WHAT IF Check report

This file was created 2012-01-19 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 pdb1z97.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  44.105  B   =  70.775  C    =  44.487
    Alpha=  90.000  Beta= 115.070  Gamma=  90.000

Dimensions of a reduced cell

    A    =  44.105  B   =  44.487  C    =  70.775
    Alpha=  90.000  Beta=  90.000  Gamma=  64.930

Dimensions of the conventional cell

    A    =  47.556  B   =  74.747  C    =  70.775
    Alpha=  90.000  Beta=  90.000  Gamma=  90.545

Transformation to conventional cell

 | -1.000000  0.000000 -1.000000|
 | -1.000000  0.000000  1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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: 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) :293.000

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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 223 ARG   ( 227-)  A
 242 ARG   ( 246-)  A

Warning: Tyrosine convention problem

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

  48 TYR   (  51-)  A
  71 TYR   (  74-)  A
  85 TYR   (  88-)  A
 124 TYR   ( 128-)  A
 190 TYR   ( 194-)  A

Warning: Phenylalanine convention problem

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

  90 PHE   (  93-)  A
 153 PHE   ( 157-)  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.

  34 ASP   (  37-)  A
  38 ASP   (  41-)  A
  49 ASP   (  52-)  A
  68 ASP   (  71-)  A
  69 ASP   (  72-)  A
  98 ASP   ( 101-)  A
  99 ASP   ( 102-)  A
 107 ASP   ( 110-)  A
 135 ASP   ( 139-)  A
 161 ASP   ( 165-)  A
 186 ASP   ( 190-)  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.

   1 GLU   (   4-)  A
  15 GLU   (  18-)  A
  23 GLU   (  26-)  A
 129 GLU   ( 133-)  A
 149 GLU   ( 153-)  A
 152 GLU   ( 156-)  A
 230 GLU   ( 234-)  A
 232 GLU   ( 236-)  A

Geometric checks

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.

   1 GLU   (   4-)  A
  15 GLU   (  18-)  A
  23 GLU   (  26-)  A
  34 ASP   (  37-)  A
  38 ASP   (  41-)  A
  49 ASP   (  52-)  A
  68 ASP   (  71-)  A
  69 ASP   (  72-)  A
  98 ASP   ( 101-)  A
  99 ASP   ( 102-)  A
 107 ASP   ( 110-)  A
 129 GLU   ( 133-)  A
 135 ASP   ( 139-)  A
 149 GLU   ( 153-)  A
 152 GLU   ( 156-)  A
 161 ASP   ( 165-)  A
 186 ASP   ( 190-)  A
 223 ARG   ( 227-)  A
 230 GLU   ( 234-)  A
 232 GLU   ( 236-)  A
 242 ARG   ( 246-)  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.

  62 THR   (  65-)  A    -2.9
  57 LEU   (  60-)  A    -2.6
  80 PRO   (  83-)  A    -2.3
 262 HIS   ( 266-)  A    -2.2
  36 ARG   (  39-)  A    -2.2
 173 THR   ( 177-)  A    -2.1
  89 GLN   (  92-)  A    -2.1
 214 VAL   ( 218-)  A    -2.1
  82 PRO   (  85-)  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.

  26 SER   (  29-)  A  PRO omega poor
 108 GLY   ( 111-)  A  Poor phi/psi
 125 ASN   ( 129-)  A  Poor phi/psi
 197 PRO   ( 201-)  A  PRO omega poor
 199 CYS   ( 203-)  A  Poor phi/psi
 239 SER   ( 243-)  A  Poor phi/psi
 248 ASN   ( 252-)  A  Poor phi/psi
 258 HIS   ( 262-)  A  Poor phi/psi
 262 HIS   ( 266-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.668

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!

   4 TYR   (   7-)  A      0
  24 ASN   (  27-)  A      0
  26 SER   (  29-)  A      0
  42 GLN   (  45-)  A      0
  46 VAL   (  49-)  A      0
  47 SER   (  50-)  A      0
  53 ALA   (  56-)  A      0
  54 LYS   (  57-)  A      0
  55 THR   (  58-)  A      0
  59 ASN   (  62-)  A      0
  61 LYS   (  64-)  A      0
  62 THR   (  65-)  A      0
  69 ASP   (  72-)  A      0
  70 THR   (  73-)  A      0
  71 TYR   (  74-)  A      0
  72 ASP   (  75-)  A      0
  73 ARG   (  76-)  A      0
  74 SER   (  77-)  A      0
  77 ARG   (  80-)  A      0
  80 PRO   (  83-)  A      0
  82 PRO   (  85-)  A      0
  88 ARG   (  91-)  A      0
  89 GLN   (  92-)  A      0
  99 ASP   ( 102-)  A      0
 100 HIS   ( 103-)  A      0
And so on for a total of 114 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 : 1.956

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.

  24 ASN   (  27-)  A      CA  <->  250 ARG   ( 254-)  A      NH1    0.88    2.22  INTRA
 258 HIS   ( 262-)  A      CE1 <->  260 HIS   ( 264-)  A      CD2    0.87    2.33  INTRA
 258 HIS   ( 262-)  A      ND1 <->  260 HIS   ( 264-)  A      CD2    0.49    2.61  INTRA
  24 ASN   (  27-)  A      C   <->  250 ARG   ( 254-)  A      NH1    0.45    2.65  INTRA
 194 LEU   ( 198-)  A      CD2 <->  203 ILE   ( 207-)  A      CD1    0.42    2.78  INTRA BL
   2 TRP   (   5-)  A      CH2 <->  196 THR   ( 200-)  A      CG2    0.38    2.82  INTRA BL
  92 LEU   (  95-)  A      CD1 <->  115 LEU   ( 118-)  A      CD1    0.34    2.86  INTRA BL
   2 TRP   (   5-)  A      CZ2 <->  196 THR   ( 200-)  A      CG2    0.30    2.90  INTRA BL
  88 ARG   (  91-)  A      CD  <->  127 PHE   ( 131-)  A      CE1    0.29    2.91  INTRA BL
  38 ASP   (  41-)  A      OD2 <->  253 ARG   ( 257-)  A      NH1    0.25    2.45  INTRA
  92 LEU   (  95-)  A      CD1 <->  115 LEU   ( 118-)  A      CA     0.25    2.95  INTRA BL
 221 LYS   ( 225-)  A      NZ  <->  265 HOH   ( 362 )  A      O      0.24    2.46  INTRA
  61 LYS   (  64-)  A      NZ  <->  265 HOH   ( 291 )  A      O      0.23    2.47  INTRA
 249 ASN   ( 253-)  A      C   <->  265 HOH   ( 352 )  A      O      0.22    2.58  INTRA
  92 LEU   (  95-)  A      CD1 <->  115 LEU   ( 118-)  A      CB     0.21    2.99  INTRA BL
  49 ASP   (  52-)  A      OD2 <->   73 ARG   (  76-)  A      NH2    0.19    2.51  INTRA
 182 PRO   ( 186-)  A      O   <->  185 ARG   ( 189-)  A      NH1    0.18    2.52  INTRA
 114 GLU   ( 117-)  A      OE2 <->  116 HIS   ( 119-)  A      NE2    0.15    2.55  INTRA BL
  72 ASP   (  75-)  A      OD1 <->   86 ARG   (  89-)  A      NE     0.14    2.56  INTRA
  97 SER   ( 100-)  A      OG  <->   99 ASP   ( 102-)  A      OD1    0.14    2.26  INTRA
 262 HIS   ( 266-)  A      CG  <->  263 HIS   ( 267-)  A      N      0.13    2.87  INTRA
  91 HIS   (  94-)  A      C   <->   92 LEU   (  95-)  A      CD2    0.12    2.98  INTRA BL
  98 ASP   ( 101-)  A      OD1 <->  223 ARG   ( 227-)  A      NH2    0.09    2.61  INTRA BL
 173 THR   ( 177-)  A      OG1 <->  174 LYS   ( 178-)  A      N      0.09    2.51  INTRA
 227 SER   ( 231-)  A      N   <->  228 SER   ( 232-)  A      N      0.09    2.51  INTRA B3
  93 HIS   (  96-)  A      ND1 <->  240 ASN   ( 244-)  A      O      0.08    2.62  INTRA BL
  88 ARG   (  91-)  A      CD  <->  127 PHE   ( 131-)  A      CD1    0.07    3.13  INTRA BL
  48 TYR   (  51-)  A      OH  <->  119 HIS   ( 122-)  A      NE2    0.07    2.63  INTRA
  13 TRP   (  16-)  A      O   <->   17 PHE   (  20-)  A      N      0.07    2.63  INTRA
 124 TYR   ( 128-)  A      O   <->  126 THR   ( 130-)  A      N      0.06    2.64  INTRA BL
  77 ARG   (  80-)  A      NH1 <->  265 HOH   ( 346 )  A      O      0.05    2.65  INTRA
 176 ASP   ( 180-)  A      OD1 <->  178 SER   ( 182-)  A      OG     0.05    2.35  INTRA
  58 ASN   (  61-)  A      OD1 <->   60 GLY   (  63-)  A      N      0.05    2.65  INTRA BL
  19 ASN   (  22-)  A      C   <->   21 LYS   (  24-)  A      N      0.05    2.85  INTRA
 196 THR   ( 200-)  A      CG2 <->  197 PRO   ( 201-)  A      N      0.05    2.95  INTRA BL
 148 HIS   ( 152-)  A      ND1 <->  265 HOH   ( 361 )  A      O      0.05    2.65  INTRA
  55 THR   (  58-)  A      O   <->   66 VAL   (  69-)  A      N      0.05    2.65  INTRA BL
 125 ASN   ( 129-)  A      C   <->  126 THR   ( 130-)  A      CG2    0.04    3.06  INTRA BL
  63 CYS   (  66-)  A      SG  <->  156 PHE   ( 160-)  A      CZ     0.04    3.36  INTRA BL
  72 ASP   (  75-)  A      N   <->  265 HOH   ( 286 )  A      O      0.04    2.66  INTRA
  55 THR   (  58-)  A      CG2 <->   56 ILE   (  59-)  A      N      0.03    2.97  INTRA
   5 ALA   (   8-)  A      CB  <->    8 ASN   (  11-)  A      ND2    0.03    3.07  INTRA BL
 104 HIS   ( 107-)  A      NE2 <->  190 TYR   ( 194-)  A      OH     0.03    2.67  INTRA BL
  86 ARG   (  89-)  A      O   <->  119 HIS   ( 122-)  A      CA     0.03    2.77  INTRA BL
 255 SER   ( 259-)  A      N   <->  256 PHE   ( 260-)  A      N      0.02    2.58  INTRA B3
  48 TYR   (  51-)  A      N   <->  265 HOH   ( 318 )  A      O      0.01    2.69  INTRA
 145 LYS   ( 149-)  A      N   <->  212 MET   ( 216-)  A      O      0.01    2.69  INTRA BL
 147 GLY   ( 151-)  A      N   <->  214 VAL   ( 218-)  A      O      0.01    2.69  INTRA BL

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.

  71 TYR   (  74-)  A      -6.02
   7 HIS   (  10-)  A      -5.74
 174 LYS   ( 178-)  A      -5.69
 134 ARG   ( 138-)  A      -5.41

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

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.

 258 HIS   ( 262-)  A   -2.62

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.

  13 TRP   (  16-)  A     -   16 LEU   (  19-)  A        -1.35
 255 SER   ( 259-)  A     -  258 HIS   ( 262-)  A        -1.65
 259 HIS   ( 263-)  A     -  262 HIS   ( 266-)  A        -1.84

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

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.

  14 HIS   (  17-)  A
 133 GLN   ( 137-)  A
 262 HIS   ( 266-)  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.

   8 ASN   (  11-)  A      ND2
  28 ILE   (  31-)  A      N
  33 LYS   (  36-)  A      N
  71 TYR   (  74-)  A      N
  97 SER   ( 100-)  A      N
 100 HIS   ( 103-)  A      ND1
 121 ASN   ( 124-)  A      ND2
 185 ARG   ( 189-)  A      NH1
 196 THR   ( 200-)  A      N
 231 ASN   ( 235-)  A      N
 241 TRP   ( 245-)  A      N
 250 ARG   ( 254-)  A      NE
 250 ARG   ( 254-)  A      NH1
 250 ARG   ( 254-)  A      NH2
 252 VAL   ( 256-)  A      N
 256 PHE   ( 260-)  A      N
 260 HIS   ( 264-)  A      N
Only metal coordination for   93 HIS  (  96-) A      NE2

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.

 260 HIS   ( 264-)  A      ND1

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.

 265 HOH   ( 329 )  A      O  1.13  K  5

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.

 158 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.545
  2nd generation packing quality :  -1.596
  Ramachandran plot appearance   :  -1.318
  chi-1/chi-2 rotamer normality  :  -0.668
  Backbone conformation          :  -1.004

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.306 (tight)
  Bond angles                    :   0.700
  Omega angle restraints         :   0.356 (tight)
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   0.535
  Inside/Outside distribution    :   0.961

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.306 (tight)
  Bond angles                    :   0.700
  Omega angle restraints         :   0.356 (tight)
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   0.535
  Inside/Outside distribution    :   0.961
==============

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.