WHAT IF Check report

This file was created 2012-01-30 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 pdb3koi.ent

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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  12 TRP   (  16-)  A    Zero
  24 GLN   (  28-)  A    Zero
  25 SER   (  29-)  A    Zero
  26 PRO   (  30-)  A    Zero
  27 VAL   (  31-)  A    Zero
  29 ILE   (  33-)  A    Zero
  47 TYR   (  51-)  A    Zero
  55 ILE   (  59-)  A    Zero
  57 ASN   (  61-)  A    Zero
  61 ALA   (  65-)  A    Zero
  62 PHE   (  66-)  A    Zero
  63 ASN   (  67-)  A    Zero
  84 TYR   (  88-)  A    Zero
  86 LEU   (  90-)  A    Zero
  87 ILE   (  91-)  A    Zero
  88 GLN   (  92-)  A    Zero
  89 PHE   (  93-)  A    Zero
  90 HIS   (  94-)  A    Zero
  91 PHE   (  95-)  A    Zero
  92 HIS   (  96-)  A    Zero
  95 SER   (  99-)  A    Zero
  97 ASP   ( 101-)  A    Zero
 100 GLY   ( 104-)  A    Zero
 101 SER   ( 105-)  A    Zero
 102 GLU   ( 106-)  A    Zero
And so on for a total of 78 lines.

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.

  10 GLU   (  14-)  A    0.30

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) :300.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 50.62

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: Tyrosine convention problem

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

   3 TYR   (   7-)  A
 186 TYR   ( 191-)  A

Warning: Phenylalanine convention problem

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

  62 PHE   (  66-)  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.

  30 ASP   (  34-)  A
  48 ASP   (  52-)  A
 160 ASP   ( 165-)  A
 170 ASP   ( 175-)  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.

 231 GLU   ( 236-)  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.

 122 LYS   ( 127-)  A      N   -C     1.24   -4.5

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: 0.328
RMS-deviation in bond distances: 0.007

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 HIS   (  10-)  A      CA   CB   CG  109.70   -4.1
  10 GLU   (  14-)  A     -C    N    CA  114.39   -4.1
  13 HIS   (  17-)  A      CA   CB   CG  109.18   -4.6
  60 HIS   (  64-)  A      CG   ND1  CE1 109.64    4.0
  89 PHE   (  93-)  A      CA   CB   CG  119.99    6.2
  90 HIS   (  94-)  A      CA   CB   CG  109.46   -4.3
  90 HIS   (  94-)  A      CG   ND1  CE1 109.98    4.4
  91 PHE   (  95-)  A      CA   CB   CG  117.83    4.0
  92 HIS   (  96-)  A      CA   CB   CG  118.42    4.6
  92 HIS   (  96-)  A      CG   ND1  CE1 110.40    4.8
 107 LYS   ( 111-)  A     -C    N    CA  133.96    6.8
 115 HIS   ( 119-)  A      CA   C    O   113.06   -4.6
 116 LEU   ( 120-)  A     -O   -C    N   131.06    5.0
 117 VAL   ( 121-)  A     -C    N    CA  129.10    4.1
 125 ASP   ( 130-)  A      CA   CB   CG  119.31    6.7
 146 GLY   ( 151-)  A     -C    N    CA  129.91    5.5
 160 ASP   ( 165-)  A      CA   CB   CG  117.81    5.2
 170 ASP   ( 175-)  A      CA   CB   CG  117.11    4.5
 173 ASN   ( 178-)  A     -C    N    CA  128.95    4.0
 173 ASN   ( 178-)  A      CA   CB   CG  108.53   -4.1
 219 LEU   ( 224-)  A     -C    N    CA  113.68   -4.5
 221 PHE   ( 226-)  A      CA   CB   CG  123.91   10.1
 222 ARG   ( 227-)  A      CD   NE   CZ  128.90    4.0
 226 PHE   ( 231-)  A      CA   CB   CG  118.69    4.9
 241 ARG   ( 246-)  A      CD   NE   CZ  130.33    4.8
 251 ILE   ( 256-)  A     -C    N    CA  114.44   -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.

  30 ASP   (  34-)  A
  48 ASP   (  52-)  A
 160 ASP   ( 165-)  A
 170 ASP   ( 175-)  A
 231 GLU   ( 236-)  A

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.

 171 PHE   ( 176-)  A    -2.5
  79 PRO   (  83-)  A    -2.4
  38 PRO   (  42-)  A    -2.2
 188 THR   ( 193-)  A    -2.2
  10 GLU   (  14-)  A    -2.2
  35 LYS   (  39-)  A    -2.2
 231 GLU   ( 236-)  A    -2.2
  56 LEU   (  60-)  A    -2.2
 162 ILE   ( 167-)  A    -2.2
 245 PRO   ( 250-)  A    -2.1
  88 GLN   (  92-)  A    -2.0
 197 PRO   ( 202-)  A    -2.0
 149 LYS   ( 154-)  A    -2.0
 247 LYS   ( 252-)  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.

  25 SER   (  29-)  A  PRO omega poor
  53 LEU   (  57-)  A  Poor phi/psi
  72 LYS   (  76-)  A  Poor phi/psi
 107 LYS   ( 111-)  A  Poor phi/psi
 173 ASN   ( 178-)  A  Poor phi/psi
 186 TYR   ( 191-)  A  omega poor
 196 PRO   ( 201-)  A  PRO omega poor
 198 LEU   ( 203-)  A  Poor phi/psi
 238 ASP   ( 243-)  A  Poor phi/psi
 247 LYS   ( 252-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.979

Warning: Unusual backbone conformations

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

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

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

   3 TYR   (   7-)  A      0
   6 HIS   (  10-)  A      0
  15 ASP   (  19-)  A      0
  16 PHE   (  20-)  A      0
  20 LYS   (  24-)  A      0
  23 ARG   (  27-)  A      0
  25 SER   (  29-)  A      0
  34 ALA   (  38-)  A      0
  46 SER   (  50-)  A      0
  48 ASP   (  52-)  A      0
  49 GLN   (  53-)  A      0
  50 ALA   (  54-)  A      0
  53 LEU   (  57-)  A      0
  58 ASN   (  62-)  A      0
  60 HIS   (  64-)  A      0
  61 ALA   (  65-)  A      0
  68 ASP   (  72-)  A      0
  69 SER   (  73-)  A      0
  71 ASP   (  75-)  A      0
  73 ALA   (  77-)  A      0
  76 LYS   (  80-)  A      0
  79 PRO   (  83-)  A      0
  81 ASP   (  85-)  A      0
  88 GLN   (  92-)  A      0
  99 GLN   ( 103-)  A      0
And so on for a total of 119 lines.

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].

  38 PRO   (  42-)  A   -58.3 half-chair C-beta/C-alpha (-54 degrees)
  42 PRO   (  46-)  A    52.3 half-chair C-delta/C-gamma (54 degrees)
 190 PRO   ( 195-)  A   -64.0 envelop C-beta (-72 degrees)
 197 PRO   ( 202-)  A    45.5 half-chair C-delta/C-gamma (54 degrees)
 210 PRO   ( 215-)  A    47.2 half-chair C-delta/C-gamma (54 degrees)
 245 PRO   ( 250-)  A   102.5 envelop C-beta (108 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.

 239 ASN   ( 244-)  A      ND2 <->  258 HOH   ( 347 )  A      O      1.19    1.51  INTRA BF
 239 ASN   ( 244-)  A      CG  <->  258 HOH   ( 347 )  A      O      0.90    1.90  INTRA BF
 224 LEU   ( 229-)  A      CB  <->  258 HOH   ( 306 )  A      O      0.87    1.93  INTRA BF
 236 MET   ( 241-)  A      CB  <->  258 HOH   ( 306 )  A      O      0.77    2.03  INTRA BF
 236 MET   ( 241-)  A      SD  <->  258 HOH   ( 306 )  A      O      0.27    2.73  INTRA BF
 183 SER   ( 188-)  A      N   <->  209 GLU   ( 214-)  A      OE1    0.21    2.49  INTRA BL
  83 THR   (  87-)  A      N   <->  258 HOH   ( 373 )  A      O      0.20    2.50  INTRA BL
 178 GLY   ( 183-)  A      N   <->  258 HOH   ( 326 )  A      O      0.20    2.50  INTRA BF
  60 HIS   (  64-)  A    A NE2 <->  258 HOH   ( 389 )  A      O      0.20    2.50  INTRA
 249 ARG   ( 254-)  A      NH2 <->  258 HOH   ( 395 )  A      O      0.20    2.50  INTRA
  70 GLN   (  74-)  A      NE2 <->  258 HOH   ( 340 )  A      O      0.20    2.50  INTRA BL
  18 ILE   (  22-)  A      N   <->  258 HOH   ( 334 )  A      O      0.20    2.50  INTRA
  67 ASP   (  71-)  A      OD2 <->   72 LYS   (  76-)  A      NZ     0.20    2.50  INTRA BL
 194 THR   ( 199-)  A      OG1 <->  258 HOH   ( 375 )  A      O      0.19    2.21  INTRA
  13 HIS   (  17-)  A      ND1 <->  258 HOH   ( 368 )  A      O      0.19    2.51  INTRA
 163 LYS   ( 168-)  A      NZ  <->  258 HOH   ( 126 )  A      O      0.18    2.52  INTRA
 254 SER   ( 259-)  A      N   <->  258 HOH   ( 308 )  A      O      0.12    2.58  INTRA
 168 SER   ( 173-)  A      N   <->  258 HOH   ( 317 )  A      O      0.11    2.59  INTRA
  54 ARG   (  58-)  A      NH2 <->   65 GLU   (  69-)  A      OE2    0.11    2.59  INTRA BL
  44 SER   (  48-)  A      OG  <->  258 HOH   ( 345 )  A      O      0.11    2.29  INTRA BL
 200 GLU   ( 205-)  A      OE1 <->  258 HOH   ( 315 )  A      O      0.10    2.30  INTRA
  30 ASP   (  34-)  A      OD1 <->  258 HOH   ( 303 )  A      O      0.10    2.30  INTRA
 106 ASP   ( 110-)  A      OD2 <->  258 HOH   ( 321 )  A      O      0.10    2.30  INTRA BL
 178 GLY   ( 183-)  A      O   <->  258 HOH   ( 291 )  A      O      0.10    2.30  INTRA
 114 LEU   ( 118-)  A      O   <->  258 HOH   ( 286 )  A      O      0.10    2.30  INTRA
And so on for a total of 55 lines.

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.

   6 HIS   (  10-)  A      -6.07
 131 GLN   ( 136-)  A      -5.46
  32 HIS   (  36-)  A      -5.14

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.

 258 HOH   ( 396 )  A      O    -26.81  -22.14   13.38

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.

 258 HOH   ( 337 )  A      O
 258 HOH   ( 399 )  A      O
Metal-coordinating Histidine residue  90 fixed to   1
Metal-coordinating Histidine residue  92 fixed to   1
Metal-coordinating Histidine residue 115 fixed to   1

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.

 132 GLN   ( 137-)  A
 173 ASN   ( 178-)  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.

  24 GLN   (  28-)  A      N
  27 VAL   (  31-)  A      N
  32 HIS   (  36-)  A      N
  40 LEU   (  44-)  A      N
  48 ASP   (  52-)  A      N
  70 GLN   (  74-)  A      N
  96 LEU   ( 100-)  A      N
 164 THR   ( 169-)  A      N
 182 GLU   ( 187-)  A      N
 195 THR   ( 200-)  A      N
 199 LEU   ( 204-)  A      N
 227 ASN   ( 232-)  A      N
 240 TRP   ( 245-)  A      N
 255 PHE   ( 260-)  A      N
Only metal coordination for   92 HIS  (  96-) A      NE2
Only metal coordination for  115 HIS  ( 119-) A      ND1

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.

  81 ASP   (  85-)  A   H-bonding suggests Asn

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 :  -0.414
  2nd generation packing quality :   0.185
  Ramachandran plot appearance   :  -2.224
  chi-1/chi-2 rotamer normality  :  -2.979
  Backbone conformation          :  -1.124

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.328 (tight)
  Bond angles                    :   1.138
  Omega angle restraints         :   1.045
  Side chain planarity           :   0.316 (tight)
  Improper dihedral distribution :   0.541
  Inside/Outside distribution    :   0.947

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 : 1.64


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -2.7
  chi-1/chi-2 rotamer normality  :  -3.5 (poor)
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.328 (tight)
  Bond angles                    :   1.138
  Omega angle restraints         :   1.045
  Side chain planarity           :   0.316 (tight)
  Improper dihedral distribution :   0.541
  Inside/Outside distribution    :   0.947
==============

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.