WHAT IF Check report

This file was created 2012-01-12 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 pdb3qcd.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some 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 two or less which PRODRUG also cannot cope with), 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.

 284 VO4   (2001-)  A  -         Atom types
 285 ACY   (2051-)  A  -         OK
 286 ACY   (2052-)  A  -         OK

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.

   8 GLN   ( 832-)  A  -   CD
   8 GLN   ( 832-)  A  -   OE1
   8 GLN   ( 832-)  A  -   NE2
  68 LYS   ( 892-)  A  -   NZ
 244 LYS   (1083-)  A  -   CD
 244 LYS   (1083-)  A  -   CE
 244 LYS   (1083-)  A  -   NZ

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: 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'.

   2 GLU   ( 826-)  A      CG
   2 GLU   ( 826-)  A      CD
   2 GLU   ( 826-)  A      OE1
   2 GLU   ( 826-)  A      OE2
  70 ARG   ( 894-)  A      CG
  70 ARG   ( 894-)  A      CD
  70 ARG   ( 894-)  A      NE
  70 ARG   ( 894-)  A      CZ
  70 ARG   ( 894-)  A      NH1
  70 ARG   ( 894-)  A      NH2
  74 SER   ( 901-)  A      OG
  75 LYS   ( 902-)  A      CG
  75 LYS   ( 902-)  A      CD
  75 LYS   ( 902-)  A      CE
  75 LYS   ( 902-)  A      NZ
 131 ARG   ( 958-)  A      CG
 131 ARG   ( 958-)  A      CD
 131 ARG   ( 958-)  A      NE
 131 ARG   ( 958-)  A      CZ
 131 ARG   ( 958-)  A      NH1
 131 ARG   ( 958-)  A      NH2
 174 GLN   (1013-)  A      CG
 174 GLN   (1013-)  A      CD
 174 GLN   (1013-)  A      OE1
 174 GLN   (1013-)  A      NE2
 213 GLU   (1052-)  A      CG
 213 GLU   (1052-)  A      CD
 213 GLU   (1052-)  A      OE1
 213 GLU   (1052-)  A      OE2
 242 LYS   (1081-)  A      CG
 242 LYS   (1081-)  A      CD
 242 LYS   (1081-)  A      CE
 242 LYS   (1081-)  A      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

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.

  33 ARG   ( 857-)  A
 170 ARG   ( 997-)  A
 204 ARG   (1043-)  A
 205 ARG   (1044-)  A

Warning: Tyrosine convention problem

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

  17 TYR   ( 841-)  A
  94 TYR   ( 921-)  A
 146 TYR   ( 973-)  A
 195 TYR   (1034-)  A
 262 TYR   (1101-)  A

Warning: Phenylalanine convention problem

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

 167 PHE   ( 994-)  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.

  30 GLU   ( 854-)  A
 128 GLU   ( 955-)  A
 144 GLU   ( 971-)  A
 267 GLU   (1106-)  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: 0.251
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: 0.524
RMS-deviation in bond angles: 0.966

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.

  30 GLU   ( 854-)  A
  33 ARG   ( 857-)  A
 128 GLU   ( 955-)  A
 144 GLU   ( 971-)  A
 170 ARG   ( 997-)  A
 204 ARG   (1043-)  A
 205 ARG   (1044-)  A
 267 GLU   (1106-)  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.

 124 THR   ( 951-)  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.

  19 ASN   ( 843-)  A  Poor phi/psi
  20 ASN   ( 844-)  A  Poor phi/psi
  21 GLN   ( 845-)  A  Poor phi/psi
  89 ASN   ( 916-)  A  Poor phi/psi
  94 TYR   ( 921-)  A  omega poor
 116 ASN   ( 943-)  A  Poor phi/psi
 142 ASN   ( 969-)  A  Poor phi/psi
 167 PHE   ( 994-)  A  omega poor
 182 TYR   (1021-)  A  omega poor
 190 MET   (1029-)  A  Poor phi/psi
 212 PRO   (1051-)  A  omega poor
 220 HIS   (1059-)  A  omega poor
 221 CYS   (1060-)  A  Poor phi/psi
 245 SER   (1084-)  A  Poor phi/psi
 262 TYR   (1101-)  A  Poor phi/psi
 264 VAL   (1103-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.015

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 206 SER   (1045-)  A    0.36

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 GLN   ( 832-)  A      0
   9 PHE   ( 833-)  A      0
  19 ASN   ( 843-)  A      0
  20 ASN   ( 844-)  A      0
  21 GLN   ( 845-)  A      0
  34 CYS   ( 858-)  A      0
  37 ASP   ( 861-)  A      0
  42 ALA   ( 866-)  A      0
  43 GLU   ( 867-)  A      0
  56 TYR   ( 880-)  A      0
  72 LEU   ( 896-)  A      0
  73 PRO   ( 897-)  A      0
  74 SER   ( 901-)  A      0
  75 LYS   ( 902-)  A      0
  76 HIS   ( 903-)  A      0
  77 SER   ( 904-)  A      0
  80 ILE   ( 907-)  A      0
  81 ASN   ( 908-)  A      0
  88 TYR   ( 915-)  A      0
  89 ASN   ( 916-)  A      0
  91 ALA   ( 918-)  A      0
  92 LYS   ( 919-)  A      0
  93 ALA   ( 920-)  A      0
 115 GLN   ( 942-)  A      0
 116 ASN   ( 943-)  A      0
And so on for a total of 110 lines.

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.

  58 ASN   ( 882-)  A      ND2 <->  287 HOH   (2232 )  A      O      0.26    2.44  INTRA BF
 110 ARG   ( 937-)  A      NH2 <->  287 HOH   (2157 )  A      O      0.17    2.53  INTRA BF
  35 THR   ( 859-)  A      O   <->   38 MET   ( 862-)  A      N      0.15    2.55  INTRA BF
 221 CYS   (1060-)  A      SG  <->  284 VO4   (2001-)  A      O2     0.15    2.85  INTRA
  70 ARG   ( 894-)  A      O   <->  110 ARG   ( 937-)  A      NH1    0.14    2.56  INTRA BF
 221 CYS   (1060-)  A      SG  <->  284 VO4   (2001-)  A      O4     0.12    2.88  INTRA BL
 197 LEU   (1036-)  A      N   <->  198 PRO   (1037-)  A      CD     0.11    2.89  INTRA BL
  53 LYS   ( 877-)  A      NZ  <->  287 HOH   (2125 )  A      O      0.10    2.60  INTRA
 221 CYS   (1060-)  A      SG  <->  284 VO4   (2001-)  A      O3     0.10    2.90  INTRA BL
  47 HIS   ( 871-)  A      ND1 <->   48 PRO   ( 872-)  A      CD     0.09    3.01  INTRA BF
 190 MET   (1029-)  A      SD  <->  265 GLN   (1104-)  A      NE2    0.09    3.21  INTRA BF
 113 TRP   ( 940-)  A      O   <->  177 ARG   (1016-)  A      NH1    0.09    2.61  INTRA BF
 222 SER   (1061-)  A      N   <->  284 VO4   (2001-)  A      O2     0.08    2.62  INTRA
 187 TRP   (1026-)  A      O   <->  227 ARG   (1066-)  A      NH1    0.08    2.62  INTRA
 118 GLY   ( 945-)  A      N   <->  287 HOH   (2111 )  A      O      0.08    2.62  INTRA BL
  30 GLU   ( 854-)  A      OE2 <->  254 LYS   (1093-)  A      NZ     0.08    2.62  INTRA BF
 133 LYS   ( 960-)  A      NZ  <->  189 ASP   (1028-)  A      OD2    0.08    2.62  INTRA BF
  33 ARG   ( 857-)  A      O   <->   36 ALA   ( 860-)  A      N      0.08    2.62  INTRA BF
  52 HIS   ( 876-)  A      ND1 <->  287 HOH   (2224 )  A      O      0.07    2.63  INTRA BF
  66 ARG   ( 890-)  A      NE  <->  287 HOH   (2151 )  A      O      0.06    2.64  INTRA
  47 HIS   ( 871-)  A      ND1 <->   49 GLU   ( 873-)  A      N      0.06    2.94  INTRA BF
 121 VAL   ( 948-)  A      N   <->  218 LEU   (1057-)  A      O      0.05    2.65  INTRA BL
 204 ARG   (1043-)  A    A NH2 <->  287 HOH   (2199 )  A      O      0.04    2.66  INTRA
  43 GLU   ( 867-)  A      N   <->   63 ASP   ( 887-)  A      OD2    0.03    2.67  INTRA
 225 VAL   (1064-)  A      N   <->  284 VO4   (2001-)  A      O3     0.03    2.67  INTRA BL
 100 PRO   ( 927-)  A      CG  <->  108 PHE   ( 935-)  A      CD1    0.03    3.17  INTRA BL
 142 ASN   ( 969-)  A      CB  <->  143 SER   ( 970-)  A      N      0.03    2.67  INTRA B3
  86 ASP   ( 913-)  A      OD2 <->  255 HIS   (1094-)  A      NE2    0.03    2.67  INTRA
 165 ARG   ( 992-)  A      NH1 <->  183 HIS   (1022-)  A      CD2    0.02    3.08  INTRA BL
  42 ALA   ( 866-)  A      N   <->  287 HOH   (2136 )  A      O      0.02    2.68  INTRA
 171 ASN   ( 998-)  A      OD1 <->  173 LYS   (1000-)  A      N      0.02    2.68  INTRA BF
 125 ASN   ( 952-)  A      ND2 <->  287 HOH   (2133 )  A      O      0.01    2.69  INTRA
   1 MET   ( 825-)  A      SD  <->  254 LYS   (1093-)  A      NZ     0.01    3.29  INTRA BF
 274 HIS   (1113-)  A      NE2 <->  287 HOH   (2161 )  A      O      0.01    2.69  INTRA
 148 ASN   ( 975-)  A      O   <->  172 THR   ( 999-)  A      N      0.01    2.69  INTRA BF
 120 ILE   ( 947-)  A      O   <->  182 TYR   (1021-)  A      N      0.01    2.69  INTRA BL
  64 HIS   ( 888-)  A      NE2 <->  258 THR   (1097-)  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

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.

  72 LEU   ( 896-)  A      -6.77
 129 LYS   ( 956-)  A      -6.62
 211 MET   (1050-)  A      -5.95
 195 TYR   (1034-)  A      -5.77
 190 MET   (1029-)  A      -5.74
 186 GLN   (1025-)  A      -5.59
 132 ARG   ( 959-)  A      -5.39
  68 LYS   ( 892-)  A      -5.37
  20 ASN   ( 844-)  A      -5.25
  19 ASN   ( 843-)  A      -5.20
  46 ASN   ( 870-)  A      -5.11

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.

  70 ARG   ( 894-)  A   -3.36
 131 ARG   ( 958-)  A   -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

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.

  20 ASN   ( 844-)  A
  89 ASN   ( 916-)  A
 136 GLN   ( 963-)  A
 183 HIS   (1022-)  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.

  21 GLN   ( 845-)  A      NE2
  35 THR   ( 859-)  A      N
  55 ARG   ( 879-)  A      NH2
  66 ARG   ( 890-)  A      NH1
  76 HIS   ( 903-)  A      N
 124 THR   ( 951-)  A      N
 138 TRP   ( 965-)  A      N
 162 TYR   ( 989-)  A      N
 181 GLN   (1020-)  A      NE2
 186 GLN   (1025-)  A      N
 223 ALA   (1062-)  A      N
 225 VAL   (1064-)  A      N
 226 GLY   (1065-)  A      N
 227 ARG   (1066-)  A      N
 227 ARG   (1066-)  A      NE
 227 ARG   (1066-)  A      NH2
 246 THR   (1085-)  A      N
 257 ARG   (1096-)  A      NH2
 265 GLN   (1104-)  A      NE2

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 :  -0.022
  2nd generation packing quality :  -0.649
  Ramachandran plot appearance   :   0.345
  chi-1/chi-2 rotamer normality  :   0.015
  Backbone conformation          :  -0.820

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.251 (tight)
  Bond angles                    :   0.524 (tight)
  Omega angle restraints         :   1.052
  Side chain planarity           :   0.130 (tight)
  Improper dihedral distribution :   0.552
  B-factor distribution          :   0.567
  Inside/Outside distribution    :   1.021

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.251 (tight)
  Bond angles                    :   0.524 (tight)
  Omega angle restraints         :   1.052
  Side chain planarity           :   0.130 (tight)
  Improper dihedral distribution :   0.552
  B-factor distribution          :   0.567
  Inside/Outside distribution    :   1.021
==============

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.