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 pdb2if4.ent

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: B-factors outside the range 0.0 - 100.0

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

 246 MET   ( 280-)  A    High
 247 ASP   ( 281-)  A    High
 248 SER   ( 282-)  A    High
 250 ARG   ( 284-)  A    High

Warning: What type of B-factor?

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

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

Crystal temperature (K) :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.

 148 ARG   ( 182-)  A

Warning: Tyrosine convention problem

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

  33 TYR   (  67-)  A
 168 TYR   ( 202-)  A
 174 TYR   ( 208-)  A
 187 TYR   ( 221-)  A

Warning: Phenylalanine convention problem

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

 104 PHE   ( 138-)  A
 156 PHE   ( 190-)  A
 253 PHE   ( 287-)  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.

  53 ASP   (  87-)  A
 114 ASP   ( 148-)  A
 178 ASP   ( 212-)  A
 252 ASP   ( 286-)  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.

 120 GLU   ( 154-)  A
 129 GLU   ( 163-)  A
 214 GLU   ( 248-)  A
 226 GLU   ( 260-)  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.

 100 LYS   ( 134-)  A      N    CA   C    97.42   -4.9
 118 GLU   ( 152-)  A      N    CA   C    99.40   -4.2
 171 ALA   ( 205-)  A      N    CA   C    99.70   -4.1

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.

  53 ASP   (  87-)  A
 114 ASP   ( 148-)  A
 120 GLU   ( 154-)  A
 129 GLU   ( 163-)  A
 148 ARG   ( 182-)  A
 178 ASP   ( 212-)  A
 214 GLU   ( 248-)  A
 226 GLU   ( 260-)  A
 252 ASP   ( 286-)  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.

 171 ALA   ( 205-)  A    8.13
 149 LYS   ( 183-)  A    7.21
 202 ILE   ( 236-)  A    6.27
 164 ALA   ( 198-)  A    6.05
 100 LYS   ( 134-)  A    5.35
 118 GLU   ( 152-)  A    4.33
 107 PRO   ( 141-)  A    4.13
  72 LEU   ( 106-)  A    4.12
 119 VAL   ( 153-)  A    4.07

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.879

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -5.236

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.

 107 PRO   ( 141-)  A    -3.0
   3 PRO   (  37-)  A    -2.9
  38 LEU   (  72-)  A    -2.7
 100 LYS   ( 134-)  A    -2.5
  52 GLU   (  86-)  A    -2.3
 202 ILE   ( 236-)  A    -2.3
  15 GLU   (  49-)  A    -2.2
 130 GLY   ( 164-)  A    -2.1
  14 ASP   (  48-)  A    -2.1
 105 SER   ( 139-)  A    -2.1
 226 GLU   ( 260-)  A    -2.1
 128 LYS   ( 162-)  A    -2.1
  99 GLY   ( 133-)  A    -2.1
  44 THR   (  78-)  A    -2.0
 106 PHE   ( 140-)  A    -2.0
 157 LYS   ( 191-)  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.

  14 ASP   (  48-)  A  Poor phi/psi
  33 TYR   (  67-)  A  Poor phi/psi
  40 TYR   (  74-)  A  Poor phi/psi
  68 GLU   ( 102-)  A  Poor phi/psi
  70 LYS   ( 104-)  A  Poor phi/psi
  85 GLY   ( 119-)  A  Poor phi/psi
  97 ALA   ( 131-)  A  Poor phi/psi
 100 LYS   ( 134-)  A  Poor phi/psi
 105 SER   ( 139-)  A  Poor phi/psi
 106 PHE   ( 140-)  A  Poor phi/psi
 132 ALA   ( 166-)  A  Poor phi/psi
 135 ASP   ( 169-)  A  Poor phi/psi
 157 LYS   ( 191-)  A  Poor phi/psi
 185 GLY   ( 219-)  A  Poor phi/psi
 198 CYS   ( 232-)  A  Poor phi/psi
 203 ALA   ( 237-)  A  Poor phi/psi
 210 LYS   ( 244-)  A  Poor phi/psi
 227 GLU   ( 261-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.144

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.144

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!

   5 LYS   (  39-)  A      0
  13 LEU   (  47-)  A      0
  16 LYS   (  50-)  A      0
  17 VAL   (  51-)  A      0
  26 HIS   (  60-)  A      0
  32 LYS   (  66-)  A      0
  33 TYR   (  67-)  A      0
  39 HIS   (  73-)  A      0
  43 TRP   (  77-)  A      0
  45 LYS   (  79-)  A      0
  50 LYS   (  84-)  A      0
  51 PHE   (  85-)  A      0
  52 GLU   (  86-)  A      0
  58 GLN   (  92-)  A      0
  59 GLN   (  93-)  A      0
  65 LEU   (  99-)  A      0
  68 GLU   ( 102-)  A      0
  70 LYS   ( 104-)  A      0
  82 MET   ( 116-)  A      0
  84 SER   ( 118-)  A      0
  87 ARG   ( 121-)  A      0
  88 ALA   ( 122-)  A      0
  96 LEU   ( 130-)  A      0
  97 ALA   ( 131-)  A      0
  98 TYR   ( 132-)  A      0
And so on for a total of 92 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 : 1.368

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].

   3 PRO   (  37-)  A  -115.7 envelop C-gamma (-108 degrees)
 107 PRO   ( 141-)  A    18.8 half-chair N/C-delta (18 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.

  36 CYS   (  70-)  A      O   <->   63 LEU   (  97-)  A      N      0.38    2.32  INTRA BL
 160 LYS   ( 194-)  A      NZ  <->  208 LYS   ( 242-)  A      CG     0.36    2.74  INTRA BF
  70 LYS   ( 104-)  A      CE  <->  100 LYS   ( 134-)  A      NZ     0.35    2.75  INTRA BF
 203 ALA   ( 237-)  A      O   <->  206 LEU   ( 240-)  A      N      0.35    2.35  INTRA BF
  41 ARG   (  75-)  A      NH1 <->   53 ASP   (  87-)  A      CG     0.30    2.80  INTRA BL
 106 PHE   ( 140-)  A      CB  <->  107 PRO   ( 141-)  A      CD     0.30    2.80  INTRA BF
 131 LYS   ( 165-)  A      CB  <->  134 SER   ( 168-)  A      CB     0.28    2.92  INTRA BF
  19 LYS   (  53-)  A      NZ  <->   81 SER   ( 115-)  A      OG     0.28    2.42  INTRA BL
 105 SER   ( 139-)  A      O   <->  106 PHE   ( 140-)  A      C      0.24    2.36  INTRA BF
 212 TYR   ( 246-)  A      CE2 <->  242 GLU   ( 276-)  A      CB     0.24    2.96  INTRA BF
 226 GLU   ( 260-)  A      O   <->  228 LYS   ( 262-)  A      N      0.24    2.46  INTRA BF
  79 VAL   ( 113-)  A      O   <->   82 MET   ( 116-)  A      N      0.24    2.46  INTRA BL
 203 ALA   ( 237-)  A      CB  <->  235 ARG   ( 269-)  A      CD     0.23    2.97  INTRA BF
  93 GLY   ( 127-)  A      C   <->   95 GLU   ( 129-)  A      N      0.23    2.67  INTRA BL
 197 PRO   ( 231-)  A      O   <->  199 HIS   ( 233-)  A      N      0.23    2.47  INTRA BL
  69 LYS   ( 103-)  A      O   <->   72 LEU   ( 106-)  A      N      0.22    2.48  INTRA BL
 245 GLN   ( 279-)  A      O   <->  249 ALA   ( 283-)  A      N      0.22    2.48  INTRA BF
 162 GLU   ( 196-)  A      O   <->  166 GLN   ( 200-)  A      N      0.22    2.48  INTRA BF
 171 ALA   ( 205-)  A      CB  <->  198 CYS   ( 232-)  A      SG     0.22    3.18  INTRA BL
 150 MET   ( 184-)  A      O   <->  153 ASN   ( 187-)  A      N      0.21    2.49  INTRA BF
  93 GLY   ( 127-)  A      O   <->   96 LEU   ( 130-)  A      N      0.21    2.49  INTRA BL
 197 PRO   ( 231-)  A      C   <->  199 HIS   ( 233-)  A      N      0.20    2.70  INTRA BL
 226 GLU   ( 260-)  A      C   <->  228 LYS   ( 262-)  A      N      0.20    2.70  INTRA BF
  14 ASP   (  48-)  A      CB  <->   17 VAL   (  51-)  A      CG2    0.20    3.00  INTRA BF
 254 ARG   ( 288-)  A      C   <->  256 ALA   ( 290-)  A      N      0.20    2.70  INTRA BF
And so on for a total of 129 lines.

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.

 184 TYR   ( 218-)  A      -6.93
 100 LYS   ( 134-)  A      -6.20
 104 PHE   ( 138-)  A      -6.02
 128 LYS   ( 162-)  A      -5.73
 129 GLU   ( 163-)  A      -5.66
   5 LYS   (  39-)  A      -5.60
 133 ARG   ( 167-)  A      -5.55
 106 PHE   ( 140-)  A      -5.52
  26 HIS   (  60-)  A      -5.18
 228 LYS   ( 262-)  A      -5.17
 257 GLN   ( 291-)  A      -5.12

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.

  57 GLU   (  91-)  A        59 - GLN     93- ( A)         -4.86

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: 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.

  97 ALA   ( 131-)  A   -2.85

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

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.

   2 VAL   (  36-)  A      N
  13 LEU   (  47-)  A      N
  21 ILE   (  55-)  A      N
  46 ASN   (  80-)  A      N
  64 VAL   (  98-)  A      N
  69 LYS   ( 103-)  A      N
  71 GLU   ( 105-)  A      N
  75 LEU   ( 109-)  A      N
  95 GLU   ( 129-)  A      N
  98 TYR   ( 132-)  A      N
 100 LYS   ( 134-)  A      N
 112 MET   ( 146-)  A      N
 113 ALA   ( 147-)  A      N
 127 THR   ( 161-)  A      OG1
 153 ASN   ( 187-)  A      ND2
 163 GLU   ( 197-)  A      N
 164 ALA   ( 198-)  A      N
 176 GLY   ( 210-)  A      N
 178 ASP   ( 212-)  A      N
 183 LEU   ( 217-)  A      N
 184 TYR   ( 218-)  A      N
 205 CYS   ( 239-)  A      N
 212 TYR   ( 246-)  A      N
 213 ASP   ( 247-)  A      N
 214 GLU   ( 248-)  A      N
 215 ALA   ( 249-)  A      N
 227 GLU   ( 261-)  A      N
 228 LYS   ( 262-)  A      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  26 HIS   (  60-)  A      ND1
 196 ASN   ( 230-)  A      OD1
 199 HIS   ( 233-)  A      ND1

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.

 101 GLU   ( 135-)  A   H-bonding suggests Gln
 189 ASP   ( 223-)  A   H-bonding suggests Asn
 251 ASP   ( 285-)  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 :  -1.499
  2nd generation packing quality :  -2.185
  Ramachandran plot appearance   :  -5.236 (bad)
  chi-1/chi-2 rotamer normality  :  -4.144 (bad)
  Backbone conformation          :  -0.870

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.360 (tight)
  Bond angles                    :   0.725
  Omega angle restraints         :   0.249 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.534
  Inside/Outside distribution    :   1.082

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 : 2.85


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.360 (tight)
  Bond angles                    :   0.725
  Omega angle restraints         :   0.249 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.534
  Inside/Outside distribution    :   1.082
==============

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

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
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      New parameters for the refinement of nucleic acid-containing structures
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DSSP
    W.Kabsch and C.Sander,
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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
    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.