WHAT IF Check report

This file was created 2012-01-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3jxf.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.700
CA-only RMS fit for the two chains : 0.472

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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

Note: Ramachandran plot

Chain identifier: B

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

Warning: B-factors outside the range 0.0 - 100.0

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

   2 GLU   (  35-)  A    High
  86 MET   ( 119-)  A    High
 129 ARG   ( 162-)  A    High
 155 GLU   ( 188-)  A    High
 194 LYS   ( 227-)  A    High
 273 GLU   (  35-)  B    High
 357 MET   ( 119-)  B    High
 373 MET   ( 135-)  B    High
 400 ARG   ( 162-)  B    High
 461 ASN   ( 223-)  B    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. 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

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

 195 TYR   ( 228-)  A
 267 TYR   ( 300-)  A
 466 TYR   ( 228-)  B

Warning: Phenylalanine convention problem

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

 125 PHE   ( 158-)  A
 130 PHE   ( 163-)  A
 160 PHE   ( 193-)  A
 173 PHE   ( 206-)  A
 216 PHE   ( 249-)  A
 230 PHE   ( 263-)  A
 396 PHE   ( 158-)  B
 431 PHE   ( 193-)  B
 453 PHE   ( 215-)  B
 487 PHE   ( 249-)  B
 501 PHE   ( 263-)  B
 535 PHE   ( 297-)  B

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   (  67-)  A
 305 ASP   (  67-)  B

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   (  34-)  A
   2 GLU   (  35-)  A
  70 GLU   ( 103-)  A
 272 GLU   (  34-)  B

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   (  34-)  A
   2 GLU   (  35-)  A
  34 ASP   (  67-)  A
  70 GLU   ( 103-)  A
 272 GLU   (  34-)  B
 305 ASP   (  67-)  B

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.

 339 THR   ( 101-)  B    -2.9
  68 THR   ( 101-)  A    -2.9
 301 PRO   (  63-)  B    -2.7
 282 LEU   (  44-)  B    -2.6
  30 PRO   (  63-)  A    -2.5
 244 LEU   ( 277-)  A    -2.3
 297 PRO   (  59-)  B    -2.3
 235 THR   ( 268-)  A    -2.3
  26 PRO   (  59-)  A    -2.3
 259 PHE   ( 292-)  A    -2.2
 461 ASN   ( 223-)  B    -2.2
 477 PRO   ( 239-)  B    -2.1
 506 THR   ( 268-)  B    -2.1
 140 LYS   ( 173-)  A    -2.1
 411 LYS   ( 173-)  B    -2.1
 188 LEU   ( 221-)  A    -2.1
 355 SER   ( 117-)  B    -2.1
  11 LEU   (  44-)  A    -2.1
 155 GLU   ( 188-)  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.

  29 SER   (  62-)  A  PRO omega poor
  91 SER   ( 124-)  A  Poor phi/psi
 100 CYS   ( 133-)  A  Poor phi/psi, omega poor
 106 GLY   ( 139-)  A  Poor phi/psi
 112 GLU   ( 145-)  A  Poor phi/psi
 140 LYS   ( 173-)  A  Poor phi/psi
 205 PRO   ( 238-)  A  PRO omega poor
 207 CYS   ( 240-)  A  Poor phi/psi
 208 THR   ( 241-)  A  omega poor
 209 ASP   ( 242-)  A  omega poor
 211 VAL   ( 244-)  A  omega poor
 260 SER   ( 293-)  A  Poor phi/psi
 270 GLY   (  32-)  B  Poor phi/psi
 279 THR   (  41-)  B  Poor phi/psi
 300 SER   (  62-)  B  PRO omega poor
 333 ILE   (  95-)  B  omega poor
 355 SER   ( 117-)  B  Poor phi/psi
 362 SER   ( 124-)  B  Poor phi/psi
 371 CYS   ( 133-)  B  Poor phi/psi
 372 ASN   ( 134-)  B  Poor phi/psi
 383 GLU   ( 145-)  B  Poor phi/psi
 476 PRO   ( 238-)  B  PRO omega poor
 478 CYS   ( 240-)  B  Poor phi/psi
 480 ASP   ( 242-)  B  omega poor
 531 SER   ( 293-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.511

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!

   5 TRP   (  38-)  A      0
   7 TYR   (  40-)  A      0
   8 THR   (  41-)  A      0
  10 ALA   (  43-)  A      0
  11 LEU   (  44-)  A      0
  12 ASN   (  45-)  A      0
  19 LYS   (  52-)  A      0
  23 CYS   (  56-)  A      0
  28 GLN   (  61-)  A      0
  29 SER   (  62-)  A      0
  46 LYS   (  79-)  A      0
  50 GLN   (  83-)  A      0
  52 TRP   (  85-)  A      0
  59 ASN   (  92-)  A      0
  67 LYS   ( 100-)  A      0
  68 THR   ( 101-)  A      0
  74 THR   ( 107-)  A      0
  76 ASP   ( 109-)  A      0
  77 TYR   ( 110-)  A      0
  80 SER   ( 113-)  A      0
  83 VAL   ( 116-)  A      0
  85 GLU   ( 118-)  A      0
  86 MET   ( 119-)  A      0
  90 ALA   ( 123-)  A      0
  91 SER   ( 124-)  A      0
And so on for a total of 237 lines.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  26 PRO   (  59-)  A    36.3 envelop C-delta (36 degrees)
  30 PRO   (  63-)  A   -63.6 envelop C-beta (-72 degrees)
 206 PRO   ( 239-)  A     7.5 envelop N (0 degrees)
 297 PRO   (  59-)  B    37.3 envelop C-delta (36 degrees)
 388 PRO   ( 150-)  B    39.8 envelop C-delta (36 degrees)
 477 PRO   ( 239-)  B    15.5 half-chair N/C-delta (18 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.

  81 GLY   ( 114-)  A      O   <->  144 ARG   ( 177-)  A      NH1    0.26    2.44  INTRA BF
 334 HIS   (  96-)  B      NE2 <->  541 HOH   ( 389 )  B      O      0.19    2.51  INTRA BF
  45 LYS   (  78-)  A      O   <->   82 GLY   ( 115-)  A      N      0.17    2.53  INTRA BF
 312 ASN   (  74-)  B      ND2 <->  314 ASN   (  76-)  B      N      0.16    2.69  INTRA BF
 380 HIS   ( 142-)  B      CE1 <->  469 TYR   ( 231-)  B      OH     0.15    2.65  INTRA BL
 269 PRO   (  31-)  B      O   <->  271 SER   (  33-)  B      N      0.15    2.55  INTRA BF
 299 GLN   (  61-)  B      NE2 <->  524 ARG   ( 286-)  B      NH1    0.13    2.72  INTRA BL
 144 ARG   ( 177-)  A      NH2 <->  540 HOH   ( 394 )  A      O      0.13    2.57  INTRA BF
 370 LYS   ( 132-)  B      C   <->  502 CYS   ( 264-)  B      SG     0.13    3.27  INTRA
  28 GLN   (  61-)  A      NE2 <->  253 ARG   ( 286-)  A      NH1    0.13    2.72  INTRA BL
  99 LYS   ( 132-)  A      C   <->  231 CYS   ( 264-)  A      SG     0.12    3.28  INTRA
 352 GLY   ( 114-)  B      O   <->  415 ARG   ( 177-)  B      NH1    0.11    2.59  INTRA BF
 144 ARG   ( 177-)  A      NH1 <->  540 HOH   ( 315 )  A      O      0.10    2.60  INTRA BF
 283 ASN   (  45-)  B      O   <->  286 ASN   (  48-)  B      N      0.10    2.60  INTRA BL
 424 GLY   ( 186-)  B      N   <->  493 ILE   ( 255-)  B      O      0.08    2.62  INTRA
 249 GLN   ( 282-)  A      NE2 <->  540 HOH   ( 407 )  A      O      0.08    2.62  INTRA BF
 471 GLY   ( 233-)  B      N   <->  482 VAL   ( 244-)  B      O      0.07    2.63  INTRA BL
 114 GLN   ( 147-)  A      CG  <->  540 HOH   ( 366 )  A      O      0.07    2.73  INTRA BF
 316 LYS   (  78-)  B      O   <->  353 GLY   ( 115-)  B      N      0.07    2.63  INTRA
 269 PRO   (  31-)  B      CB  <->  270 GLY   (  32-)  B      N      0.06    2.64  INTRA BF
   8 THR   (  41-)  A      N   <->  540 HOH   ( 361 )  A      O      0.05    2.65  INTRA
  17 GLY   (  50-)  A      CA  <->   24 ASN   (  57-)  A      ND2    0.04    3.06  INTRA
  41 ASN   (  74-)  A      ND2 <->   43 ASN   (  76-)  A      N      0.03    2.82  INTRA BF
 108 GLU   ( 141-)  A      N   <->  119 GLU   ( 152-)  A      OE1    0.03    2.67  INTRA BL
   1 GLU   (  34-)  A      CB  <->    2 GLU   (  35-)  A      N      0.02    2.68  INTRA BF
 281 ALA   (  43-)  B      C   <->  282 LEU   (  44-)  B      C      0.02    2.78  INTRA BF
 203 THR   ( 236-)  A      N   <->  540 HOH   ( 307 )  A      O      0.02    2.68  INTRA
 381 SER   ( 143-)  B      OG  <->  526 GLN   ( 288-)  B      NE2    0.02    2.68  INTRA
 363 LYS   ( 125-)  B      NZ  <->  405 GLU   ( 167-)  B      OE2    0.01    2.69  INTRA BF
 110 SER   ( 143-)  A      OG  <->  255 GLN   ( 288-)  A      NE2    0.01    2.69  INTRA
 153 GLY   ( 186-)  A      N   <->  222 ILE   ( 255-)  A      O      0.01    2.69  INTRA BL
 529 LYS   ( 291-)  B      NZ  <->  541 HOH   ( 336 )  B      O      0.01    2.69  INTRA BF

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 538 TYR   ( 300-)  B      -7.64
 267 TYR   ( 300-)  A      -7.12
 512 TYR   ( 274-)  B      -7.11
 241 TYR   ( 274-)  A      -6.99
 373 MET   ( 135-)  B      -5.58
   2 GLU   (  35-)  A      -5.57
 295 ASN   (  57-)  B      -5.47
  24 ASN   (  57-)  A      -5.46
 273 GLU   (  35-)  B      -5.30
 190 ASN   ( 223-)  A      -5.19
 530 PHE   ( 292-)  B      -5.11

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: 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: B

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.

 346 ASN   ( 108-)  B   -3.24
  75 ASN   ( 108-)  A   -3.11
 372 ASN   ( 134-)  B   -2.78
 262 GLN   ( 295-)  A   -2.76
 302 ILE   (  64-)  B   -2.72
  31 ILE   (  64-)  A   -2.68
 258 LYS   ( 291-)  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

Note: Second generation quality Z-score plot

Chain identifier: B

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.

 541 HOH   ( 378 )  B      O     27.95   13.81    4.45

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.

  28 GLN   (  61-)  A
  41 ASN   (  74-)  A
 238 GLN   ( 271-)  A
 250 ASN   ( 283-)  A
 283 ASN   (  45-)  B
 286 ASN   (  48-)  B
 299 GLN   (  61-)  B
 312 ASN   (  74-)  B
 380 HIS   ( 142-)  B
 461 ASN   ( 223-)  B
 509 GLN   ( 271-)  B
 521 ASN   ( 283-)  B

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 ILE   (  36-)  A      N
  25 SER   (  58-)  A      OG
  31 ILE   (  64-)  A      N
  83 VAL   ( 116-)  A      N
  84 SER   ( 117-)  A      N
  91 SER   ( 124-)  A      OG
 102 MET   ( 135-)  A      N
 118 LEU   ( 151-)  A      N
 132 SER   ( 165-)  A      N
 144 ARG   ( 177-)  A      NH1
 155 GLU   ( 188-)  A      N
 191 SER   ( 224-)  A      N
 204 SER   ( 237-)  A      N
 210 THR   ( 243-)  A      N
 272 GLU   (  34-)  B      N
 296 SER   (  58-)  B      OG
 302 ILE   (  64-)  B      N
 323 TRP   (  85-)  B      N
 323 TRP   (  85-)  B      NE1
 354 VAL   ( 116-)  B      N
 355 SER   ( 117-)  B      N
 376 ASP   ( 138-)  B      N
 377 GLY   ( 139-)  B      N
 389 LEU   ( 151-)  B      N
 403 SER   ( 165-)  B      N
 415 ARG   ( 177-)  B      NE
 415 ARG   ( 177-)  B      NH1
 426 GLU   ( 188-)  B      N
 434 ILE   ( 196-)  B      N
 475 SER   ( 237-)  B      N
 481 THR   ( 243-)  B      N
 512 TYR   ( 274-)  B      OH
 523 PHE   ( 285-)  B      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.

 540 HOH   (   7 )  A      O  1.02  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.

 108 GLU   ( 141-)  A   H-bonding suggests Gln
 165 ASP   ( 198-)  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 :  -0.218
  2nd generation packing quality :  -1.694
  Ramachandran plot appearance   :  -0.361
  chi-1/chi-2 rotamer normality  :  -1.511
  Backbone conformation          :  -1.224

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.286 (tight)
  Bond angles                    :   0.489 (tight)
  Omega angle restraints         :   0.955
  Side chain planarity           :   0.345 (tight)
  Improper dihedral distribution :   0.541
  B-factor distribution          :   1.380
  Inside/Outside distribution    :   1.033

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 :  -1.1
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -1.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.286 (tight)
  Bond angles                    :   0.489 (tight)
  Omega angle restraints         :   0.955
  Side chain planarity           :   0.345 (tight)
  Improper dihedral distribution :   0.541
  B-factor distribution          :   1.380
  Inside/Outside distribution    :   1.033
==============

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.