WHAT IF Check report

This file was created 2011-12-13 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 pdb1cyn.ent

Checks that need to be done early-on in validation

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.

 186 SAR   (   7-)  C  -
 187 ABA   (   6-)  C  -
 188 BMT   (   5-)  C  -
 189 MVA   (   4-)  C  -
 190 DSN   (   1-)  C  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  19 VAL   (  25-)  A  -
 119 VAL   ( 125-)  A  -
 144 VAL   ( 150-)  A  -
 157 LYS   ( 163-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  19 VAL   (  25-)  A  -
 119 VAL   ( 125-)  A  -
 144 VAL   ( 150-)  A  -
 157 LYS   ( 163-)  A  -

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.

 179 MLE   (   2-)  C  -   N   bound to  190 DSN   (   1-)  C  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 179 MLE   (   2-)  C
 180 MLE   (   3-)  C
 181 MLE   (   8-)  C
 183 MLE   (  10-)  C

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.

 144 VAL   ( 150-)  A    1.19

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.

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Nomenclature related problems

Warning: Valine nomenclature problem

The valine residues listed in the table below have their C-gamma-1 and C-gamma-2 swapped.

 144 VAL   ( 150-)  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.

  58 VAL   (  64-)  A      CA   CB    1.64    5.4
 140 VAL   ( 146-)  A      CA   CB    1.64    5.7

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.

   6 VAL   (  12-)  A      N    CA   CB  121.20    6.3
   6 VAL   (  12-)  A      C    CA   CB   98.28   -6.2
   7 LYS   (  13-)  A      CB   CG   CD   99.70   -5.0
  10 PHE   (  16-)  A      CA   CB   CG  120.77    7.0
  19 VAL   (  25-)  A      N    CA   CB  102.80   -4.5
  51 LYS   (  57-)  A      CA   CB   CG  104.98   -4.6
  52 ASN   (  58-)  A      CB   CG   ND2 126.07    6.4
  52 ASN   (  58-)  A      ND2  CG   OD1 116.42   -6.2
  60 LYS   (  66-)  A      CA   CB   CG  103.67   -5.2
  73 ASP   (  79-)  A      CA   CB   CG  117.17    4.6
  83 GLU   (  89-)  A      CA   CB   CG  106.04   -4.0
  85 PHE   (  91-)  A      CA   CB   CG  119.98    6.2
  89 ASN   (  95-)  A      CA   CB   CG  116.63    4.0
  94 HIS   ( 100-)  A      CB   CG   ND1 131.16    6.4
  94 HIS   ( 100-)  A      ND1  CE1  NE2 106.40   -4.1
  94 HIS   ( 100-)  A      CB   CG   CD2 122.31   -5.2
  99 TRP   ( 105-)  A      CG   CD2  CE2 102.23   -4.1
 104 ASN   ( 110-)  A      CB   CG   ND2 124.42    5.3
 104 ASN   ( 110-)  A      ND2  CG   OD1 116.87   -5.7
 115 PHE   ( 121-)  A      CA   CB   CG  119.01    5.2
 123 TRP   ( 129-)  A      CB   CG   CD1 119.73   -4.8
 123 TRP   ( 129-)  A      CD1  CG   CD2 112.74    4.0
 123 TRP   ( 129-)  A      CE3  CD2  CG  139.02    5.1
 123 TRP   ( 129-)  A      CG   CD2  CE2 101.27   -4.9
 142 ARG   ( 148-)  A      CA   CB   CG  102.71   -5.7
 144 VAL   ( 150-)  A      CG1  CB   CG2   7.74  -46.8
 147 THR   ( 153-)  A      N    CA   CB  120.78    6.0
 147 THR   ( 153-)  A      C    CA   CB   96.50   -7.2
 147 THR   ( 153-)  A      CG2  CB   OG1 118.88    4.8
 148 LYS   ( 154-)  A      CB   CG   CD  101.73   -4.2
 150 ASP   ( 156-)  A      CA   CB   CG  117.45    4.9
 177 LYS   ( 183-)  A     -CA  -C    N   105.36   -5.4
 177 LYS   ( 183-)  A      N    CA   C   125.11    5.0
 178 GLU   ( 184-)  A     -CA  -C    N   107.23   -4.5

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.

 144 VAL   ( 150-)  A

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.

 177 LYS   ( 183-)  A    5.31

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.

 119 VAL   ( 125-)  A    -2.4
   6 VAL   (  12-)  A    -2.3
  63 MET   (  69-)  A    -2.3
 152 ARG   ( 158-)  A    -2.3
  71 ARG   (  77-)  A    -2.3
  62 PHE   (  68-)  A    -2.2
 111 GLY   ( 117-)  A    -2.2
 166 LYS   ( 172-)  A    -2.1
 104 ASN   ( 110-)  A    -2.1
 140 VAL   ( 146-)  A    -2.1
  31 VAL   (  37-)  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.

  52 ASN   (  58-)  A  Poor phi/psi
  61 ASP   (  67-)  A  Poor phi/psi
  62 PHE   (  68-)  A  Poor phi/psi
 153 ASP   ( 159-)  A  Poor phi/psi
 176 ALA   ( 182-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -0.500

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 THR   (  11-)  A      0
  14 ILE   (  20-)  A      0
  16 ASP   (  22-)  A      0
  19 VAL   (  25-)  A      0
  27 PHE   (  33-)  A      0
  30 THR   (  36-)  A      0
  31 VAL   (  37-)  A      0
  45 GLU   (  51-)  A      0
  46 LYS   (  52-)  A      0
  48 PHE   (  54-)  A      0
  50 TYR   (  56-)  A      0
  51 LYS   (  57-)  A      0
  52 ASN   (  58-)  A      0
  55 PHE   (  61-)  A      0
  56 HIS   (  62-)  A      0
  62 PHE   (  68-)  A      0
  63 MET   (  69-)  A      0
  70 THR   (  76-)  A      0
  73 ASP   (  79-)  A      0
  75 THR   (  81-)  A      0
  81 TYR   (  87-)  A      0
  83 GLU   (  89-)  A      0
  88 GLU   (  94-)  A      0
  89 ASN   (  95-)  A      0
  90 PHE   (  96-)  A      0
And so on for a total of 94 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 184 ALA   (  11-)  C      C   <->  190 DSN   (   1-)  C      N      1.37    1.33  INTRA B3
 186 SAR   (   7-)  C      N   <->  187 ABA   (   6-)  C      C      1.37    1.33  INTRA B3
 187 ABA   (   6-)  C      N   <->  188 BMT   (   5-)  C      C      1.36    1.34  INTRA B3
 181 MLE   (   8-)  C      N   <->  186 SAR   (   7-)  C      C      1.36    1.34  INTRA B3
 180 MLE   (   3-)  C      C   <->  189 MVA   (   4-)  C      N      1.36    1.34  INTRA B3
 179 MLE   (   2-)  C      N   <->  190 DSN   (   1-)  C      C      1.35    1.35  INTRA B3
 188 BMT   (   5-)  C      N   <->  189 MVA   (   4-)  C      C      1.35    1.35  INTRA B3
 181 MLE   (   8-)  C      CA  <->  186 SAR   (   7-)  C      C      0.81    2.39  INTRA
 188 BMT   (   5-)  C      CA  <->  189 MVA   (   4-)  C      C      0.79    2.41  INTRA
 179 MLE   (   2-)  C      CA  <->  190 DSN   (   1-)  C      C      0.76    2.44  INTRA
 188 BMT   (   5-)  C      CN  <->  189 MVA   (   4-)  C      C      0.72    2.48  INTRA
 181 MLE   (   8-)  C      CN  <->  186 SAR   (   7-)  C      C      0.69    2.51  INTRA
 179 MLE   (   2-)  C      CN  <->  190 DSN   (   1-)  C      C      0.69    2.51  INTRA
 187 ABA   (   6-)  C      CA  <->  188 BMT   (   5-)  C      C      0.68    2.42  INTRA
 184 ALA   (  11-)  C      CA  <->  190 DSN   (   1-)  C      N      0.66    2.44  INTRA
 186 SAR   (   7-)  C      CN  <->  187 ABA   (   6-)  C      C      0.60    2.50  INTRA
 186 SAR   (   7-)  C      CA  <->  187 ABA   (   6-)  C      C      0.60    2.40  INTRA
 180 MLE   (   3-)  C      CA  <->  189 MVA   (   4-)  C      N      0.60    2.50  INTRA
 184 ALA   (  11-)  C      O   <->  190 DSN   (   1-)  C      N      0.47    2.23  INTRA
 180 MLE   (   3-)  C      O   <->  189 MVA   (   4-)  C      N      0.47    2.23  INTRA
 188 BMT   (   5-)  C      CN  <->  189 MVA   (   4-)  C      CA     0.34    2.86  INTRA
 180 MLE   (   3-)  C      CA  <->  189 MVA   (   4-)  C      CN     0.25    2.95  INTRA
 179 MLE   (   2-)  C      CN  <->  190 DSN   (   1-)  C      CA     0.24    2.96  INTRA
 181 MLE   (   8-)  C      CN  <->  186 SAR   (   7-)  C      CA     0.23    2.97  INTRA
 186 SAR   (   7-)  C      CN  <->  187 ABA   (   6-)  C      CA     0.19    2.91  INTRA
 181 MLE   (   8-)  C      CA  <->  186 SAR   (   7-)  C      O      0.16    2.64  INTRA
 180 MLE   (   3-)  C      O   <->  189 MVA   (   4-)  C      CA     0.15    2.65  INTRA
 154 LYS   ( 160-)  A      NZ  <->  191 HOH   (2168 )  A      O      0.13    2.57  INTRA BF
 188 BMT   (   5-)  C      CA  <->  189 MVA   (   4-)  C      O      0.10    2.70  INTRA
 184 ALA   (  11-)  C      O   <->  190 DSN   (   1-)  C      CA     0.09    2.71  INTRA
   1 GLY   (   7-)  A      N   <->  191 HOH   (2001 )  A      O      0.07    2.63  INTRA BF
  54 LYS   (  60-)  A      NZ  <->  154 LYS   ( 160-)  A      NZ     0.07    2.78  INTRA
 179 MLE   (   2-)  C      CA  <->  190 DSN   (   1-)  C      O      0.05    2.75  INTRA
 143 LYS   ( 149-)  A    A NZ  <->  191 HOH   (2147 )  A      O      0.03    2.67  INTRA

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  95 TYR   ( 101-)  A      -6.26
 177 LYS   ( 183-)  A      -6.13
 170 GLU   ( 176-)  A      -5.62
  84 ARG   (  90-)  A      -5.54
 182 VAL   (   9-)  C      -5.34
  71 ARG   (  77-)  A      -5.33

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

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.

 191 HOH   (2009 )  A      O      9.43   16.46   55.06
 191 HOH   (2016 )  A      O     12.06   21.55   29.57
 191 HOH   (2076 )  A      O     16.06  -10.41   44.80
 191 HOH   (2077 )  A      O     16.76  -11.84   42.11
 191 HOH   (2139 )  A      O      7.03   19.96   52.37

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.

 104 ASN   ( 110-)  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.

   6 VAL   (  12-)  A      N
  48 PHE   (  54-)  A      N
  89 ASN   (  95-)  A      N
  96 GLY   ( 102-)  A      N
 104 ASN   ( 110-)  A      N
 119 VAL   ( 125-)  A      N

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.

 191 HOH   (2142 )  A      O  0.88  K  4 Ion-B
 191 HOH   (2156 )  A      O  0.92  K  5

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 :  -1.156
  2nd generation packing quality :  -1.895
  Ramachandran plot appearance   :  -1.224
  chi-1/chi-2 rotamer normality  :  -0.500
  Backbone conformation          :  -0.516

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.725
  Bond angles                    :   1.436
  Omega angle restraints         :   0.873
  Side chain planarity           :   0.515 (tight)
  Improper dihedral distribution :   1.136
  B-factor distribution          :   0.731
  Inside/Outside distribution    :   0.919

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 : 1.85


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.725
  Bond angles                    :   1.436
  Omega angle restraints         :   0.873
  Side chain planarity           :   0.515 (tight)
  Improper dihedral distribution :   1.136
  B-factor distribution          :   0.731
  Inside/Outside distribution    :   0.919
==============

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.