WHAT IF Check report

This file was created 2013-12-09 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 pdb3vx0.ent

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: Tyrosine convention problem

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

  51 TYR   (  51-)  A

Warning: Phenylalanine convention problem

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

 317 PHE   ( 317-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

   5 ASP   (   5-)  A
 144 ASP   ( 144-)  A
 270 ASP   ( 270-)  A
 391 ASP   ( 391-)  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.

  92 GLU   (  92-)  A
 294 GLU   ( 294-)  A
 467 GLU   ( 467-)  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.

 216 TRP   ( 216-)  A      NE1  CE2   1.50   11.7

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: 0.372
RMS-deviation in bond distances: 0.009

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.

   2 THR   (   2-)  A     -O   -C    N   114.31   -5.4
 148 PRO   ( 148-)  A      N    CA   CB  107.52    4.1
 217 PRO   ( 217-)  A      N    CA   CB  107.93    4.5
 317 PHE   ( 317-)  A      CA   CB   CG  109.63   -4.2
 353 PRO   ( 353-)  A     -O   -C    N   115.59   -4.6
 438 ILE   ( 438-)  A     -O   -C    N   116.56   -4.0

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.

   5 ASP   (   5-)  A
  92 GLU   (  92-)  A
 144 ASP   ( 144-)  A
 270 ASP   ( 270-)  A
 294 GLU   ( 294-)  A
 391 ASP   ( 391-)  A
 467 GLU   ( 467-)  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.

   1 ALA   (   1-)  A      C     -7.4   -11.27     0.08
The average deviation= 0.910

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.

  11 ILE   (  11-)  A    5.10
 213 LYS   ( 213-)  A    4.47
  18 ARG   (  18-)  A    4.07

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.

 207 THR   ( 207-)  A    -3.4
 334 HIS   ( 334-)  A    -2.9
 341 PRO   ( 341-)  A    -2.7
 389 LYS   ( 389-)  A    -2.6
 419 TYR   ( 419-)  A    -2.5
 139 PRO   ( 139-)  A    -2.5
 305 THR   ( 305-)  A    -2.5
 440 CYS   ( 440-)  A    -2.4
  14 LEU   (  14-)  A    -2.4
 174 PRO   ( 174-)  A    -2.4
 308 ILE   ( 308-)  A    -2.3
  48 LYS   (  48-)  A    -2.2
 199 SER   ( 199-)  A    -2.1
  94 TYR   (  94-)  A    -2.0
 136 VAL   ( 136-)  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.

  71 GLN   (  71-)  A  omega poor
  85 GLN   (  85-)  A  Poor phi/psi
 122 HIS   ( 122-)  A  omega poor
 138 LYS   ( 138-)  A  PRO omega poor
 140 PHE   ( 140-)  A  Poor phi/psi
 168 ASP   ( 168-)  A  Poor phi/psi
 215 PHE   ( 215-)  A  omega poor
 334 HIS   ( 334-)  A  Poor phi/psi
 340 ASP   ( 340-)  A  PRO omega poor
 352 TYR   ( 352-)  A  Poor phi/psi
 390 ASP   ( 390-)  A  Poor phi/psi
 440 CYS   ( 440-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.331

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.

 104 SER   ( 104-)  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!

   9 GLN   (   9-)  A      0
  19 PHE   (  19-)  A      0
  29 THR   (  29-)  A      0
  30 CYS   (  30-)  A      0
  34 ASP   (  34-)  A      0
  36 LYS   (  36-)  A      0
  38 CYS   (  38-)  A      0
  42 TRP   (  42-)  A      0
  48 LYS   (  48-)  A      0
  49 LEU   (  49-)  A      0
  55 MET   (  55-)  A      0
  57 PHE   (  57-)  A      0
  63 THR   (  63-)  A      0
  65 VAL   (  65-)  A      0
  68 GLN   (  68-)  A      0
  70 PRO   (  70-)  A      0
  75 TYR   (  75-)  A      0
  77 ASP   (  77-)  A      0
  78 ALA   (  78-)  A      0
  82 TYR   (  82-)  A      0
  83 TRP   (  83-)  A      0
  84 GLN   (  84-)  A      0
  88 TYR   (  88-)  A      0
  94 TYR   (  94-)  A      0
 120 ALA   ( 120-)  A      0
And so on for a total of 189 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 : 3.350

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.

 433 GLN   ( 433-)  A      NE2 <->  442 THR   ( 442-)  A      CB     0.62    2.48  INTRA
  92 GLU   (  92-)  A      OE2 <->  484 HOH   (1270 )  A      O      0.44    1.96  INTRA
 484 HOH   (1604 )  A      O   <->  484 HOH   (1684 )  A      O      0.36    1.84  INTRA
 357 GLU   ( 357-)  A      CD  <->  484 HOH   (1605 )  A      O      0.35    2.45  INTRA
 280 LYS   ( 280-)  A      NZ  <->  484 HOH   (1560 )  A      O      0.33    2.37  INTRA
 397 ARG   ( 397-)  A      NH2 <->  401 ASP   ( 401-)  A      OD1    0.29    2.41  INTRA
 433 GLN   ( 433-)  A      NE2 <->  442 THR   ( 442-)  A      CG2    0.29    2.81  INTRA
 312 LYS   ( 312-)  A      NZ  <->  357 GLU   ( 357-)  A      OE2    0.28    2.42  INTRA
   1 ALA   (   1-)  A      N   <->  201 ASP   ( 201-)  A      O      0.27    2.43  INTRA BL
 252 TYR   ( 252-)  A      N   <->  253 PRO   ( 253-)  A      CD     0.26    2.74  INTRA BL
  48 LYS   (  48-)  A      NZ  <->  484 HOH   (1496 )  A      O      0.26    2.44  INTRA
 357 GLU   ( 357-)  A      OE1 <->  484 HOH   (1605 )  A      O      0.25    2.15  INTRA
 150 CYS   ( 150-)  A      O   <->  165 TRP   ( 165-)  A      N      0.23    2.47  INTRA
 432 GLN   ( 432-)  A      NE2 <->  484 HOH   (1429 )  A      O      0.23    2.47  INTRA
 182 VAL   ( 182-)  A      CG1 <->  183 VAL   ( 183-)  A      N      0.17    2.83  INTRA
 375 LYS   ( 375-)  A      NZ  <->  484 HOH   (1452 )  A      O      0.16    2.54  INTRA
 321 ASN   ( 321-)  A      CG  <->  322 ASP   ( 322-)  A      N      0.16    2.84  INTRA BL
  61 TRP   (  61-)  A      CZ2 <->  204 ARG   ( 204-)  A      NE     0.16    2.94  INTRA BL
 484 HOH   (1585 )  A      O   <->  484 HOH   (1634 )  A      O      0.15    2.05  INTRA
 216 TRP   ( 216-)  A      N   <->  217 PRO   ( 217-)  A      CD     0.14    2.86  INTRA BL
   9 GLN   (   9-)  A      NE2 <->   58 THR   (  58-)  A      OG1    0.13    2.57  INTRA BL
 388 TYR   ( 388-)  A      CG  <->  389 LYS   ( 389-)  A      N      0.13    2.87  INTRA
 352 TYR   ( 352-)  A      N   <->  353 PRO   ( 353-)  A      CD     0.12    2.88  INTRA BL
 169 ASN   ( 169-)  A      ND2 <->  484 HOH   (1271 )  A      O      0.11    2.59  INTRA
  93 ASN   (  93-)  A      ND2 <->  484 HOH   (1214 )  A      O      0.11    2.59  INTRA
And so on for a total of 63 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.

  88 TYR   (  88-)  A      -6.33
 232 LEU   ( 232-)  A      -6.04
 333 GLN   ( 333-)  A      -5.39
 244 ASN   ( 244-)  A      -5.06

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.

 245 VAL   ( 245-)  A   -2.65
 151 PHE   ( 151-)  A   -2.63
 288 LEU   ( 288-)  A   -2.51

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.

  91 ASN   (  91-)  A     -   94 TYR   (  94-)  A        -1.32

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.

 484 HOH   (1196 )  A      O     15.99   14.37   -0.80
 484 HOH   (1325 )  A      O    -17.31   18.40   24.91
 484 HOH   (1347 )  A      O     18.84   30.44   -7.54
 484 HOH   (1358 )  A      O     -6.19   45.38   18.66
 484 HOH   (1359 )  A      O     -3.73   48.88   17.45
 484 HOH   (1389 )  A      O     -1.93    1.13    9.73
 484 HOH   (1397 )  A      O     11.96   57.22   -9.82
 484 HOH   (1553 )  A      O     15.59   28.18  -10.53
 484 HOH   (1577 )  A      O     15.33   51.51   -0.60
 484 HOH   (1616 )  A      O      4.24   39.63   27.60
 484 HOH   (1622 )  A      O      6.44   39.57   29.14
 484 HOH   (1637 )  A      O     29.57   11.67   13.75
 484 HOH   (1641 )  A      O     10.26   54.39   -9.18
 484 HOH   (1653 )  A      O     17.83   49.76   -0.39
 484 HOH   (1668 )  A      O      5.56   56.22   -8.70

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.

   9 GLN   (   9-)  A
  93 ASN   (  93-)  A
 143 GLN   ( 143-)  A
 212 GLN   ( 212-)  A
 296 HIS   ( 296-)  A
 333 GLN   ( 333-)  A
 370 ASN   ( 370-)  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.

  16 THR   (  16-)  A      OG1
  79 TYR   (  79-)  A      N
  80 HIS   (  80-)  A      N
 122 HIS   ( 122-)  A      N
 130 SER   ( 130-)  A      OG
 140 PHE   ( 140-)  A      N
 142 SER   ( 142-)  A      N
 175 ASP   ( 175-)  A      N
 204 ARG   ( 204-)  A      NE
 249 VAL   ( 249-)  A      N
 264 SER   ( 264-)  A      N
 322 ASP   ( 322-)  A      N
 343 ASN   ( 343-)  A      N
 343 ASN   ( 343-)  A      ND2
 348 TRP   ( 348-)  A      N
 366 ASN   ( 366-)  A      ND2
 384 ASN   ( 384-)  A      N
 399 GLY   ( 399-)  A      N
 428 TYR   ( 428-)  A      N
Only metal coordination for  121 ASN  ( 121-) 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+.

 483  CA   (1008-)  A     0.65   0.88 Scores about as good as NA

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.

 484 HOH   (1122 )  A      O  0.90  K  4
 484 HOH   (1144 )  A      O  0.86 NA  5 (or CA *1 and *2)
 484 HOH   (1216 )  A      O  0.99  K  5
 484 HOH   (1270 )  A      O  0.94 NA  6 (or CA *1 and *2) Ion-B
 484 HOH   (1453 )  A      O  0.90  K  4 Ion-B
 484 HOH   (1471 )  A      O  0.98  K  5 Ion-B
 484 HOH   (1538 )  A      O  0.99  K  5 Ion-B
 484 HOH   (1605 )  A      O  0.99 NA  5
 484 HOH   (1614 )  A      O  1.11 CA  4 *1 and *2 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 :  -0.397
  2nd generation packing quality :  -2.352
  Ramachandran plot appearance   :  -1.386
  chi-1/chi-2 rotamer normality  :  -2.331
  Backbone conformation          :  -1.122

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.372 (tight)
  Bond angles                    :   0.734
  Omega angle restraints         :   0.609 (tight)
  Side chain planarity           :   0.500 (tight)
  Improper dihedral distribution :   0.776
  B-factor distribution          :   0.429
  Inside/Outside distribution    :   0.968

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 : 1.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -2.0
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.372 (tight)
  Bond angles                    :   0.734
  Omega angle restraints         :   0.609 (tight)
  Side chain planarity           :   0.500 (tight)
  Improper dihedral distribution :   0.776
  B-factor distribution          :   0.429
  Inside/Outside distribution    :   0.968
==============

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.