WHAT IF Check report

This file was created 2012-03-13 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 pdb3kcl.ent

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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) :293.000

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.

  10 ARG   (  10-)  A
 387 ARG   ( 387-)  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   (   8-)  A
  38 GLU   (  38-)  A
  69 GLU   (  69-)  A
  70 GLU   (  70-)  A
 359 GLU   ( 359-)  A

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.

 387 ARG   ( 387-)  A      CD   NE    1.39   -4.0
 387 ARG   ( 387-)  A      CZ   NH2   1.25   -4.3

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

 |  0.998011 -0.000025  0.000070|
 | -0.000025  0.998518  0.000167|
 |  0.000070  0.000167  0.999186|
Proposed new scale matrix

 |  0.010637  0.000000  0.000000|
 |  0.000000  0.010072 -0.000002|
 |  0.000000 -0.000002  0.009718|
With corresponding cell

    A    =  94.010  B   =  99.286  C    = 102.903
    Alpha=  89.981  Beta=  90.001  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  94.196  B   =  99.430  C    = 102.986
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 27.894
(Under-)estimated Z-score: 3.892

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.

  54 HIS   (  54-)  A      N    CA   C    99.01   -4.4
  71 HIS   (  71-)  A      CG   ND1  CE1 109.69    4.1
  98 VAL   (  98-)  A      N    CA   CB  121.83    6.7
  98 VAL   (  98-)  A      C    CA   CB   93.94   -8.5
  98 VAL   (  98-)  A      CA   CB   CG2 118.81    4.9
 111 VAL   ( 111-)  A      N    CA   CB  121.34    6.4
 111 VAL   ( 111-)  A      CA   CB   CG1 117.93    4.4
 198 HIS   ( 198-)  A      CG   ND1  CE1 109.79    4.2
 382 HIS   ( 382-)  A      CG   ND1  CE1 109.69    4.1
 387 ARG   ( 387-)  A      NE   CZ   NH1 112.01   -4.2

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   (   8-)  A
  10 ARG   (  10-)  A
  38 GLU   (  38-)  A
  69 GLU   (  69-)  A
  70 GLU   (  70-)  A
 359 GLU   ( 359-)  A
 387 ARG   ( 387-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  98 VAL   (  98-)  A      CB    11.7   -17.64   -32.96
 111 VAL   ( 111-)  A      CA   -10.2    18.37    33.23
 111 VAL   ( 111-)  A      CB     7.1   -23.63   -32.96
The average deviation= 0.986

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.

 146 GLY   ( 146-)  A    5.31
  54 HIS   (  54-)  A    4.59
 284 ARG   ( 284-)  A    4.08

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.

 187 PRO   ( 187-)  A    -2.6
  10 ARG   (  10-)  A    -2.6
  90 THR   (  90-)  A    -2.4
 186 GLU   ( 186-)  A    -2.1
 288 PHE   ( 288-)  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.

  10 ARG   (  10-)  A  Poor phi/psi
  94 PHE   (  94-)  A  Poor phi/psi
 186 GLU   ( 186-)  A  Poor phi/psi, PRO omega poor
 193 LEU   ( 193-)  A  Poor phi/psi
 253 LYS   ( 253-)  A  Poor phi/psi
 334 ARG   ( 334-)  A  Poor phi/psi
 371 ALA   ( 371-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.593

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.

  66 SER   (  66-)  A    0.35

Warning: Unusual backbone conformations

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

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

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

   3 TYR   (   3-)  A      0
  11 PHE   (  11-)  A      0
  16 TRP   (  16-)  A      0
  17 THR   (  17-)  A      0
  20 TRP   (  20-)  A      0
  21 GLN   (  21-)  A      0
  23 ARG   (  23-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  28 ASP   (  28-)  A      0
  46 LEU   (  46-)  A      0
  49 HIS   (  49-)  A      0
  61 PHE   (  61-)  A      0
  84 MET   (  84-)  A      0
  87 PRO   (  87-)  A      0
  88 MET   (  88-)  A      0
  93 LEU   (  93-)  A      0
  94 PHE   (  94-)  A      0
  95 THR   (  95-)  A      0
 101 ASP   ( 101-)  A      0
 104 PHE   ( 104-)  A      0
 105 THR   ( 105-)  A      0
 107 ASN   ( 107-)  A      0
 109 ARG   ( 109-)  A      0
 111 VAL   ( 111-)  A      0
And so on for a total of 125 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 : 2.291

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  25 PRO   (  25-)  A    0.12 LOW
  36 PRO   (  36-)  A    0.13 LOW
 184 PRO   ( 184-)  A    0.14 LOW

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].

   7 PRO   (   7-)  A   101.1 envelop C-beta (108 degrees)
  87 PRO   (  87-)  A    40.1 envelop C-delta (36 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.

 382 HIS   ( 382-)  A      ND1 <->  394 DOD   (1061 )  A      O      0.23    2.47  INTRA
 289 LYS   ( 289-)  A      NZ  <->  394 DOD   (1084 )  A      O      0.23    2.47  INTRA BF
 340 ARG   ( 340-)  A      NE  <->  394 DOD   (1101 )  A      O      0.17    2.53  INTRA BF
 389 GLC   ( 401-)  A      C6  <->  394 DOD   (1106 )  A      O      0.09    2.71  INTRA
 266 ARG   ( 266-)  A      NH2 <->  376 ASP   ( 376-)  A      OD2    0.08    2.62  INTRA BL
 208 ARG   ( 208-)  A      NH1 <->  394 DOD   (1127 )  A      O      0.07    2.63  INTRA
  71 HIS   (  71-)  A      ND1 <->  394 DOD   (1180 )  A      O      0.06    2.64  INTRA BF
 109 ARG   ( 109-)  A      NH2 <->  394 DOD   (1058 )  A      O      0.06    2.64  INTRA
 387 ARG   ( 387-)  A      O   <->  390 GLY   ( 388-)  A      O''    0.05    2.35  INTRA BF
 215 ASN   ( 215-)  A      OD1 <->  243 HIS   ( 243-)  A      ND1    0.05    2.65  INTRA BL
  64 SER   (  64-)  A      C   <->   66 SER   (  66-)  A      N      0.04    2.86  INTRA BF
  32 ARG   (  32-)  A      NH1 <->   33 ALA   (  33-)  A      O      0.04    2.56  INTRA
 152 ARG   ( 152-)  A      NE  <->  394 DOD   (1149 )  A      O      0.04    2.66  INTRA BF
 101 ASP   ( 101-)  A      OD2 <->  149 LYS   ( 149-)  A      NZ     0.03    2.67  INTRA BL
 315 GLU   ( 315-)  A      OE1 <->  316 ARG   ( 316-)  A      NE     0.03    2.67  INTRA
   6 THR   (   6-)  A      O   <->    9 ASP   (   9-)  A      N      0.02    2.68  INTRA
 250 ASN   ( 250-)  A      O   <->  253 LYS   ( 253-)  A      NZ     0.02    2.68  INTRA
 250 ASN   ( 250-)  A      N   <->  256 GLN   ( 256-)  A      OE1    0.02    2.68  INTRA BL
  76 ARG   (  76-)  A      CD  <->  394 DOD   (1181 )  A      O      0.02    2.78  INTRA BF
  88 MET   (  88-)  A      SD  <->   89 ALA   (  89-)  A      N      0.02    3.18  INTRA BL
  96 HIS   (  96-)  A      ND1 <->   98 VAL   (  98-)  A      N      0.01    2.99  INTRA
 387 ARG   ( 387-)  A      C   <->  390 GLY   ( 388-)  A      O''    0.01    2.79  INTRA BF
 323 ASP   ( 323-)  A      OD2 <->  382 HIS   ( 382-)  A      NE2    0.01    2.69  INTRA
 337 GLU   ( 337-)  A      CG  <->  340 ARG   ( 340-)  A      NH2    0.01    3.09  INTRA

Packing, accessibility and threading

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.

 387 ARG   ( 387-)  A      -7.12
  26 PHE   (  26-)  A      -6.95
  61 PHE   (  61-)  A      -6.93
  23 ARG   (  23-)  A      -6.33
 237 TRP   ( 237-)  A      -6.25
 254 TYR   ( 254-)  A      -6.21
 140 ARG   ( 140-)  A      -5.68
 172 GLN   ( 172-)  A      -5.47
 100 LYS   ( 100-)  A      -5.34
 144 GLU   ( 144-)  A      -5.27
 368 ARG   ( 368-)  A      -5.17

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.

 224 ALA   ( 224-)  A   -2.63

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.

   3 TYR   (   3-)  A      N
   8 GLU   (   8-)  A      N
  16 TRP   (  16-)  A      N
  22 GLY   (  22-)  A      N
  88 MET   (  88-)  A      N
 122 ASN   ( 122-)  A      ND2
 149 LYS   ( 149-)  A      N
 185 ASN   ( 185-)  A      N
 188 ARG   ( 188-)  A      N
 195 THR   ( 195-)  A      N
 195 THR   ( 195-)  A      OG1
 196 VAL   ( 196-)  A      N
 215 ASN   ( 215-)  A      ND2
 244 ILE   ( 244-)  A      N
 247 ASN   ( 247-)  A      N
 253 LYS   ( 253-)  A      N
 288 PHE   ( 288-)  A      N
 337 GLU   ( 337-)  A      N
 361 ASP   ( 361-)  A      N
 363 ASP   ( 363-)  A      N
Only metal coordination for  217 GLU  ( 217-) A      OE1
Only metal coordination for  220 HIS  ( 220-) A      NE2

Warning: Unusual water packing

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

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

 394 DOD   (1012 )  A      O  0.94  K  4
 394 DOD   (1078 )  A      O  1.02  K  4
 394 DOD   (1139 )  A      O  1.00  K  4 Ion-B

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 :  -0.543
  2nd generation packing quality :   1.044
  Ramachandran plot appearance   :  -0.330
  chi-1/chi-2 rotamer normality  :  -1.593
  Backbone conformation          :   0.067

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.440 (tight)
  Bond angles                    :   0.762
  Omega angle restraints         :   0.417 (tight)
  Side chain planarity           :   0.682
  Improper dihedral distribution :   0.953
  B-factor distribution          :   0.495
  Inside/Outside distribution    :   1.046

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 :   0.6
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.440 (tight)
  Bond angles                    :   0.762
  Omega angle restraints         :   0.417 (tight)
  Side chain planarity           :   0.682
  Improper dihedral distribution :   0.953
  B-factor distribution          :   0.495
  Inside/Outside distribution    :   1.046
==============

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.