
==============

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.