WHAT IF Check report

This file was created 2011-12-16 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 pdb1kgs.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.

 221 SCN   ( 301-)  A  -
 222 SCN   ( 302-)  A  -
 223 SCN   ( 303-)  A  -
 224 SCN   ( 304-)  A  -
 225 SCN   ( 305-)  A  -
 226 SCN   ( 306-)  A  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 ASN   (   2-)  A  -   CG
   1 ASN   (   2-)  A  -   OD1
   1 ASN   (   2-)  A  -   ND2
 107 ARG   ( 108-)  A  -   CG
 107 ARG   ( 108-)  A  -   CD
 107 ARG   ( 108-)  A  -   NE
 107 ARG   ( 108-)  A  -   CZ
 107 ARG   ( 108-)  A  -   NH1
 107 ARG   ( 108-)  A  -   NH2
 120 LYS   ( 121-)  A  -   CG
 120 LYS   ( 121-)  A  -   CD
 120 LYS   ( 121-)  A  -   CE
 120 LYS   ( 121-)  A  -   NZ
 122 GLU   ( 123-)  A  -   CB
 122 GLU   ( 123-)  A  -   CG
 122 GLU   ( 123-)  A  -   CD
 122 GLU   ( 123-)  A  -   OE1
 122 GLU   ( 123-)  A  -   OE2
 123 SER   ( 124-)  A  -   CB
 123 SER   ( 124-)  A  -   OG
 124 LYS   ( 125-)  A  -   CB
 124 LYS   ( 125-)  A  -   CG
 124 LYS   ( 125-)  A  -   CD
 124 LYS   ( 125-)  A  -   CE
 124 LYS   ( 125-)  A  -   NZ
And so on for a total of 54 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 123 SER   ( 124-)  A  -   N
 123 SER   ( 124-)  A  -   C
 123 SER   ( 124-)  A  -   O
 124 LYS   ( 125-)  A  -   N
 124 LYS   ( 125-)  A  -   C
 124 LYS   ( 125-)  A  -   O
 181 VAL   ( 187-)  A  -   N
 181 VAL   ( 187-)  A  -   CA
 181 VAL   ( 187-)  A  -   C
 181 VAL   ( 187-)  A  -   O

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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 123 SER   ( 124-)  A      CA
 124 LYS   ( 125-)  A      CA
 125 SER   ( 126-)  A      CB
 177 GLU   ( 178-)  A      CG
 199 LYS   ( 205-)  A      CD

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 2

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 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.

 123 SER   ( 124-)  A      N   -C     1.24   -4.4

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.

   1 ASN   (   2-)  A      CA   CB   CG  107.52   -5.1
  88 ARG   (  89-)  A      CG   CD   NE  119.95    5.6
  88 ARG   (  89-)  A      CD   NE   CZ  131.46    5.4

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.

 198 ASP   ( 204-)  A    4.31

Torsion-related checks

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.

  57 VAL   (  58-)  A  Poor phi/psi
 102 LYS   ( 103-)  A  PRO omega poor
 123 SER   ( 124-)  A  Impossible phi
 124 LYS   ( 125-)  A  Impossible phi
 146 SER   ( 147-)  A  Poor phi/psi
 167 ASN   ( 168-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.657

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.

 215 VAL   ( 221-)  A    0.36
 183 SER   ( 189-)  A    0.38

Warning: Unusual backbone conformations

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

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

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

   9 ASP   (  10-)  A      0
  11 ARG   (  12-)  A      0
  24 GLU   (  25-)  A      0
  25 MSE   (  26-)  A      0
  26 PHE   (  27-)  A      0
  32 TYR   (  33-)  A      0
  38 MSE   (  39-)  A      0
  40 MSE   (  41-)  A      0
  46 PHE   (  47-)  A      0
  53 ILE   (  54-)  A      0
  54 MSE   (  55-)  A      0
  56 PRO   (  57-)  A      0
  57 VAL   (  58-)  A      0
  67 MSE   (  68-)  A      0
  70 SER   (  71-)  A      0
  78 MSE   (  79-)  A      0
  81 ALA   (  82-)  A      0
  82 LEU   (  83-)  A      0
  90 LYS   (  91-)  A      0
  94 MSE   (  95-)  A      0
  96 ALA   (  97-)  A      0
  97 ASP   (  98-)  A      0
  98 ASP   (  99-)  A      0
 104 PHE   ( 105-)  A      0
 122 GLU   ( 123-)  A      0
And so on for a total of 72 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

  60 GLY   (  61-)  A   1.62   10

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]

  56 PRO   (  57-)  A    0.14 LOW
  75 PRO   (  76-)  A    0.14 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].

 103 PRO   ( 104-)  A   -62.7 half-chair C-beta/C-alpha (-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.

 217 ARG   ( 223-)  A      NH1 <->  223 SCN   ( 303-)  A      S      0.43    2.87  INTRA
 181 VAL   ( 187-)  A      CG1 <->  182 PHE   ( 188-)  A      N      0.34    2.66  INTRA
 172 LYS   ( 173-)  A      NZ  <->  227 HOH   ( 505 )  A      O      0.32    2.38  INTRA
 183 SER   ( 189-)  A      O   <->  227 HOH   ( 463 )  A      O      0.32    2.08  INTRA
 167 ASN   ( 168-)  A      O   <->  223 SCN   ( 303-)  A      S      0.31    2.69  INTRA
  75 PRO   (  76-)  A      CB  <->  120 LYS   ( 121-)  A      NZ     0.29    2.81  INTRA BL
 219 GLU   ( 225-)  A      O   <->  225 SCN   ( 305-)  A      N      0.25    2.45  INTRA
 124 LYS   ( 125-)  A      NZ  <->  227 HOH   ( 401 )  A      O      0.24    2.46  INTRA
 222 SCN   ( 302-)  A      S   <->  227 HOH   ( 333 )  A      O      0.20    2.80  INTRA
 194 ARG   ( 200-)  A      NH1 <->  227 HOH   ( 459 )  A      O      0.20    2.50  INTRA
 102 LYS   ( 103-)  A      NZ  <->  227 HOH   ( 412 )  A      O      0.17    2.53  INTRA
 222 SCN   ( 302-)  A      S   <->  227 HOH   ( 316 )  A      O      0.16    2.84  INTRA
 118 ARG   ( 119-)  A      NH1 <->  221 SCN   ( 301-)  A      N      0.16    2.84  INTRA BL
 116 LEU   ( 117-)  A      O   <->  120 LYS   ( 121-)  A      CD     0.16    2.64  INTRA BL
 119 ARG   ( 120-)  A      C   <->  120 LYS   ( 121-)  A      CD     0.16    2.94  INTRA BL
  58 HIS   (  59-)  A      ND1 <->   62 GLU   (  63-)  A      OE1    0.15    2.55  INTRA
 224 SCN   ( 304-)  A      S   <->  227 HOH   ( 406 )  A      O      0.14    2.86  INTRA
 195 LYS   ( 201-)  A      NZ  <->  227 HOH   ( 434 )  A      O      0.13    2.57  INTRA
 129 VAL   ( 130-)  A      CG1 <->  227 HOH   ( 414 )  A      O      0.11    2.69  INTRA
 119 ARG   ( 120-)  A      NE  <->  227 HOH   ( 420 )  A      O      0.11    2.59  INTRA
 172 LYS   ( 173-)  A      NZ  <->  214 TYR   ( 220-)  A      OH     0.10    2.60  INTRA BL
 225 SCN   ( 305-)  A      N   <->  227 HOH   ( 426 )  A      O      0.10    2.60  INTRA BF
  43 ASN   (  44-)  A      ND2 <->  224 SCN   ( 304-)  A      N      0.10    2.90  INTRA
 202 LYS   ( 208-)  A      CG  <->  203 LYS   ( 209-)  A      N      0.09    2.91  INTRA
  23 LYS   (  24-)  A      NZ  <->  226 SCN   ( 306-)  A      N      0.08    2.92  INTRA
 154 LYS   ( 155-)  A      NZ  <->  227 HOH   ( 438 )  A      O      0.08    2.62  INTRA
 212 ILE   ( 218-)  A      O   <->  227 HOH   ( 473 )  A      O      0.07    2.33  INTRA
 168 ARG   ( 169-)  A      NE  <->  227 HOH   ( 491 )  A      O      0.06    2.64  INTRA
  70 SER   (  71-)  A      OG  <->  227 HOH   ( 424 )  A      O      0.06    2.34  INTRA
 124 LYS   ( 125-)  A      N   <->  227 HOH   ( 503 )  A      O      0.05    2.65  INTRA
  48 VAL   (  49-)  A    A CG1 <->   49 VAL   (  50-)  A      N      0.05    2.95  INTRA BL
 122 GLU   ( 123-)  A      C   <->  123 SER   ( 124-)  A      C      0.05    2.75  INTRA B3
 140 LYS   ( 141-)  A      NZ  <->  227 HOH   ( 395 )  A      O      0.04    2.66  INTRA
 132 ASP   ( 133-)  A      OD1 <->  227 HOH   ( 432 )  A      O      0.04    2.36  INTRA
 219 GLU   ( 225-)  A      OE2 <->  227 HOH   ( 397 )  A      O      0.04    2.36  INTRA
 207 HIS   ( 213-)  A      CE1 <->  225 SCN   ( 305-)  A      S      0.02    3.38  INTRA
 189 HIS   ( 195-)  A      ND1 <->  227 HOH   ( 341 )  A      O      0.02    2.68  INTRA
 118 ARG   ( 119-)  A      CZ  <->  143 TYR   ( 144-)  A      CE2    0.02    3.18  INTRA BL
 155 GLU   ( 156-)  A      OE1 <->  196 LYS   ( 202-)  A      NZ     0.02    2.68  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.

 210 ARG   ( 216-)  A      -6.77
 122 GLU   ( 123-)  A      -6.19
 178 HIS   ( 179-)  A      -5.96
 102 LYS   ( 103-)  A      -5.52
  99 TYR   ( 100-)  A      -5.49
  43 ASN   (  44-)  A      -5.45
  93 ASN   (  94-)  A      -5.12

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.

 227 HOH   ( 418 )  A      O     14.29   50.91   74.09

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.

  93 ASN   (  94-)  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.

  33 ASP   (  34-)  A      N
  43 ASN   (  44-)  A      ND2
 127 LYS   ( 128-)  A      N
 146 SER   ( 147-)  A      N
 203 LYS   ( 209-)  A      N

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.

 227 HOH   ( 307 )  A      O  1.01  K  5 *2
 227 HOH   ( 309 )  A      O  0.89  K  4 *2
 227 HOH   ( 327 )  A      O  1.19  K  4 *2
 227 HOH   ( 353 )  A      O  0.91  K  4 *2
 227 HOH   ( 355 )  A      O  0.98  K  5 *2
 227 HOH   ( 358 )  A      O  1.20  K  6 *2
 227 HOH   ( 393 )  A      O  1.04  K  4 *2 Ion-B

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.468
  2nd generation packing quality :  -0.291
  Ramachandran plot appearance   :   1.019
  chi-1/chi-2 rotamer normality  :   0.657
  Backbone conformation          :   0.637

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.686
  Bond angles                    :   0.852
  Omega angle restraints         :   0.812
  Side chain planarity           :   1.005
  Improper dihedral distribution :   0.951
  B-factor distribution          :   0.680
  Inside/Outside distribution    :   0.976

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.686
  Bond angles                    :   0.852
  Omega angle restraints         :   0.812
  Side chain planarity           :   1.005
  Improper dihedral distribution :   0.951
  B-factor distribution          :   0.680
  Inside/Outside distribution    :   0.976
==============

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.