WHAT IF Check report

This file was created 2013-12-10 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb4fpg.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.

 659 DMS   ( 702-)  A  -
 660 IH9   ( 701-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 368 ASP   ( 406-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 368 ASP   ( 406-)  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. 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: 0

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

  10 TYR   (  48-)  A
  63 TYR   ( 101-)  A
 212 TYR   ( 250-)  A
 227 TYR   ( 265-)  A
 354 TYR   ( 392-)  A
 420 TYR   ( 458-)  A
 471 TYR   ( 509-)  A
 633 TYR   ( 671-)  A

Warning: Phenylalanine convention problem

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

 173 PHE   ( 211-)  A
 195 PHE   ( 233-)  A
 324 PHE   ( 362-)  A
 343 PHE   ( 381-)  A
 388 PHE   ( 426-)  A
 407 PHE   ( 445-)  A
 497 PHE   ( 535-)  A
 518 PHE   ( 556-)  A
 630 PHE   ( 668-)  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.

 232 ASP   ( 270-)  A
 273 ASP   ( 311-)  A
 387 ASP   ( 425-)  A
 651 ASP   ( 689-)  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.

 105 GLU   ( 143-)  A
 445 GLU   ( 483-)  A
 475 GLU   ( 513-)  A
 503 GLU   ( 541-)  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.

 105 GLU   ( 143-)  A
 232 ASP   ( 270-)  A
 273 ASP   ( 311-)  A
 387 ASP   ( 425-)  A
 445 GLU   ( 483-)  A
 475 GLU   ( 513-)  A
 503 GLU   ( 541-)  A
 651 ASP   ( 689-)  A

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

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

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

 190 PRO   ( 228-)  A    -2.9
 642 HIS   ( 680-)  A    -2.8
 633 TYR   ( 671-)  A    -2.7
 472 THR   ( 510-)  A    -2.7
 208 ILE   ( 246-)  A    -2.7
 418 THR   ( 456-)  A    -2.6
  78 ILE   ( 116-)  A    -2.5
 161 TYR   ( 199-)  A    -2.4
 574 THR   ( 612-)  A    -2.3
 230 THR   ( 268-)  A    -2.3
 510 ARG   ( 548-)  A    -2.3
   9 SER   (  47-)  A    -2.3
 293 VAL   ( 331-)  A    -2.2
 267 LEU   ( 305-)  A    -2.2
 455 GLY   ( 493-)  A    -2.2
  74 ILE   ( 112-)  A    -2.2
 172 LEU   ( 210-)  A    -2.2
 618 ILE   ( 656-)  A    -2.2
  46 LEU   (  84-)  A    -2.1
 394 ARG   ( 432-)  A    -2.1
 314 ASN   ( 352-)  A    -2.1
 188 SER   ( 226-)  A    -2.1
  88 LEU   ( 126-)  A    -2.1
 533 SER   ( 571-)  A    -2.1
 135 THR   ( 173-)  A    -2.1
 475 GLU   ( 513-)  A    -2.0
 484 SER   ( 522-)  A    -2.0
 387 ASP   ( 425-)  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.

   9 SER   (  47-)  A  Poor phi/psi
  14 ASN   (  52-)  A  Poor phi/psi
  51 GLY   (  89-)  A  omega poor
  53 SER   (  91-)  A  omega poor
 100 LYS   ( 138-)  A  Poor phi/psi
 117 LYS   ( 155-)  A  Poor phi/psi
 148 ALA   ( 186-)  A  omega poor
 156 GLU   ( 194-)  A  Poor phi/psi
 161 TYR   ( 199-)  A  Poor phi/psi
 163 ALA   ( 201-)  A  omega poor
 174 ASN   ( 212-)  A  Poor phi/psi
 202 GLN   ( 240-)  A  Poor phi/psi
 208 ILE   ( 246-)  A  Poor phi/psi
 231 HIS   ( 269-)  A  omega poor
 233 SER   ( 271-)  A  omega poor
 235 SER   ( 273-)  A  Poor phi/psi
 247 ASN   ( 285-)  A  Poor phi/psi
 281 ILE   ( 319-)  A  omega poor
 289 ASP   ( 327-)  A  Poor phi/psi
 320 ALA   ( 358-)  A  Poor phi/psi
 328 ASN   ( 366-)  A  Poor phi/psi
 350 ASN   ( 388-)  A  Poor phi/psi
 359 ASN   ( 397-)  A  Poor phi/psi
 373 LEU   ( 411-)  A  omega poor
 417 PRO   ( 455-)  A  Poor phi/psi
 442 PHE   ( 480-)  A  Poor phi/psi
 456 GLN   ( 494-)  A  omega poor
 474 GLY   ( 512-)  A  Poor phi/psi
 484 SER   ( 522-)  A  Poor phi/psi
 496 PRO   ( 534-)  A  Poor phi/psi
 502 ALA   ( 540-)  A  Poor phi/psi
 520 THR   ( 558-)  A  Poor phi/psi
 565 ASP   ( 603-)  A  Poor phi/psi
 585 GLN   ( 623-)  A  omega poor
 596 ASP   ( 634-)  A  Poor phi/psi
 600 TRP   ( 638-)  A  omega poor
 614 ALA   ( 652-)  A  Poor phi/psi
 624 HIS   ( 662-)  A  Poor phi/psi
 629 LEU   ( 667-)  A  omega poor
 633 TYR   ( 671-)  A  Poor phi/psi
 642 HIS   ( 680-)  A  Poor phi/psi
 645 ASN   ( 683-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.757

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!

   4 ILE   (  42-)  A      0
   5 PHE   (  43-)  A      0
   6 GLN   (  44-)  A      0
   9 SER   (  47-)  A      0
  13 ASN   (  51-)  A      0
  14 ASN   (  52-)  A      0
  19 ILE   (  57-)  A      0
  30 GLU   (  68-)  A      0
  31 SER   (  69-)  A      0
  40 ALA   (  78-)  A      0
  41 ASP   (  79-)  A      0
  42 LYS   (  80-)  A      0
  45 SER   (  83-)  A      0
  46 LEU   (  84-)  A      0
  50 PHE   (  88-)  A      0
  55 SER   (  93-)  A      0
  57 ALA   (  95-)  A      0
  59 PHE   (  97-)  A      0
  61 ASN   (  99-)  A      0
  62 ASN   ( 100-)  A      0
  63 TYR   ( 101-)  A      0
  71 SER   ( 109-)  A      0
  74 ILE   ( 112-)  A      0
  80 ASP   ( 118-)  A      0
  85 ILE   ( 123-)  A      0
And so on for a total of 307 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].

 190 PRO   ( 228-)  A   -59.9 half-chair C-beta/C-alpha (-54 degrees)
 271 PRO   ( 309-)  A  -116.1 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.

  13 ASN   (  51-)  A      OD1 <->  164 LYS   ( 202-)  A      NZ     0.39    2.31  INTRA
 510 ARG   ( 548-)  A      NH2 <->  596 ASP   ( 634-)  A      OD2    0.36    2.34  INTRA BF
 132 THR   ( 170-)  A      N   <->  661 HOH   ( 965 )  A      O      0.34    2.36  INTRA BL
 404 MET   ( 442-)  A      SD  <->  412 LEU   ( 450-)  A      N      0.29    3.01  INTRA
 525 ILE   ( 563-)  A      N   <->  661 HOH   ( 916 )  A      O      0.26    2.44  INTRA BL
 334 LYS   ( 372-)  A      NZ  <->  661 HOH   ( 889 )  A      O      0.25    2.45  INTRA
 582 LYS   ( 620-)  A      NZ  <->  661 HOH   ( 958 )  A      O      0.24    2.46  INTRA BL
 207 ARG   ( 245-)  A      NE  <->  631 GLU   ( 669-)  A      OE2    0.24    2.46  INTRA BL
  22 LEU   (  60-)  A      O   <->   26 LYS   (  64-)  A      NZ     0.24    2.46  INTRA BF
 387 ASP   ( 425-)  A      OD1 <->  389 ASP   ( 427-)  A      N      0.23    2.47  INTRA
 261 ASN   ( 299-)  A      O   <->  383 GLN   ( 421-)  A      NE2    0.22    2.48  INTRA BL
 210 THR   ( 248-)  A      OG1 <->  222 SER   ( 260-)  A      N      0.21    2.49  INTRA BL
 418 THR   ( 456-)  A      OG1 <->  419 ASN   ( 457-)  A      N      0.20    2.40  INTRA BL
 565 ASP   ( 603-)  A      OD2 <->  602 TYR   ( 640-)  A      OH     0.19    2.21  INTRA
 547 GLN   ( 585-)  A      N   <->  576 ASN   ( 614-)  A      OD1    0.19    2.51  INTRA
 465 ARG   ( 503-)  A      NH1 <->  535 GLU   ( 573-)  A      OE2    0.18    2.52  INTRA BL
 265 GLU   ( 303-)  A      OE1 <->  661 HOH   ( 821 )  A      O      0.16    2.24  INTRA
 180 GLN   ( 218-)  A      O   <->  183 SER   ( 221-)  A      OG     0.15    2.25  INTRA
 238 ASN   ( 276-)  A      ND2 <->  265 GLU   ( 303-)  A      OE2    0.15    2.55  INTRA BL
 325 LYS   ( 363-)  A      N   <->  332 TYR   ( 370-)  A      O      0.15    2.55  INTRA
 553 THR   ( 591-)  A      OG1 <->  581 ARG   ( 619-)  A      NE     0.14    2.56  INTRA BL
 301 THR   ( 339-)  A      OG1 <->  661 HOH   ( 928 )  A      O      0.14    2.26  INTRA
 416 THR   ( 454-)  A      O   <->  418 THR   ( 456-)  A      N      0.13    2.57  INTRA
  62 ASN   ( 100-)  A      OD1 <->   81 ALA   ( 119-)  A      N      0.13    2.57  INTRA
 130 SER   ( 168-)  A      O   <->  661 HOH   ( 975 )  A      O      0.13    2.27  INTRA
And so on for a total of 88 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.

 269 TYR   ( 307-)  A      -7.58
 551 TYR   ( 589-)  A      -6.00
 578 ARG   ( 616-)  A      -5.73
  82 GLN   ( 120-)  A      -5.45
 350 ASN   ( 388-)  A      -5.32
 638 ARG   ( 676-)  A      -5.32
 510 ARG   ( 548-)  A      -5.15
 341 ASN   ( 379-)  A      -5.13
 443 LEU   ( 481-)  A      -5.09

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

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.

 661 HOH   ( 941 )  A      O

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.

 192 GLN   ( 230-)  A
 486 GLN   ( 524-)  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.

  15 LYS   (  53-)  A      N
  22 LEU   (  60-)  A      N
  28 SER   (  66-)  A      N
  60 LYS   (  98-)  A      N
  71 SER   ( 109-)  A      N
  73 GLU   ( 111-)  A      N
  97 GLY   ( 135-)  A      N
 112 SER   ( 150-)  A      OG
 116 ASP   ( 154-)  A      N
 139 ILE   ( 177-)  A      N
 142 ILE   ( 180-)  A      N
 152 ALA   ( 190-)  A      N
 156 GLU   ( 194-)  A      N
 180 GLN   ( 218-)  A      N
 191 PHE   ( 229-)  A      N
 207 ARG   ( 245-)  A      NH2
 222 SER   ( 260-)  A      N
 228 GLY   ( 266-)  A      N
 231 HIS   ( 269-)  A      N
 237 ILE   ( 275-)  A      N
 263 TYR   ( 301-)  A      N
 291 SER   ( 329-)  A      OG
 297 LYS   ( 335-)  A      N
 314 ASN   ( 352-)  A      N
 321 ASP   ( 359-)  A      N
 337 LYS   ( 375-)  A      N
 341 ASN   ( 379-)  A      N
 342 ASP   ( 380-)  A      N
 344 ARG   ( 382-)  A      NE
 345 TYR   ( 383-)  A      N
 360 LYS   ( 398-)  A      N
 366 ILE   ( 404-)  A      N
 390 SER   ( 428-)  A      N
 405 ASN   ( 443-)  A      N
 411 SER   ( 449-)  A      N
 419 ASN   ( 457-)  A      ND2
 516 THR   ( 554-)  A      OG1
 546 ILE   ( 584-)  A      N
 549 THR   ( 587-)  A      OG1
 550 SER   ( 588-)  A      N
 554 GLN   ( 592-)  A      N
 555 VAL   ( 593-)  A      N
 562 GLN   ( 600-)  A      N
 569 ALA   ( 607-)  A      N
 581 ARG   ( 619-)  A      NH1
 581 ARG   ( 619-)  A      NH2
 643 LEU   ( 681-)  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.

  32 GLN   (  70-)  A      OE1
 289 ASP   ( 327-)  A      OD1
 306 ASP   ( 344-)  A      OD2
 340 ASP   ( 378-)  A      OD2

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.

  25 ASP   (  63-)  A   H-bonding suggests Asn
 199 ASP   ( 237-)  A   H-bonding suggests Asn; but Alt-Rotamer
 246 ASP   ( 284-)  A   H-bonding suggests Asn; but Alt-Rotamer
 483 ASP   ( 521-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.065
  2nd generation packing quality :  -1.141
  Ramachandran plot appearance   :  -1.119
  chi-1/chi-2 rotamer normality  :  -2.757
  Backbone conformation          :  -0.552

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.340 (tight)
  Bond angles                    :   0.559 (tight)
  Omega angle restraints         :   1.168
  Side chain planarity           :   0.339 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   1.223
  Inside/Outside distribution    :   0.964

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 : 2.58


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.3
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.340 (tight)
  Bond angles                    :   0.559 (tight)
  Omega angle restraints         :   1.168
  Side chain planarity           :   0.339 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   1.223
  Inside/Outside distribution    :   0.964
==============

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.