WHAT IF Check report

This file was created 2011-12-18 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 pdb1z4v.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 49759.715
Volume of the Unit Cell V= 3041622.0
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.094
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.340

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.

 451 DAN   ( 601-)  A  -
 452 NDG   (   1-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 445 NAG   (   2-)  A  -   O4  bound to  446 NAG   (   3-)  A  -   C1
 447 NAG   (   4-)  A  -   O4  bound to  448 NAG   (   5-)  A  -   C1

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. 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

Nomenclature related problems

Warning: Phenylalanine convention problem

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

  34 PHE   ( 151-)  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.

  61 HIS   ( 178-)  A      CG   ND1  CE1 109.88    4.3

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.

  27 PRO   ( 144-)  A      N     -6.6   -24.01    -2.48
The average deviation= 0.877

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.

 168 PRO   ( 289-)  A    4.43
  13 PHE   ( 130-)  A    4.28

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.

 436 PRO   ( 557-)  A    -2.9
 375 ILE   ( 496-)  A    -2.7
  47 ILE   ( 164-)  A    -2.7
 170 THR   ( 291-)  A    -2.7
 370 THR   ( 491-)  A    -2.7
 320 PRO   ( 441-)  A    -2.5
 321 ARG   ( 442-)  A    -2.4
 105 SER   ( 226-)  A    -2.4
 232 PHE   ( 353-)  A    -2.3
 341 VAL   ( 462-)  A    -2.3
  88 PHE   ( 209-)  A    -2.3
 339 THR   ( 460-)  A    -2.3
  96 TYR   ( 217-)  A    -2.3
  60 THR   ( 177-)  A    -2.3
 290 PRO   ( 411-)  A    -2.2
 316 THR   ( 437-)  A    -2.2
 185 TYR   ( 306-)  A    -2.2
 414 VAL   ( 535-)  A    -2.1
 200 ASN   ( 321-)  A    -2.1
 403 GLY   ( 524-)  A    -2.1
  53 THR   ( 170-)  A    -2.1
 147 ASP   ( 268-)  A    -2.0
  61 HIS   ( 178-)  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.

  47 ILE   ( 164-)  A  Poor phi/psi
 147 ASP   ( 268-)  A  Poor phi/psi
 161 ASP   ( 282-)  A  Poor phi/psi
 170 THR   ( 291-)  A  Poor phi/psi
 200 ASN   ( 321-)  A  Poor phi/psi
 234 ASN   ( 355-)  A  Poor phi/psi
 287 SER   ( 408-)  A  Poor phi/psi
 303 ASN   ( 424-)  A  Poor phi/psi
 319 VAL   ( 440-)  A  Poor phi/psi
 332 ARG   ( 453-)  A  Poor phi/psi
 376 ASN   ( 497-)  A  Poor phi/psi
 385 THR   ( 506-)  A  Poor phi/psi
 401 ALA   ( 522-)  A  Poor phi/psi
 414 VAL   ( 535-)  A  Poor phi/psi
 428 LEU   ( 549-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.875

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!

   6 TYR   ( 123-)  A      0
  10 ILE   ( 127-)  A      0
  11 ASN   ( 128-)  A      0
  12 GLN   ( 129-)  A      0
  14 TYR   ( 131-)  A      0
  23 LEU   ( 140-)  A      0
  31 MET   ( 148-)  A      0
  34 PHE   ( 151-)  A      0
  46 ARG   ( 163-)  A      0
  47 ILE   ( 164-)  A      0
  48 PRO   ( 165-)  A      0
  55 THR   ( 172-)  A      0
  56 HIS   ( 173-)  A      0
  61 HIS   ( 178-)  A      0
  66 ASN   ( 183-)  A      0
  68 CYS   ( 185-)  A      0
  69 GLN   ( 186-)  A      0
  70 SER   ( 191-)  A      0
  71 ASN   ( 192-)  A      0
  76 MET   ( 197-)  A      0
  80 GLU   ( 201-)  A      0
  86 PHE   ( 207-)  A      0
  87 PRO   ( 208-)  A      0
  92 LEU   ( 213-)  A      0
  98 SER   ( 219-)  A      0
And so on for a total of 202 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 : 1.666

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

  43 GLY   ( 160-)  A   1.66   20

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].

  27 PRO   ( 144-)  A   153.8 half-chair C-alpha/N (162 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.

  22 ASN   ( 139-)  A      ND2 <->  452 NDG   (   1-)  A      C1     1.24    1.46  INTRA BF
  22 ASN   ( 139-)  A      CG  <->  452 NDG   (   1-)  A      C1     0.78    2.42  INTRA BF
 207 MET   ( 328-)  A      CE  <->  317 GLN   ( 438-)  A      NE2    0.35    2.75  INTRA
 321 ARG   ( 442-)  A      NH2 <->  327 CYS   ( 448-)  A      O      0.33    2.37  INTRA BF
 198 GLN   ( 319-)  A      CG  <->  261 ASN   ( 382-)  A      ND2    0.27    2.83  INTRA
  53 THR   ( 170-)  A      CG2 <->   54 LYS   ( 171-)  A      N      0.22    2.78  INTRA BL
  14 TYR   ( 131-)  A      O   <->  409 ARG   ( 530-)  A      NH2    0.22    2.48  INTRA
 370 THR   ( 491-)  A      CG2 <->  373 GLN   ( 494-)  A      O      0.19    2.61  INTRA
 264 VAL   ( 385-)  A      CG1 <->  283 GLN   ( 404-)  A      NE2    0.18    2.92  INTRA BL
 247 ARG   ( 368-)  A      NH1 <->  249 ASP   ( 370-)  A      OD1    0.18    2.52  INTRA BF
  37 THR   ( 154-)  A      CG2 <->   38 ALA   ( 155-)  A      N      0.16    2.84  INTRA BL
 410 ASP   ( 531-)  A      OD1 <->  412 GLY   ( 533-)  A      N      0.16    2.54  INTRA BL
 247 ARG   ( 368-)  A      NH1 <->  249 ASP   ( 370-)  A      CG     0.16    2.94  INTRA BF
 391 GLN   ( 512-)  A      OE1 <->  439 ARG   ( 560-)  A      NH1    0.13    2.57  INTRA
 370 THR   ( 491-)  A      CG2 <->  373 GLN   ( 494-)  A      N      0.12    2.98  INTRA
 318 GLN   ( 439-)  A      CG  <->  385 THR   ( 506-)  A      C      0.12    3.08  INTRA
 264 VAL   ( 385-)  A      CG1 <->  265 LEU   ( 386-)  A      N      0.11    2.89  INTRA BL
   1 ILE   ( 118-)  A      N   <->  453 HOH   ( 610 )  A      O      0.10    2.60  INTRA
 300 THR   ( 421-)  A      O   <->  307 SER   ( 428-)  A      N      0.10    2.60  INTRA BF
 317 GLN   ( 438-)  A      N   <->  318 GLN   ( 439-)  A      N      0.09    2.51  INTRA B3
 415 MET   ( 536-)  A      CB  <->  440 GLN   ( 561-)  A      NE2    0.09    3.01  INTRA
   1 ILE   ( 118-)  A      CG1 <->    2 ASN   ( 119-)  A      N      0.09    2.91  INTRA BL
 375 ILE   ( 496-)  A      CG2 <->  376 ASN   ( 497-)  A      CG     0.09    3.11  INTRA
 130 TYR   ( 251-)  A      O   <->  235 ARG   ( 356-)  A      NE     0.08    2.62  INTRA
 212 CYS   ( 333-)  A      SG  <->  333 CYS   ( 454-)  A      SG     0.08    3.37  INTRA BF
And so on for a total of 56 lines.

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.

  65 LEU   ( 182-)  A      -6.11
 428 LEU   ( 549-)  A      -5.92
 321 ARG   ( 442-)  A      -5.52
 393 PHE   ( 514-)  A      -5.49
 160 LEU   ( 281-)  A      -5.35
 177 LEU   ( 298-)  A      -5.30
  30 ASN   ( 147-)  A      -5.17
 247 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.

   7 ILE   ( 124-)  A   -2.68

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.

   8 ASN   ( 125-)  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.

  12 GLN   ( 129-)  A      N
  30 ASN   ( 147-)  A      ND2
  34 PHE   ( 151-)  A      N
  40 THR   ( 157-)  A      OG1
  46 ARG   ( 163-)  A      NH2
  56 HIS   ( 173-)  A      N
  86 PHE   ( 207-)  A      N
 165 THR   ( 286-)  A      OG1
 166 LEU   ( 287-)  A      N
 233 GLY   ( 354-)  A      N
 247 ARG   ( 368-)  A      NH1
 254 CYS   ( 375-)  A      N
 289 TRP   ( 410-)  A      N
 289 TRP   ( 410-)  A      NE1
 291 MET   ( 412-)  A      N
 305 GLN   ( 426-)  A      N
 321 ARG   ( 442-)  A      NH2
 335 GLY   ( 456-)  A      N
 341 VAL   ( 462-)  A      N
 342 TYR   ( 463-)  A      N
 345 ALA   ( 466-)  A      N
 362 THR   ( 483-)  A      N
 373 GLN   ( 494-)  A      N
 407 CYS   ( 528-)  A      N
 428 LEU   ( 549-)  A      N
 439 ARG   ( 560-)  A      NE

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.

 167 ASN   ( 288-)  A      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 450  CA   ( 600-)  A     0.79   1.02 Scores about as good as NA *2

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.

 453 HOH   ( 630 )  A      O  0.93  K  4
 453 HOH   ( 771 )  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 :  -0.201
  2nd generation packing quality :  -1.225
  Ramachandran plot appearance   :  -1.459
  chi-1/chi-2 rotamer normality  :  -1.875
  Backbone conformation          :  -0.083

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.368 (tight)
  Bond angles                    :   0.669
  Omega angle restraints         :   0.303 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.733
  B-factor distribution          :   0.453
  Inside/Outside distribution    :   1.026

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.368 (tight)
  Bond angles                    :   0.669
  Omega angle restraints         :   0.303 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.733
  B-factor distribution          :   0.453
  Inside/Outside distribution    :   1.026
==============

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.