WHAT IF Check report

This file was created 2011-12-15 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 pdb2htr.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 388 DAN   (1850-)  A  -

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) :100.000

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.

  25 ARG   ( 107-)  A
  36 ARG   ( 118-)  A
  48 ARG   ( 130-)  A
  70 ARG   ( 152-)  A
  74 ARG   ( 156-)  A
  91 ARG   ( 172-)  A
 143 ARG   ( 224-)  A
 211 ARG   ( 292-)  A
 219 ARG   ( 300-)  A
 245 ARG   ( 327-)  A
 281 ARG   ( 364-)  A
 288 ARG   ( 371-)  A
 348 ARG   ( 428-)  A

Warning: Tyrosine convention problem

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

   2 TYR   (  84-)  A
  88 TYR   (  69-)  A
 126 TYR   ( 207-)  A
 174 TYR   ( 255-)  A

Warning: Phenylalanine convention problem

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

  33 PHE   ( 115-)  A
  73 PHE   ( 155-)  A
 271 PHE   ( 354-)  A
 342 PHE   ( 422-)  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.

  11 ASP   (  93-)  A
 162 ASP   ( 243-)  A
 212 ASP   ( 293-)  A
 242 ASP   ( 324-)  A
 379 ASP   ( 460-)  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.

  93 GLU   ( 174-)  A
 195 GLU   ( 276-)  A
 207 GLU   ( 288-)  A
 306 GLU   ( 389-)  A

Error: Decreasing residue numbers

At least one residue in each of the chains mentioned below has a residue number that is lower than the previous residue in that chain ('-' represents a chain without chain identifier).

Chain identifier(s): A

Geometric checks

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.

  34 VAL   ( 116-)  A      N    CA   C    97.66   -4.8
 145 GLN   ( 226-)  A      N    CA   C   125.32    5.0
 229 SER   ( 311-)  A      N    CA   C    98.63   -4.5

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  11 ASP   (  93-)  A
  25 ARG   ( 107-)  A
  36 ARG   ( 118-)  A
  48 ARG   ( 130-)  A
  70 ARG   ( 152-)  A
  74 ARG   ( 156-)  A
  91 ARG   ( 172-)  A
  93 GLU   ( 174-)  A
 143 ARG   ( 224-)  A
 162 ASP   ( 243-)  A
 195 GLU   ( 276-)  A
 207 GLU   ( 288-)  A
 211 ARG   ( 292-)  A
 212 ASP   ( 293-)  A
 219 ARG   ( 300-)  A
 242 ASP   ( 324-)  A
 245 ARG   ( 327-)  A
 281 ARG   ( 364-)  A
 288 ARG   ( 371-)  A
 306 GLU   ( 389-)  A
 348 ARG   ( 428-)  A
 379 ASP   ( 460-)  A

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 145 GLN   ( 226-)  A    5.48
  34 VAL   ( 116-)  A    5.04
 229 SER   ( 311-)  A    4.95
  87 VAL   ( 169-)  A    4.31

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 189 PHE   ( 270-)  A    -3.0
 228 LEU   ( 310-)  A    -2.7
 385 PHE   ( 466-)  A    -2.7
 375 TRP   ( 456-)  A    -2.7
 114 THR   ( 195-)  A    -2.7
 144 THR   ( 225-)  A    -2.5
 367 GLY   ( 448-)  A    -2.5
  36 ARG   ( 118-)  A    -2.4
 100 THR   ( 181-)  A    -2.4
  74 ARG   ( 156-)  A    -2.1
 266 VAL   ( 349-)  A    -2.1
 326 PHE   ( 410-)  A    -2.1
 146 GLU   ( 227-)  A    -2.0
 368 VAL   ( 449-)  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.

  22 ASN   ( 104-)  A  Poor phi/psi
  36 ARG   ( 118-)  A  Poor phi/psi
  37 GLU   ( 119-)  A  Poor phi/psi
  45 ILE   ( 127-)  A  Poor phi/psi
  59 ASN   ( 141-)  A  Poor phi/psi
  64 ASN   ( 146-)  A  Poor phi/psi
  65 GLY   ( 147-)  A  Poor phi/psi
  66 THR   ( 148-)  A  Poor phi/psi
  67 VAL   ( 149-)  A  Poor phi/psi
  69 ASP   ( 151-)  A  Poor phi/psi
  71 SER   ( 153-)  A  Poor phi/psi
  85 PRO   ( 167-)  A  Poor phi/psi
 144 THR   ( 225-)  A  Poor phi/psi
 146 GLU   ( 227-)  A  Poor phi/psi
 153 GLN   ( 234-)  A  Poor phi/psi
 166 ASN   ( 247-)  A  Poor phi/psi
 167 ARG   ( 248-)  A  Poor phi/psi
 210 CYS   ( 291-)  A  Poor phi/psi
 228 LEU   ( 310-)  A  Poor phi/psi
 238 GLY   ( 320-)  A  Poor phi/psi
 243 THR   ( 325-)  A  PRO omega poor
 264 TYR   ( 347-)  A  Poor phi/psi
 281 ARG   ( 364-)  A  Poor phi/psi
 298 ASN   ( 381-)  A  Poor phi/psi
 303 THR   ( 386-)  A  Poor phi/psi
 320 SER   ( 404-)  A  Poor phi/psi
 326 PHE   ( 410-)  A  Poor phi/psi
 334 GLY   ( 414-)  A  Poor phi/psi
 350 LYS   ( 430-)  A  PRO omega poor
 367 GLY   ( 448-)  A  Poor phi/psi
 368 VAL   ( 449-)  A  Poor phi/psi
 383 LEU   ( 464-)  A  PRO omega poor
 386 ASP   ( 467-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.396

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.

 277 VAL   ( 360-)  A    0.36

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!

   6 THR   (  88-)  A      0
  18 PHE   ( 100-)  A      0
  19 SER   ( 101-)  A      0
  21 ASP   ( 103-)  A      0
  22 ASN   ( 104-)  A      0
  28 SER   ( 110-)  A      0
  29 ARG   ( 111-)  A      0
  33 PHE   ( 115-)  A      0
  35 ILE   ( 117-)  A      0
  36 ARG   ( 118-)  A      0
  37 GLU   ( 119-)  A      0
  38 PRO   ( 120-)  A      0
  45 ILE   ( 127-)  A      0
  54 GLN   ( 136-)  A      0
  58 LEU   ( 140-)  A      0
  64 ASN   ( 146-)  A      0
  66 THR   ( 148-)  A      0
  67 VAL   ( 149-)  A      0
  68 LYS   ( 150-)  A      0
  69 ASP   ( 151-)  A      0
  70 ARG   ( 152-)  A      0
  74 ARG   ( 156-)  A      0
  81 VAL   ( 163-)  A      0
  85 PRO   ( 167-)  A      0
  86 ASN   ( 168-)  A      0
And so on for a total of 206 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 : 1.531

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].

 220 PRO   ( 301-)  A  -114.9 envelop C-gamma (-108 degrees)
 226 PRO   ( 308-)  A  -113.9 envelop C-gamma (-108 degrees)
 329 PRO   (  12-)  A  -120.0 half-chair C-delta/C-gamma (-126 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.

 385 PHE   ( 466-)  A      C   <->  387 ILE   ( 468-)  A      N      0.43    2.47  INTRA
 247 GLU   ( 329-)  A      CG  <->  285 ARG   ( 368-)  A      NH1    0.43    2.67  INTRA
 385 PHE   ( 466-)  A      O   <->  387 ILE   ( 468-)  A      N      0.35    2.35  INTRA
 168 GLN   ( 249-)  A      NE2 <->  191 GLY   ( 272-)  A      N      0.34    2.51  INTRA
 101 ALA   ( 182-)  A      C   <->  149 CYS   ( 230-)  A      SG     0.32    3.08  INTRA BL
   1 THR   (  83-)  A      CG2 <->    2 TYR   (  84-)  A      N      0.29    2.71  INTRA
  14 GLY   (  96-)  A      O   <->  367 GLY   ( 448-)  A      O      0.23    2.02  INTRA
 346 MET   ( 426-)  A      CE  <->  378 HIS   ( 459-)  A      CA     0.19    3.01  INTRA BL
 319 TRP   ( 403-)  A      CH2 <->  352 GLU   ( 432-)  A      CG     0.19    3.01  INTRA
 254 SER   ( 336-)  A      CB  <->  259 MET   ( 341-)  A      SD     0.18    3.22  INTRA
 376 SER   ( 457-)  A      OG  <->  378 HIS   ( 459-)  A      ND1    0.17    2.53  INTRA
  53 THR   ( 135-)  A      CG2 <->   77 MET   ( 159-)  A      CE     0.17    3.03  INTRA BL
 302 GLN   ( 385-)  A      C   <->  304 SER   ( 387-)  A      N      0.16    2.74  INTRA BL
 103 HIS   ( 184-)  A      CD2 <->  105 GLY   ( 186-)  A      N      0.15    2.95  INTRA BL
 133 VAL   ( 214-)  A      CG1 <->  134 VAL   ( 215-)  A      N      0.15    2.85  INTRA BL
 264 TYR   ( 347-)  A      CG  <->  265 GLY   ( 348-)  A      N      0.15    2.85  INTRA
  18 PHE   ( 100-)  A      N   <->  364 VAL   ( 445-)  A      O      0.14    2.56  INTRA BL
 196 GLU   ( 277-)  A      OE1 <->  211 ARG   ( 292-)  A      NH1    0.13    2.57  INTRA BL
 272 ARG   ( 355-)  A      CD  <->  274 GLY   ( 357-)  A      O      0.13    2.67  INTRA BL
  84 SER   ( 166-)  A      O   <->   86 ASN   ( 168-)  A      N      0.13    2.57  INTRA BL
 131 THR   ( 212-)  A      O   <->  180 ARG   ( 261-)  A      NE     0.13    2.57  INTRA
 193 HIS   ( 274-)  A      ND1 <->  213 GLY   ( 294-)  A      N      0.12    2.88  INTRA BL
 145 GLN   ( 226-)  A      NE2 <->  158 TRP   ( 239-)  A      CA     0.12    2.98  INTRA BL
  31 HIS   ( 113-)  A      ND1 <->   88 TYR   (  69-)  A      OH     0.12    2.58  INTRA BL
 150 THR   ( 231-)  A      O   <->  157 TYR   ( 238-)  A      N      0.12    2.58  INTRA BL
And so on for a total of 82 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.

 264 TYR   ( 347-)  A      -7.73
  29 ARG   ( 111-)  A      -6.50
 354 LYS   ( 435-)  A      -6.30
 167 ARG   ( 248-)  A      -5.87
 261 ASN   ( 344-)  A      -5.77
 190 ASN   ( 271-)  A      -5.54
 250 GLN   ( 330-)  A      -5.53
  89 GLN   ( 170-)  A      -5.52
 168 GLN   ( 249-)  A      -5.41
 317 LEU   ( 401-)  A      -5.20
  70 ARG   ( 152-)  A      -5.16
 382 ILE   ( 463-)  A      -5.10

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.

 373 ALA   ( 454-)  A   -2.51

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.

  22 ASN   ( 104-)  A
  62 HIS   ( 144-)  A
 103 HIS   ( 184-)  A
 145 GLN   ( 226-)  A
 311 GLN   ( 395-)  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.

   2 TYR   (  84-)  A      N
   7 GLU   (  89-)  A      N
  20 LYS   ( 102-)  A      N
  24 ILE   ( 106-)  A      N
  25 ARG   ( 107-)  A      N
  36 ARG   ( 118-)  A      NH2
  40 VAL   ( 122-)  A      N
  53 THR   ( 135-)  A      OG1
  56 SER   ( 138-)  A      N
  69 ASP   ( 151-)  A      N
  70 ARG   ( 152-)  A      N
  74 ARG   ( 156-)  A      NE
  74 ARG   ( 156-)  A      NH1
  95 VAL   ( 176-)  A      N
  98 SER   ( 179-)  A      N
 101 ALA   ( 182-)  A      N
 114 THR   ( 195-)  A      OG1
 120 ALA   ( 201-)  A      N
 142 LEU   ( 223-)  A      N
 147 SER   ( 228-)  A      N
 147 SER   ( 228-)  A      OG
 154 GLY   ( 235-)  A      N
 166 ASN   ( 247-)  A      N
 168 GLN   ( 249-)  A      N
 168 GLN   ( 249-)  A      NE2
And so on for a total of 54 lines.

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.

  37 GLU   ( 119-)  A      OE2
 195 GLU   ( 276-)  A      OE1

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.

 104 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 146 GLU   ( 227-)  A   H-bonding suggests Gln
 162 ASP   ( 243-)  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 :  -0.919
  2nd generation packing quality :  -1.449
  Ramachandran plot appearance   :  -2.937
  chi-1/chi-2 rotamer normality  :  -2.396
  Backbone conformation          :  -0.969

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.685
  Omega angle restraints         :   0.278 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.635
  B-factor distribution          :   0.717
  Inside/Outside distribution    :   1.072

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.685
  Omega angle restraints         :   0.278 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.635
  B-factor distribution          :   0.717
  Inside/Outside distribution    :   1.072
==============

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.