WHAT IF Check report

This file was created 2012-01-05 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 pdb1ose.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: 56395.039
Volume of the Unit Cell V= 959635.375
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.254
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.330

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.

 499 AC1   ( 990-)  A  -
 500 BGC   ( 993-)  A  -
 503 BGC   ( 996-)  A  -
 504 AC1   ( 992-)  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.

 497 GLC   ( 991-)  A  -   O4  bound to  499 AC1   ( 990-)  A  -   C1

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 347 ASN   ( 347-)  A    0.50
 348 PHE   ( 348-)  A    0.50
 349 VAL   ( 349-)  A    0.50
 351 GLY   ( 351-)  A    0.50

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.39

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.

 195 ARG   ( 195-)  A      N    CA   C    99.76   -4.1
 323 VAL   ( 323-)  A      CA   CB   CG1 117.31    4.0
 323 VAL   ( 323-)  A      CA   CB   CG2 132.32   12.8

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.

 323 VAL   ( 323-)  A      CB    14.8   -13.62   -32.96
The average deviation= 0.949

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.

 292 ALA   ( 292-)  A    4.69
 336 THR   ( 336-)  A    4.61
 195 ARG   ( 195-)  A    4.47
 318 ALA   ( 318-)  A    4.45
 382 TRP   ( 382-)  A    4.15
 293 LEU   ( 293-)  A    4.02

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.

 376 THR   ( 376-)  A    -3.0
  92 ARG   (  92-)  A    -2.3
 163 VAL   ( 163-)  A    -2.2
 227 ARG   ( 227-)  A    -2.2
  56 ARG   (  56-)  A    -2.2
  66 SER   (  66-)  A    -2.1
 270 SER   ( 270-)  A    -2.1
 341 SER   ( 341-)  A    -2.1
 237 LEU   ( 237-)  A    -2.1
  69 LEU   (  69-)  A    -2.1
 401 VAL   ( 401-)  A    -2.1

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.

   5 GLN   (   5-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
 102 MET   ( 102-)  A  Poor phi/psi
 124 ARG   ( 124-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 221 TRP   ( 221-)  A  Poor phi/psi
 268 LYS   ( 268-)  A  Poor phi/psi
 350 ASN   ( 350-)  A  Poor phi/psi
 364 ASN   ( 364-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 486 PRO   ( 486-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.974

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 GLN   (   5-)  A      0
   8 SER   (   8-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  30 ARG   (  30-)  A      0
  35 LYS   (  35-)  A      0
  45 PRO   (  45-)  A      0
  48 ASN   (  48-)  A      0
  52 THR   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 SER   (  55-)  A      0
  56 ARG   (  56-)  A      0
  58 TRP   (  58-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
  73 SER   (  73-)  A      0
  75 ASN   (  75-)  A      0
And so on for a total of 216 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 : 1.496

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.

 500 BGC   ( 993-)  A      O4  <->  504 AC1   ( 992-)  A      C1     1.00    1.40  INTRA B3
 500 BGC   ( 993-)  A      C4  <->  504 AC1   ( 992-)  A      C1     0.78    2.42  INTRA
  10 ARG   (  10-)  A      NH2 <->   33 GLY   (  33-)  A      O      0.24    2.46  INTRA
 404 GLU   ( 404-)  A      O   <->  421 ARG   ( 421-)  A      NH1    0.24    2.46  INTRA
 195 ARG   ( 195-)  A      NH1 <->  501  CL   ( 498-)  A     CL      0.20    2.90  INTRA BL
 100 ASN   ( 100-)  A      ND2 <->  101 HIS   ( 101-)  A      CD2    0.11    2.99  INTRA BL
  11 THR   (  11-)  A      OG1 <->  399 ASN   ( 399-)  A      ND2    0.10    2.60  INTRA BL
 170 LEU   ( 170-)  A      O   <->  176 ARG   ( 176-)  A      CD     0.09    2.71  INTRA BL
 421 ARG   ( 421-)  A      NH2 <->  505 HOH   (1069 )  A      O      0.09    2.61  INTRA
 158 ARG   ( 158-)  A      NH1 <->  247 TYR   ( 247-)  A      OH     0.08    2.62  INTRA BL
 214 LEU   ( 214-)  A      O   <->  227 ARG   ( 227-)  A      NH2    0.07    2.63  INTRA
 103 CYS   ( 103-)  A      SG  <->  121 PRO   ( 121-)  A      CG     0.06    3.34  INTRA
 291 ARG   ( 291-)  A      N   <->  292 ALA   ( 292-)  A      N      0.05    2.55  INTRA BL
 389 ARG   ( 389-)  A      NH1 <->  453 ILE   ( 453-)  A      O      0.05    2.65  INTRA
 494 SER   ( 494-)  A      N   <->  495 LYS   ( 495-)  A      N      0.04    2.56  INTRA BL
 201 HIS   ( 201-)  A      NE2 <->  504 AC1   ( 992-)  A      O2     0.03    2.67  INTRA
 259 GLY   ( 259-)  A      N   <->  505 HOH   (1012 )  A      O      0.02    2.68  INTRA
 195 ARG   ( 195-)  A      NH2 <->  197 ASP   ( 197-)  A      OD1    0.02    2.68  INTRA BL
 337 ARG   ( 337-)  A      NH2 <->  501  CL   ( 498-)  A     CL      0.02    3.08  INTRA BL

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.

  72 ARG   (  72-)  A      -6.98
   7 GLN   (   7-)  A      -5.74
   2 TYR   (   2-)  A      -5.64
 118 TYR   ( 118-)  A      -5.42
 284 TRP   ( 284-)  A      -5.38
  30 ARG   (  30-)  A      -5.33
 279 ASN   ( 279-)  A      -5.32
  88 ASN   (  88-)  A      -5.30
 302 GLN   ( 302-)  A      -5.29
 343 ARG   ( 343-)  A      -5.26
 303 ARG   ( 303-)  A      -5.24
  53 ASN   (  53-)  A      -5.22
 267 ARG   ( 267-)  A      -5.12

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 235 ILE   ( 235-)  A     -  238 GLY   ( 238-)  A        -1.86

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

 506 HOH   (1240 )  A      O     54.12   28.39   10.72
 507 HOH   (1271 )  A      O     46.84   -1.07   31.08
 507 HOH   (1366 )  A      O     22.99   44.01  -10.18
 507 HOH   (1382 )  A      O     40.20   36.17   -9.55

Error: Water molecules without hydrogen bonds

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

 507 HOH   (1279 )  A      O
 507 HOH   (1304 )  A      O
 507 HOH   (1375 )  A      O
 507 HOH   (1380 )  A      O
 507 HOH   (1382 )  A      O
 507 HOH   (1396 )  A      O
Marked this atom as acceptor  501  CL  ( 498-) A     CL
Strange metal coordination for HIS 201

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.

  15 HIS   (  15-)  A
 101 HIS   ( 101-)  A
 152 ASN   ( 152-)  A
 279 ASN   ( 279-)  A
 373 ASN   ( 373-)  A
 399 ASN   ( 399-)  A
 408 ASN   ( 408-)  A
 435 GLN   ( 435-)  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.

  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
 101 HIS   ( 101-)  A      N
 158 ARG   ( 158-)  A      NE
 175 VAL   ( 175-)  A      N
 193 GLY   ( 193-)  A      N
 195 ARG   ( 195-)  A      NH1
 241 ALA   ( 241-)  A      N
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 299 HIS   ( 299-)  A      NE2
 308 GLY   ( 308-)  A      N
 314 THR   ( 314-)  A      N
 316 TRP   ( 316-)  A      NE1
 337 ARG   ( 337-)  A      NH2
 344 TRP   ( 344-)  A      N
 364 ASN   ( 364-)  A      ND2
 370 VAL   ( 370-)  A      N
 434 TRP   ( 434-)  A      N
Only metal coordination for  100 ASN  ( 100-) A      OD1

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.

 201 HIS   ( 201-)  A      NE2
 300 ASP   ( 300-)  A      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 505 HOH   (1032 )  A      O  0.95  K  4
 505 HOH   (1070 )  A      O  1.12  K  4
 507 HOH   (1339 )  A      O  1.00  K  4
 507 HOH   (1394 )  A      O  0.96  K  4 ION-B

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.

 181 ASP   ( 181-)  A   H-bonding suggests Asn
 352 GLU   ( 352-)  A   H-bonding suggests Gln

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 :  -0.997
  2nd generation packing quality :  -1.846
  Ramachandran plot appearance   :  -1.426
  chi-1/chi-2 rotamer normality  :  -1.974
  Backbone conformation          :  -1.001

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.309 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   0.272 (tight)
  Side chain planarity           :   0.299 (tight)
  Improper dihedral distribution :   0.880
  B-factor distribution          :   1.078
  Inside/Outside distribution    :   0.996

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 :  -0.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.309 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   0.272 (tight)
  Side chain planarity           :   0.299 (tight)
  Improper dihedral distribution :   0.880
  B-factor distribution          :   1.078
  Inside/Outside distribution    :   0.996
==============

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.