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 pdb2fo0.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.

 469 P16   (   2-)  A  -
 470 MYR   (   1-)  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: Tyrosine convention problem

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

  48 TYR   ( 112-)  A
 181 TYR   ( 245-)  A
 208 TYR   ( 272-)  A
 219 TYR   ( 283-)  A
 267 TYR   ( 331-)  A
 368 TYR   ( 432-)  A
 395 TYR   ( 459-)  A

Warning: Phenylalanine convention problem

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

 266 PHE   ( 330-)  A
 314 PHE   ( 378-)  A
 356 PHE   ( 420-)  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.

 410 ASP   ( 474-)  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.

  56 GLU   ( 120-)  A
 213 GLU   ( 277-)  A
 271 GLU   ( 335-)  A
 289 GLU   ( 353-)  A
 307 GLU   ( 371-)  A
 405 GLU   ( 469-)  A

Geometric checks

Error: Nomenclature error(s)

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

  56 GLU   ( 120-)  A
 213 GLU   ( 277-)  A
 271 GLU   ( 335-)  A
 289 GLU   ( 353-)  A
 307 GLU   ( 371-)  A
 405 GLU   ( 469-)  A
 410 ASP   ( 474-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  18 PRO   (  82-)  A      N      6.7    19.40    -2.48
The average deviation= 0.717

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.

 358 ILE   ( 422-)  A    5.39
 158 SER   ( 222-)  A    4.39

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.

 166 THR   ( 230-)  A    -3.0
 105 LEU   ( 169-)  A    -2.6
 232 THR   ( 296-)  A    -2.5
  43 LEU   ( 107-)  A    -2.4
 263 GLU   ( 327-)  A    -2.3
  70 TYR   ( 134-)  A    -2.3
  72 THR   ( 136-)  A    -2.2
 188 ASP   ( 252-)  A    -2.2
  18 PRO   (  82-)  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.

 200 LYS   ( 264-)  A  Poor phi/psi
 205 GLY   ( 269-)  A  Poor phi/psi
 264 PRO   ( 328-)  A  PRO omega poor
 313 ASN   ( 377-)  A  Poor phi/psi
 317 ARG   ( 381-)  A  Poor phi/psi
 329 ASN   ( 393-)  A  Poor phi/psi
 346 ASP   ( 410-)  A  Poor phi/psi
 369 ASN   ( 433-)  A  Poor phi/psi
 390 TYR   ( 454-)  A  Poor phi/psi
 410 ASP   ( 474-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.249

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 TRP   (  67-)  A      0
   4 ASN   (  68-)  A      0
   5 SEP   (  69-)  A      0
  15 GLU   (  79-)  A      0
  16 ASN   (  80-)  A      0
  25 TYR   (  89-)  A      0
  39 LYS   ( 103-)  A      0
  48 TYR   ( 112-)  A      0
  61 ASN   ( 125-)  A      0
  63 GLN   ( 127-)  A      0
  65 TRP   ( 129-)  A      0
  66 VAL   ( 130-)  A      0
  70 TYR   ( 134-)  A      0
  71 ILE   ( 135-)  A      0
  82 TRP   ( 146-)  A      0
  86 PRO   ( 150-)  A      0
  96 LEU   ( 160-)  A      0
  97 SER   ( 161-)  A      0
  98 SER   ( 162-)  A      0
 100 ILE   ( 164-)  A      0
 101 ASN   ( 165-)  A      0
 103 SER   ( 167-)  A      0
 104 PHE   ( 168-)  A      0
 113 PRO   ( 177-)  A      0
 122 TYR   ( 186-)  A      0
And so on for a total of 184 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 : 1.416

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!

 345 GLY   ( 409-)  A   2.07   11

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].

  13 PRO   (  77-)  A   106.6 envelop C-beta (108 degrees)
 435 PRO   ( 499-)  A  -113.6 envelop C-gamma (-108 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.

 169 HIS   ( 233-)  A      ND1 <->  471 HOH   ( 659 )  A      O      0.23    2.47  INTRA
 316 HIS   ( 380-)  A      ND1 <->  318 ASN   ( 382-)  A      N      0.20    2.80  INTRA BL
 271 GLU   ( 335-)  A      OE2 <->  333 LYS   ( 397-)  A      NZ     0.19    2.51  INTRA BL
 273 MET   ( 337-)  A      N   <->  469 P16   (   2-)  A      N11    0.18    2.82  INTRA BL
  16 ASN   (  80-)  A      OD1 <->   75 ASN   ( 139-)  A      ND2    0.17    2.53  INTRA BF
 176 ASN   ( 240-)  A      CG  <->  177 LYS   ( 241-)  A      N      0.15    2.85  INTRA BF
 141 VAL   ( 205-)  A      N   <->  471 HOH   ( 554 )  A      O      0.15    2.55  INTRA BL
 318 ASN   ( 382-)  A      O   <->  323 ASN   ( 387-)  A      ND2    0.15    2.55  INTRA BL
 108 GLU   ( 172-)  A      CG  <->  109 SER   ( 173-)  A      N      0.14    2.86  INTRA BF
 194 ARG   ( 258-)  A      NH2 <->  263 GLU   ( 327-)  A      O      0.14    2.56  INTRA BF
  94 TYR   ( 158-)  A      OH  <->  330 HIS   ( 394-)  A      ND1    0.14    2.56  INTRA BL
 190 TRP   ( 254-)  A      NE1 <->  471 HOH   ( 678 )  A      O      0.11    2.59  INTRA BF
 234 GLU   ( 298-)  A      N   <->  235 VAL   ( 299-)  A      N      0.11    2.49  INTRA BF
 256 LEU   ( 320-)  A      N   <->  471 HOH   ( 633 )  A      O      0.09    2.61  INTRA
 250 HIS   ( 314-)  A      ND1 <->  252 ASN   ( 316-)  A      N      0.09    2.91  INTRA BL
 234 GLU   ( 298-)  A      O   <->  237 GLU   ( 301-)  A      N      0.09    2.61  INTRA BF
 398 ILE   ( 462-)  A      N   <->  471 HOH   ( 594 )  A      O      0.08    2.62  INTRA BF
  17 ASP   (  81-)  A      CA  <->   18 PRO   (  82-)  A      CD     0.08    2.72  INTRA BF
  12 GLY   (  76-)  A      CA  <->   13 PRO   (  77-)  A      CD     0.08    2.72  INTRA BF
 194 ARG   ( 258-)  A      NH2 <->  265 PRO   ( 329-)  A      O      0.08    2.62  INTRA BF
  57 ALA   ( 121-)  A      N   <->   64 GLY   ( 128-)  A      O      0.07    2.63  INTRA BL
 158 SER   ( 222-)  A      N   <->  159 THR   ( 223-)  A      N      0.06    2.54  INTRA BL
 412 ARG   ( 476-)  A      NH2 <->  471 HOH   ( 540 )  A      O      0.06    2.64  INTRA BL
 219 TYR   ( 283-)  A      O   <->  220 SER   ( 284-)  A      C      0.06    2.54  INTRA BL
 360 TRP   ( 424-)  A      NE1 <->  386 GLU   ( 450-)  A      OE2    0.06    2.64  INTRA BL
  58 GLN   ( 122-)  A      NE2 <->   63 GLN   ( 127-)  A      OE1    0.05    2.65  INTRA BF
 138 LYS   ( 202-)  A      NZ  <->  148 ASN   ( 212-)  A      OD1    0.05    2.65  INTRA BF
 175 ARG   ( 239-)  A      CG  <->  176 ASN   ( 240-)  A      N      0.05    2.95  INTRA BF
 155 HIS   ( 219-)  A      ND1 <->  471 HOH   ( 623 )  A      O      0.05    2.65  INTRA BF
 107 ARG   ( 171-)  A      NH2 <->  128 HIS   ( 192-)  A      ND1    0.05    2.95  INTRA BL
  75 ASN   ( 139-)  A      N   <->  471 HOH   ( 588 )  A      O      0.04    2.66  INTRA
 418 GLY   ( 482-)  A      N   <->  471 HOH   ( 652 )  A      O      0.04    2.66  INTRA
 286 ASN   ( 350-)  A      N   <->  471 HOH   ( 578 )  A      O      0.04    2.66  INTRA BF
 219 TYR   ( 283-)  A      C   <->  220 SER   ( 284-)  A      C      0.04    2.76  INTRA BL
 120 LEU   ( 184-)  A      O   <->  127 TYR   ( 191-)  A      N      0.04    2.66  INTRA BL
 339 LEU   ( 403-)  A      O   <->  471 HOH   ( 566 )  A      O      0.03    2.37  INTRA BL
 395 TYR   ( 459-)  A      N   <->  413 MET   ( 477-)  A      SD     0.03    3.27  INTRA BL
 257 LEU   ( 321-)  A      N   <->  269 ILE   ( 333-)  A      O      0.03    2.67  INTRA BL
 456 SER   ( 520-)  A      C   <->  458 SER   ( 522-)  A      N      0.03    2.87  INTRA BF
 316 HIS   ( 380-)  A      N   <->  376 ASP   ( 440-)  A      OD2    0.02    2.68  INTRA BL
  70 TYR   ( 134-)  A      N   <->   71 ILE   ( 135-)  A      N      0.02    2.58  INTRA BL
 232 THR   ( 296-)  A      O   <->  234 GLU   ( 298-)  A      N      0.02    2.68  INTRA BF
 343 MET   ( 407-)  A      O   <->  345 GLY   ( 409-)  A      N      0.02    2.68  INTRA BF
  53 GLU   ( 117-)  A      OE2 <->  249 LYS   ( 313-)  A      NZ     0.02    2.68  INTRA
 230 GLU   ( 294-)  A      C   <->  232 THR   ( 296-)  A      N      0.01    2.89  INTRA BF
  35 LEU   (  99-)  A      N   <->   65 TRP   ( 129-)  A      O      0.01    2.69  INTRA BL
   8 ASN   (  72-)  A      N   <->    9 LEU   (  73-)  A      N      0.01    2.59  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

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.

 175 ARG   ( 239-)  A      -7.74
 187 TYR   ( 251-)  A      -7.10
 262 ARG   ( 326-)  A      -7.05
 207 GLN   ( 271-)  A      -6.71
 355 LYS   ( 419-)  A      -6.19
  60 LYS   ( 124-)  A      -6.14
 208 TYR   ( 272-)  A      -5.70
 392 MET   ( 456-)  A      -5.66
 181 TYR   ( 245-)  A      -5.65
 360 TRP   ( 424-)  A      -5.48
 233 MET   ( 297-)  A      -5.44
  10 LEU   (  74-)  A      -5.16
 329 ASN   ( 393-)  A      -5.14
  61 ASN   ( 125-)  A      -5.08
 395 TYR   ( 459-)  A      -5.07
 100 ILE   ( 164-)  A      -5.05

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 328 GLU   ( 392-)  A       330 - HIS    394- ( A)         -4.67

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.

   9 LEU   (  73-)  A   -2.98
  87 VAL   ( 151-)  A   -2.58
 254 VAL   ( 318-)  A   -2.56

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.

 471 HOH   ( 641 )  A      O     29.22   35.62   -1.47

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.

 471 HOH   ( 594 )  A      O
 471 HOH   ( 676 )  A      O
Marked this atom as acceptor  469 P16  (   2-) A     CL28
Marked this atom as acceptor  469 P16  (   2-) A     CL29

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.

  51 ASN   ( 115-)  A      N
  82 TRP   ( 146-)  A      N
  98 SER   ( 162-)  A      N
 144 GLU   ( 208-)  A      N
 166 THR   ( 230-)  A      N
 176 ASN   ( 240-)  A      N
 177 LYS   ( 241-)  A      N
 231 ASP   ( 295-)  A      N
 233 MET   ( 297-)  A      N
 235 VAL   ( 299-)  A      N
 263 GLU   ( 327-)  A      N
 273 MET   ( 337-)  A      N
 320 ALA   ( 384-)  A      N
 336 ASP   ( 400-)  A      N
 337 PHE   ( 401-)  A      N
 452 PHE   ( 516-)  A      N

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.

 336 ASP   ( 400-)  A      OD1

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.

 284 GLU   ( 348-)  A   H-bonding suggests Gln
 336 ASP   ( 400-)  A   H-bonding suggests Asn
 454 GLU   ( 518-)  A   H-bonding suggests Gln

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 :  -1.167
  2nd generation packing quality :  -1.334
  Ramachandran plot appearance   :  -1.613
  chi-1/chi-2 rotamer normality  :  -1.249
  Backbone conformation          :  -0.518

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.295 (tight)
  Bond angles                    :   0.623 (tight)
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.298 (tight)
  Improper dihedral distribution :   0.611
  B-factor distribution          :   0.487
  Inside/Outside distribution    :   0.974

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 : 2.27


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.295 (tight)
  Bond angles                    :   0.623 (tight)
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.298 (tight)
  Improper dihedral distribution :   0.611
  B-factor distribution          :   0.487
  Inside/Outside distribution    :   0.974
==============

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.