WHAT IF Check report

This file was created 2011-12-15 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 pdb3fko.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.

 344 FKO   ( 361-)  A  -

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 1

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  19 ARG   (  23-)  A
  66 ARG   (  70-)  A
 130 ARG   ( 136-)  A
 143 ARG   ( 149-)  A
 180 ARG   ( 189-)  A
 228 ARG   ( 237-)  A
 287 ARG   ( 296-)  A

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

   5 TYR   (   9-)  A
 173 TYR   ( 182-)  A
 191 TYR   ( 200-)  A
 302 TYR   ( 311-)  A
 333 TYR   ( 342-)  A

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

   4 PHE   (   8-)  A
  55 PHE   (  59-)  A
  95 PHE   (  99-)  A
 214 PHE   ( 223-)  A
 265 PHE   ( 274-)  A
 318 PHE   ( 327-)  A
 339 PHE   ( 348-)  A

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.

  84 ASP   (  88-)  A
  97 ASP   ( 101-)  A
 118 ASP   ( 124-)  A
 119 ASP   ( 125-)  A
 144 ASP   ( 150-)  A
 155 ASP   ( 161-)  A
 162 ASP   ( 168-)  A
 167 ASP   ( 176-)  A
 218 ASP   ( 227-)  A
 221 ASP   ( 230-)  A
 283 ASP   ( 292-)  A
 285 ASP   ( 294-)  A
 306 ASP   ( 315-)  A
 307 ASP   ( 316-)  A
 312 ASP   ( 321-)  A
 315 ASP   ( 324-)  A
 326 ASP   ( 335-)  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.

   8 GLU   (  12-)  A
  77 GLU   (  81-)  A
  94 GLU   (  98-)  A
 157 GLU   ( 163-)  A
 183 GLU   ( 192-)  A
 236 GLU   ( 245-)  A
 327 GLU   ( 336-)  A

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.996581 -0.000063  0.000138|
 | -0.000063  0.997036  0.000282|
 |  0.000138  0.000282  0.996788|
Proposed new scale matrix

 |  0.022157  0.000001 -0.000003|
 |  0.000000  0.011580 -0.000003|
 | -0.000001 -0.000002  0.008130|
With corresponding cell

    A    =  45.133  B   =  86.353  C    = 122.999
    Alpha=  89.968  Beta=  89.984  Gamma=  90.004

The CRYST1 cell dimensions

    A    =  45.288  B   =  86.613  C    = 123.396
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 118.828
(Under-)estimated Z-score: 8.034

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.

   8 GLU   (  12-)  A
  19 ARG   (  23-)  A
  66 ARG   (  70-)  A
  77 GLU   (  81-)  A
  84 ASP   (  88-)  A
  94 GLU   (  98-)  A
  97 ASP   ( 101-)  A
 118 ASP   ( 124-)  A
 119 ASP   ( 125-)  A
 130 ARG   ( 136-)  A
 143 ARG   ( 149-)  A
 144 ASP   ( 150-)  A
 155 ASP   ( 161-)  A
 157 GLU   ( 163-)  A
 162 ASP   ( 168-)  A
 167 ASP   ( 176-)  A
 180 ARG   ( 189-)  A
 183 GLU   ( 192-)  A
 218 ASP   ( 227-)  A
 221 ASP   ( 230-)  A
 228 ARG   ( 237-)  A
 236 GLU   ( 245-)  A
 283 ASP   ( 292-)  A
 285 ASP   ( 294-)  A
 287 ARG   ( 296-)  A
 306 ASP   ( 315-)  A
 307 ASP   ( 316-)  A
 312 ASP   ( 321-)  A
 315 ASP   ( 324-)  A
 326 ASP   ( 335-)  A
 327 GLU   ( 336-)  A

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.

 156 CYS   ( 162-)  A    -2.5
 102 THR   ( 106-)  A    -2.4
 321 ARG   ( 330-)  A    -2.3
  27 GLY   (  31-)  A    -2.2
   9 LEU   (  13-)  A    -2.0
 110 ASN   ( 114-)  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.

   9 LEU   (  13-)  A  Poor phi/psi
  10 ASN   (  14-)  A  Poor phi/psi
  11 LYS   (  15-)  A  Poor phi/psi
  22 ASN   (  26-)  A  Poor phi/psi
  96 ASN   ( 100-)  A  Poor phi/psi
 112 ILE   ( 116-)  A  Poor phi/psi
 139 ASP   ( 145-)  A  Poor phi/psi
 143 ARG   ( 149-)  A  Poor phi/psi
 156 CYS   ( 162-)  A  Poor phi/psi
 162 ASP   ( 168-)  A  Poor phi/psi
 189 MET   ( 198-)  A  omega poor
 194 THR   ( 203-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -1.160

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 GLU   (  12-)  A      0
   9 LEU   (  13-)  A      0
  10 ASN   (  14-)  A      0
  11 LYS   (  15-)  A      0
  20 TYR   (  24-)  A      0
  21 GLN   (  25-)  A      0
  22 ASN   (  26-)  A      0
  26 VAL   (  30-)  A      0
  27 GLY   (  31-)  A      0
  28 SER   (  32-)  A      0
  31 TYR   (  35-)  A      0
  33 SER   (  37-)  A      0
  36 ALA   (  40-)  A      0
  52 SER   (  56-)  A      0
  53 LYS   (  57-)  A      0
  55 PHE   (  59-)  A      0
  56 GLN   (  60-)  A      0
  73 HIS   (  77-)  A      0
  74 MET   (  78-)  A      0
  75 LYS   (  79-)  A      0
  76 HIS   (  80-)  A      0
  84 ASP   (  88-)  A      0
  88 PRO   (  92-)  A      0
  94 GLU   (  98-)  A      0
  95 PHE   (  99-)  A      0
And so on for a total of 120 lines.

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].

 343 PRO   ( 352-)  A    -7.3 envelop N (0 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.

 114 GLN   ( 120-)  A      NE2 <->  345 HOH   (2034 )  A      O      0.41    2.29  INTRA
 277 GLU   ( 286-)  A      OE2 <->  345 HOH   (3291 )  A      O      0.34    2.06  INTRA
  51 LEU   (  55-)  A      O   <->  345 HOH   (2051 )  A      O      0.17    2.23  INTRA
 192 ASN   ( 201-)  A      ND2 <->  194 THR   ( 203-)  A      OG1    0.11    2.59  INTRA
 110 ASN   ( 114-)  A      ND2 <->  345 HOH   (3300 )  A      O      0.10    2.60  INTRA BF
 146 LYS   ( 152-)  A      NZ  <->  345 HOH   (3127 )  A      O      0.09    2.61  INTRA
 142 HIS   ( 148-)  A      NE2 <->  161 LEU   ( 167-)  A      O      0.08    2.62  INTRA
 122 GLN   ( 128-)  A      NE2 <->  345 HOH   (3099 )  A      O      0.08    2.62  INTRA
 105 MET   ( 109-)  A      N   <->  344 FKO   ( 361-)  A      NAN    0.07    2.93  INTRA BL
 122 GLN   ( 128-)  A      NE2 <->  301 GLN   ( 310-)  A      OE1    0.05    2.65  INTRA
 321 ARG   ( 330-)  A      NE  <->  345 HOH   (2017 )  A      O      0.05    2.65  INTRA
  10 ASN   (  14-)  A      C   <->   12 THR   (  16-)  A      N      0.05    2.85  INTRA BF
 240 LYS   ( 249-)  A      NZ  <->  283 ASP   ( 292-)  A      OD2    0.05    2.65  INTRA
  69 ARG   (  73-)  A      NH2 <->  315 ASP   ( 324-)  A      O      0.05    2.65  INTRA
  24 SER   (  28-)  A      O   <->   36 ALA   (  40-)  A      N      0.04    2.66  INTRA
 200 VAL   ( 209-)  A      O   <->  204 MET   ( 213-)  A      N      0.03    2.67  INTRA BL
 258 LYS   ( 267-)  A      NZ  <->  345 HOH   (3291 )  A      O      0.03    2.67  INTRA
  76 HIS   (  80-)  A      ND1 <->   78 ASN   (  82-)  A      N      0.02    2.98  INTRA BL
 153 ASN   ( 159-)  A      ND2 <->  157 GLU   ( 163-)  A      OE1    0.02    2.68  INTRA
 169 GLU   ( 178-)  A      O   <->  176 THR   ( 185-)  A      OG1    0.02    2.38  INTRA
  18 GLU   (  22-)  A      O   <->   21 GLN   (  25-)  A      NE2    0.01    2.69  INTRA BL
  72 LYS   (  76-)  A      NZ  <->  335 GLU   ( 344-)  A      O      0.01    2.69  INTRA BL
  66 ARG   (  70-)  A      NH1 <->  345 HOH   (1053 )  A      O      0.01    2.69  INTRA

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.

  90 ARG   (  94-)  A      -7.63
 173 TYR   ( 182-)  A      -7.12
  31 TYR   (  35-)  A      -6.98
 190 HIS   ( 199-)  A      -5.92
 255 GLN   ( 264-)  A      -5.90
  73 HIS   (  77-)  A      -5.86
  56 GLN   (  60-)  A      -5.72
  75 LYS   (  79-)  A      -5.49
 266 ILE   ( 275-)  A      -5.02
 340 VAL   ( 349-)  A      -5.00

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.

 183 GLU   ( 192-)  A     -  186 LEU   ( 195-)  A        -1.46

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 345 HOH   (1010 )  A      O     65.58   63.73   83.41
 345 HOH   (3189 )  A      O     59.96   62.83   87.44

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 345 HOH   (3224 )  A      O
 345 HOH   (3237 )  A      O
Marked this atom as acceptor  344 FKO  ( 361-) A     CLB
Marked this atom as acceptor  344 FKO  ( 361-) A      FAA

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.

   7 GLN   (  11-)  A
 103 HIS   ( 107-)  A
 111 ASN   ( 115-)  A
 114 GLN   ( 120-)  A
 122 GLN   ( 128-)  A
 149 ASN   ( 155-)  A
 248 ASN   ( 257-)  A
 260 ASN   ( 269-)  A
 263 ASN   ( 272-)  A
 301 GLN   ( 310-)  A
 316 GLN   ( 325-)  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.

  10 ASN   (  14-)  A      N
  12 THR   (  16-)  A      N
  14 TRP   (  18-)  A      NE1
  21 GLN   (  25-)  A      NE2
  31 TYR   (  35-)  A      N
  57 SER   (  61-)  A      N
  69 ARG   (  73-)  A      NH2
  91 SER   (  95-)  A      N
 105 MET   ( 109-)  A      N
 187 ASN   ( 196-)  A      N
 192 ASN   ( 201-)  A      ND2
 197 ILE   ( 206-)  A      N
 211 ARG   ( 220-)  A      NH1
 218 ASP   ( 227-)  A      N
 248 ASN   ( 257-)  A      ND2

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.

  97 ASP   ( 101-)  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 :  -0.560
  2nd generation packing quality :  -0.642
  Ramachandran plot appearance   :  -0.303
  chi-1/chi-2 rotamer normality  :  -1.160
  Backbone conformation          :  -0.220

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.383 (tight)
  Bond angles                    :   0.565 (tight)
  Omega angle restraints         :   0.931
  Side chain planarity           :   0.305 (tight)
  Improper dihedral distribution :   0.528
  B-factor distribution          :   0.352
  Inside/Outside distribution    :   1.023

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.383 (tight)
  Bond angles                    :   0.565 (tight)
  Omega angle restraints         :   0.931
  Side chain planarity           :   0.305 (tight)
  Improper dihedral distribution :   0.528
  B-factor distribution          :   0.352
  Inside/Outside distribution    :   1.023
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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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
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      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
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      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.