WHAT IF Check report

This file was created 2013-12-10 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 pdb4duo.ent

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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.

   1 MET   (   1-)  A    High
   2 ASN   (   2-)  A    High
   4 GLN   (   4-)  A    High
   8 GLU   (   8-)  A    High
  23 ARG   (  23-)  A    High
  41 ARG   (  41-)  A    High
  45 GLU   (  45-)  A    High
  69 GLU   (  69-)  A    High
  70 GLU   (  70-)  A    High
  73 LYS   (  73-)  A    High
 328 GLU   ( 328-)  A    High
 388 GLY   ( 388-)  A    High

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

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.882 over 2710 bonds
Average difference in B over a bond : 4.43
RMS difference in B over a bond : 6.17

Nomenclature related problems

Warning: Phenylalanine convention problem

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

  61 PHE   (  61-)  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.

 207 GLU   ( 207-)  A
 328 GLU   ( 328-)  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.

 389 XYL   ( 403-)  A      C1   O5    5.17   73.8

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.

   3 TYR   (   3-)  A     -C    N    CA  131.92    5.7
  13 PHE   (  13-)  A      CA   CB   CG  118.53    4.7
  24 ASP   (  24-)  A      C    CA   CB  119.04    4.7
  25 PRO   (  25-)  A     -CA  -C    N   124.54    5.1
  41 ARG   (  41-)  A      CD   NE   CZ  134.94    7.4
  42 ARG   (  42-)  A      CD   NE   CZ  129.71    4.5
  49 HIS   (  49-)  A      CG   ND1  CE1 110.26    4.7
  55 ASP   (  55-)  A      CA   CB   CG  117.73    5.1
  71 HIS   (  71-)  A      CG   ND1  CE1 109.71    4.1
  74 ARG   (  74-)  A      CD   NE   CZ  129.50    4.3
 157 ARG   ( 157-)  A      CD   NE   CZ  129.91    4.6
 188 ARG   ( 188-)  A     -CA  -C    N   124.29    4.0
 188 ARG   ( 188-)  A      CD   NE   CZ  129.00    4.1
 227 ASN   ( 227-)  A      CA   CB   CG  116.84    4.2
 243 HIS   ( 243-)  A      CA   CB   CG  118.79    5.0
 243 HIS   ( 243-)  A      CG   ND1  CE1 109.73    4.1
 260 PHE   ( 260-)  A      CA   CB   CG  109.61   -4.2
 266 ARG   ( 266-)  A      CD   NE   CZ  140.77   10.6
 285 HIS   ( 285-)  A      CG   ND1  CE1 110.65    5.0
 340 ARG   ( 340-)  A      CD   NE   CZ  129.43    4.3
 387 ARG   ( 387-)  A      CD   NE   CZ  129.20    4.2
 389 XYL   ( 403-)  A      C2   C1   O5   48.31  -12.1
 389 XYL   ( 403-)  A      C1   O5   C5   75.55   -7.4

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.

 207 GLU   ( 207-)  A
 328 GLU   ( 328-)  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.

 187 PRO   ( 187-)  A    -2.7
  90 THR   (  90-)  A    -2.6
 334 ARG   ( 334-)  A    -2.5
 186 GLU   ( 186-)  A    -2.4
 357 PHE   ( 357-)  A    -2.3
 288 PHE   ( 288-)  A    -2.2
  41 ARG   (  41-)  A    -2.2
  10 ARG   (  10-)  A    -2.1
 284 ARG   ( 284-)  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.

   2 ASN   (   2-)  A  omega poor
  10 ARG   (  10-)  A  Poor phi/psi
  53 PHE   (  53-)  A  omega poor
  94 PHE   (  94-)  A  Poor phi/psi
 186 GLU   ( 186-)  A  Poor phi/psi, PRO omega poor
 193 LEU   ( 193-)  A  Poor phi/psi
 294 GLU   ( 294-)  A  omega poor
 334 ARG   ( 334-)  A  Poor phi/psi
 371 ALA   ( 371-)  A  Poor phi/psi
 387 ARG   ( 387-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.742

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.

  39 SER   (  39-)  A    0.39

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   (   3-)  A      0
  11 PHE   (  11-)  A      0
  20 TRP   (  20-)  A      0
  21 GLN   (  21-)  A      0
  23 ARG   (  23-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  29 ALA   (  29-)  A      0
  31 ARG   (  31-)  A      0
  46 LEU   (  46-)  A      0
  49 HIS   (  49-)  A      0
  61 PHE   (  61-)  A      0
  84 MET   (  84-)  A      0
  87 PRO   (  87-)  A      0
  88 MET   (  88-)  A      0
  93 LEU   (  93-)  A      0
  94 PHE   (  94-)  A      0
  95 THR   (  95-)  A      0
 101 ASP   ( 101-)  A      0
 104 PHE   ( 104-)  A      0
 105 THR   ( 105-)  A      0
 107 ASN   ( 107-)  A      0
 109 ARG   ( 109-)  A      0
 129 LEU   ( 129-)  A      0
 132 GLU   ( 132-)  A      0
And so on for a total of 120 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

   5 PRO   (   5-)  A    0.16 LOW
 182 PRO   ( 182-)  A    0.19 LOW
 184 PRO   ( 184-)  A    0.14 LOW
 283 PRO   ( 283-)  A    0.18 LOW

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].

   7 PRO   (   7-)  A   106.5 envelop C-beta (108 degrees)
  60 PRO   (  60-)  A  -122.9 half-chair C-delta/C-gamma (-126 degrees)
  87 PRO   (  87-)  A    37.5 envelop C-delta (36 degrees)
 187 PRO   ( 187-)  A   -63.1 envelop C-beta (-72 degrees)
 216 PRO   ( 216-)  A    49.7 half-chair C-delta/C-gamma (54 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.

  96 HIS   (  96-)  A      ND1 <->   98 VAL   (  98-)  A      N      0.30    2.70  INTRA BL
  42 ARG   (  42-)  A      NH1 <->  393 HOH   (1211 )  A      O      0.21    2.49  INTRA BF
 208 ARG   ( 208-)  A      NH1 <->  393 HOH   (1151 )  A      O      0.21    2.49  INTRA
  68 ARG   (  68-)  A      NH2 <->  393 HOH   (1064 )  A      O      0.21    2.49  INTRA
  41 ARG   (  41-)  A      NH2 <->  393 HOH   (1150 )  A      O      0.21    2.49  INTRA BF
 331 ARG   ( 331-)  A      NH1 <->  393 HOH   (1107 )  A      O      0.20    2.50  INTRA
 331 ARG   ( 331-)  A      NH2 <->  393 HOH   (1079 )  A      O      0.20    2.50  INTRA BF
   1 MET   (   1-)  A      N   <->  393 HOH   (1222 )  A      O      0.20    2.50  INTRA BF
 109 ARG   ( 109-)  A      NH2 <->  393 HOH   (1052 )  A      O      0.20    2.50  INTRA
 386 ALA   ( 386-)  A      O   <->  388 GLY   ( 388-)  A      N      0.20    2.50  INTRA BF
 387 ARG   ( 387-)  A      NH1 <->  393 HOH   (1130 )  A      O      0.20    2.50  INTRA BF
 323 ASP   ( 323-)  A      OD2 <->  387 ARG   ( 387-)  A      NH2    0.19    2.51  INTRA
 328 GLU   ( 328-)  A      OE2 <->  393 HOH   (1107 )  A      O      0.11    2.29  INTRA BF
 337 GLU   ( 337-)  A      CG  <->  340 ARG   ( 340-)  A      NH2    0.11    2.99  INTRA BF
  32 ARG   (  32-)  A      NH1 <->   33 ALA   (  33-)  A      O      0.10    2.50  INTRA BF
 250 ASN   ( 250-)  A      N   <->  256 GLN   ( 256-)  A      OE1    0.09    2.61  INTRA BL
 152 ARG   ( 152-)  A      NE  <->  393 HOH   (1197 )  A      O      0.08    2.62  INTRA
 163 ASP   ( 163-)  A      OD1 <->  207 GLU   ( 207-)  A      N      0.08    2.62  INTRA
 246 LEU   ( 246-)  A      N   <->  285 HIS   ( 285-)  A      O      0.06    2.64  INTRA BL
   6 THR   (   6-)  A      O   <->    9 ASP   (   9-)  A      N      0.06    2.64  INTRA
 374 ARG   ( 374-)  A      N   <->  393 HOH   (1047 )  A      O      0.05    2.65  INTRA BL
 186 GLU   ( 186-)  A      OE1 <->  255 ASP   ( 255-)  A    A OD1    0.04    2.36  INTRA
 144 GLU   ( 144-)  A      N   <->  393 HOH   (1021 )  A      O      0.04    2.66  INTRA BL
 249 GLN   ( 249-)  A      NE2 <->  251 GLY   ( 251-)  A      O      0.04    2.66  INTRA BL
 300 TRP   ( 300-)  A      NE1 <->  393 HOH   (1147 )  A      O      0.03    2.67  INTRA
 183 LYS   ( 183-)  A      NZ  <->  255 ASP   ( 255-)  A    A OD2    0.02    2.68  INTRA BL
 183 LYS   ( 183-)  A      NZ  <->  186 GLU   ( 186-)  A      O      0.02    2.68  INTRA BL
 195 THR   ( 195-)  A      OG1 <->  198 HIS   ( 198-)  A      ND1    0.02    2.68  INTRA BL
 390  MG   ( 401-)  A     MG   <->  392 XYL   ( 403-)  A      O1     0.01    2.79  INTRA

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.

  26 PHE   (  26-)  A      -7.20
 387 ARG   ( 387-)  A      -6.85
  23 ARG   (  23-)  A      -6.68
  61 PHE   (  61-)  A      -6.61
 254 TYR   ( 254-)  A      -6.57
 237 TRP   ( 237-)  A      -6.19
 140 ARG   ( 140-)  A      -5.71
 172 GLN   ( 172-)  A      -5.50
 144 GLU   ( 144-)  A      -5.33
 100 LYS   ( 100-)  A      -5.30
 368 ARG   ( 368-)  A      -5.16

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.

 224 ALA   ( 224-)  A   -2.63

Water, ion, and hydrogenbond related checks

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.

 393 HOH   (1227 )  A      O
Metal-coordinating Histidine residue 220 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.

 185 ASN   ( 185-)  A
 285 HIS   ( 285-)  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.

   3 TYR   (   3-)  A      N
  16 TRP   (  16-)  A      N
  22 GLY   (  22-)  A      N
  53 PHE   (  53-)  A      N
  88 MET   (  88-)  A      N
 122 ASN   ( 122-)  A      ND2
 137 TRP   ( 137-)  A      NE1
 188 ARG   ( 188-)  A      N
 195 THR   ( 195-)  A      N
 244 ILE   ( 244-)  A      N
 247 ASN   ( 247-)  A      N
 253 LYS   ( 253-)  A      N
 340 ARG   ( 340-)  A      NH2
Only metal coordination for  181 GLU  ( 181-) A      OE2
Only metal coordination for  217 GLU  ( 217-) A      OE1
Only metal coordination for  220 HIS  ( 220-) A      NE2

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+.

 390  MG   ( 401-)  A     0.31   1.27 Is perhaps  K

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.

 393 HOH   (1071 )  A      O  1.08  K  4
 393 HOH   (1089 )  A      O  1.10  K  4

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.

   9 ASP   (   9-)  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 :  -0.538
  2nd generation packing quality :   0.858
  Ramachandran plot appearance   :  -0.258
  chi-1/chi-2 rotamer normality  :  -1.742
  Backbone conformation          :  -0.038

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.348 (tight)
  Bond angles                    :   1.122
  Omega angle restraints         :   0.897
  Side chain planarity           :   0.336 (tight)
  Improper dihedral distribution :   0.556
  B-factor distribution          :   1.882 (loose)
  Inside/Outside distribution    :   1.046

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.348 (tight)
  Bond angles                    :   1.122
  Omega angle restraints         :   0.897
  Side chain planarity           :   0.336 (tight)
  Improper dihedral distribution :   0.556
  B-factor distribution          :   1.882 (loose)
  Inside/Outside distribution    :   1.046
==============

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.