WHAT IF Check report

This file was created 2011-12-13 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 pdb3bkk.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.

 596 KAF   ( 704-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 588 NAG   ( 693-)  A  -   O4  bound to  589 NAG   ( 694-)  A  -   C1

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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

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.

 216 ARG   ( 253-)  A
 452 ARG   ( 489-)  A

Warning: Tyrosine convention problem

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

 138 TYR   ( 175-)  A
 176 TYR   ( 213-)  A
 222 TYR   ( 259-)  A
 323 TYR   ( 360-)  A
 353 TYR   ( 390-)  A
 444 TYR   ( 481-)  A
 455 TYR   ( 492-)  A
 486 TYR   ( 523-)  A
 558 TYR   ( 595-)  A
 582 TYR   ( 619-)  A

Warning: Phenylalanine convention problem

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

  65 PHE   ( 102-)  A
 159 PHE   ( 196-)  A
 256 PHE   ( 293-)  A
 279 PHE   ( 316-)  A
 285 PHE   ( 322-)  A
 286 PHE   ( 323-)  A
 298 PHE   ( 335-)  A
 328 PHE   ( 365-)  A
 354 PHE   ( 391-)  A
 435 PHE   ( 472-)  A
 559 PHE   ( 596-)  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.

 284 ASP   ( 321-)  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.

  86 GLU   ( 123-)  A

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999191  0.000088  0.000338|
 |  0.000088  0.998789 -0.000333|
 |  0.000338 -0.000333  0.998501|
Proposed new scale matrix

 |  0.016574 -0.000001 -0.000006|
 | -0.000001  0.011769  0.000004|
 | -0.000003  0.000002  0.007391|
With corresponding cell

    A    =  60.334  B   =  84.967  C    = 135.298
    Alpha=  90.038  Beta=  89.961  Gamma=  89.990

The CRYST1 cell dimensions

    A    =  60.383  B   =  85.070  C    = 135.506
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 29.529
(Under-)estimated Z-score: 4.005

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.

  86 GLU   ( 123-)  A
 216 ARG   ( 253-)  A
 284 ASP   ( 321-)  A
 452 ARG   ( 489-)  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.

 375 ALA   ( 412-)  A    5.01
 492 ILE   ( 529-)  A    4.11
 301 LYS   ( 338-)  A    4.06

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.506

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.

 548 PRO   ( 585-)  A    -3.0
 126 PRO   ( 163-)  A    -2.8
 444 TYR   ( 481-)  A    -2.6
 576 LYS   ( 613-)  A    -2.6
  86 GLU   ( 123-)  A    -2.6
 480 SER   ( 517-)  A    -2.3
 308 THR   ( 345-)  A    -2.3
 484 ILE   ( 521-)  A    -2.3
 465 THR   ( 502-)  A    -2.2
 357 TYR   ( 394-)  A    -2.2

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.

  68 ASN   ( 105-)  A  Poor phi/psi
  69 GLN   ( 106-)  A  Poor phi/psi
  86 GLU   ( 123-)  A  Poor phi/psi
 125 GLU   ( 162-)  A  PRO omega poor
 188 GLU   ( 225-)  A  Poor phi/psi
 326 LYS   ( 363-)  A  Poor phi/psi
 394 ASN   ( 431-)  A  Poor phi/psi
 517 GLN   ( 554-)  A  Poor phi/psi
 581 GLN   ( 618-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.339

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.

 424 SER   ( 461-)  A    0.36
   8 SER   (  45-)  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!

  34 THR   (  71-)  A      0
  65 PHE   ( 102-)  A      0
  68 ASN   ( 105-)  A      0
  69 GLN   ( 106-)  A      0
  71 GLN   ( 108-)  A      0
  86 GLU   ( 123-)  A      0
  87 ARG   ( 124-)  A      0
 116 HIS   ( 153-)  A      0
 117 PRO   ( 154-)  A      0
 118 GLN   ( 155-)  A      0
 120 SER   ( 157-)  A      0
 124 LEU   ( 161-)  A      0
 125 GLU   ( 162-)  A      0
 135 SER   ( 172-)  A      0
 176 TYR   ( 213-)  A      0
 177 VAL   ( 214-)  A      0
 222 TYR   ( 259-)  A      0
 226 HIS   ( 263-)  A      0
 230 GLU   ( 267-)  A      0
 236 HIS   ( 273-)  A      0
 237 LEU   ( 274-)  A      0
 242 TRP   ( 279-)  A      0
 244 GLN   ( 281-)  A      0
 245 THR   ( 282-)  A      0
 246 TRP   ( 283-)  A      0
And so on for a total of 162 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 : 1.477

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].

 126 PRO   ( 163-)  A   -32.5 envelop C-alpha (-36 degrees)
 161 PRO   ( 198-)  A   109.2 envelop C-beta (108 degrees)
 275 PRO   ( 312-)  A   110.5 envelop C-beta (108 degrees)
 370 PRO   ( 407-)  A   123.1 half-chair C-beta/C-alpha (126 degrees)
 463 PRO   ( 500-)  A   154.6 half-chair C-alpha/N (162 degrees)
 548 PRO   ( 585-)  A   -64.6 envelop C-beta (-72 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.

 276 ARG   ( 313-)  A    A CG  <->  597 HOH   (1046 )  A      O      0.39    2.41  INTRA
 125 GLU   ( 162-)  A      O   <->  306 LYS   ( 343-)  A      NZ     0.29    2.41  INTRA
 350 HIS   ( 387-)  A      ND1 <->  373 HIS   ( 410-)  A      ND1    0.26    2.74  INTRA BL
 441 LYS   ( 478-)  A      NZ  <->  442 GLU   ( 479-)  A      OE2    0.25    2.45  INTRA
 511 HIS   ( 548-)  A      ND1 <->  597 HOH   (1006 )  A      O      0.25    2.45  INTRA BL
 146 GLU   ( 183-)  A    A OE1 <->  462 VAL   ( 499-)  A      CG2    0.25    2.55  INTRA BL
 567 ARG   ( 604-)  A      NH1 <->  597 HOH   (1183 )  A      O      0.24    2.46  INTRA
 580 PRO   ( 617-)  A      O   <->  582 TYR   ( 619-)  A      N      0.24    2.46  INTRA BF
 251 ASP   ( 288-)  A      OD1 <->  597 HOH   (1184 )  A      O      0.20    2.20  INTRA
 202 GLU   ( 239-)  A      OE2 <->  597 HOH   (1069 )  A      O      0.19    2.21  INTRA
 314 VAL   ( 351-)  A      O   <->  331 LYS   ( 368-)  A      NZ     0.17    2.53  INTRA BL
 195 ASP   ( 232-)  A      OD1 <->  198 ARG   ( 235-)  A      NH2    0.16    2.54  INTRA
  11 VAL   (  48-)  A      CG1 <->  597 HOH   (1207 )  A      O      0.16    2.64  INTRA
 202 GLU   ( 239-)  A      OE1 <->  597 HOH   (1209 )  A      O      0.16    2.24  INTRA
 470 ASP   ( 507-)  A      N   <->  471 PRO   ( 508-)  A      CD     0.16    2.84  INTRA BL
 136 ARG   ( 173-)  A      NH2 <->  251 ASP   ( 288-)  A      OD1    0.14    2.56  INTRA
 432 TRP   ( 469-)  A      NE1 <->  597 HOH   (1080 )  A      O      0.14    2.56  INTRA BL
 266 GLU   ( 303-)  A      OE1 <->  597 HOH   (1126 )  A      O      0.14    2.26  INTRA
 398 SER   ( 435-)  A      OG  <->  400 GLY   ( 437-)  A      N      0.14    2.56  INTRA BF
  67 VAL   ( 104-)  A      O   <->   69 GLN   ( 106-)  A      N      0.13    2.57  INTRA BF
 399 GLU   ( 436-)  A      N   <->  400 GLY   ( 437-)  A      N      0.13    2.47  INTRA BF
  69 GLN   ( 106-)  A      N   <->   70 LEU   ( 107-)  A      N      0.12    2.48  INTRA BF
 369 ASN   ( 406-)  A      OD1 <->  371 GLY   ( 408-)  A      N      0.11    2.59  INTRA BL
 537 TRP   ( 574-)  A      N   <->  538 PRO   ( 575-)  A      CD     0.11    2.89  INTRA BL
 244 GLN   ( 281-)  A      OE1 <->  474 LYS   ( 511-)  A      NZ     0.10    2.60  INTRA BL
And so on for a total of 67 lines.

Packing, accessibility and threading

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.

 118 GLN   ( 155-)  A      -7.53
 466 GLN   ( 503-)  A      -6.24
 576 LYS   ( 613-)  A      -5.85
 225 GLN   ( 262-)  A      -5.62
 221 HIS   ( 258-)  A      -5.62
 464 ARG   ( 501-)  A      -5.37
 399 GLU   ( 436-)  A      -5.17
 456 GLN   ( 493-)  A      -5.12
 506 HIS   ( 543-)  A      -5.10
 229 LEU   ( 266-)  A      -5.02

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.

 220 ARG   ( 257-)  A       222 - TYR    259- ( A)         -4.80

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.

  85 LEU   ( 122-)  A   -2.95

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.

  23 ASN   (  60-)  A
  69 GLN   ( 106-)  A
 116 HIS   ( 153-)  A
 123 GLN   ( 160-)  A
 502 GLN   ( 539-)  A
 573 HIS   ( 610-)  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.

 109 TYR   ( 146-)  A      OH
 127 ASP   ( 164-)  A      N
 178 ASP   ( 215-)  A      N
 236 HIS   ( 273-)  A      NE2
 240 ASN   ( 277-)  A      N
 245 THR   ( 282-)  A      N
 258 SER   ( 295-)  A      N
 274 THR   ( 311-)  A      N
 305 GLU   ( 342-)  A      N
 319 ALA   ( 356-)  A      N
 332 GLN   ( 369-)  A      NE2
 369 ASN   ( 406-)  A      N
 369 ASN   ( 406-)  A      ND2
 396 LEU   ( 433-)  A      N
 423 PHE   ( 460-)  A      N
 452 ARG   ( 489-)  A      NE
 462 VAL   ( 499-)  A      N
 464 ARG   ( 501-)  A      NH1
 483 TYR   ( 520-)  A      OH
 485 ARG   ( 522-)  A      N
 511 HIS   ( 548-)  A      NE2
 585 THR   ( 622-)  A      N
Only metal coordination for  346 HIS  ( 383-) A      NE2
Only metal coordination for  350 HIS  ( 387-) A      NE2
Only metal coordination for  374 GLU  ( 411-) A      OE1

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.

 146 GLU   ( 183-)  A    A OE1
 281 GLU   ( 318-)  A      OE1
 332 GLN   ( 369-)  A      OE1
 345 HIS   ( 382-)  A      NE2
 347 GLU   ( 384-)  A      OE1
 347 GLU   ( 384-)  A      OE2

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.

 150 ASP   ( 187-)  A   H-bonding suggests Asn
 195 ASP   ( 232-)  A   H-bonding suggests Asn; but Alt-Rotamer
 297 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 436 ASP   ( 473-)  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 :  -0.189
  2nd generation packing quality :  -1.000
  Ramachandran plot appearance   :  -0.734
  chi-1/chi-2 rotamer normality  :  -1.339
  Backbone conformation          :   0.066

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.269 (tight)
  Side chain planarity           :   0.273 (tight)
  Improper dihedral distribution :   0.562
  B-factor distribution          :   0.548
  Inside/Outside distribution    :   0.994

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 : 2.17


Structure Z-scores, positive is better than average:

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

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.269 (tight)
  Side chain planarity           :   0.273 (tight)
  Improper dihedral distribution :   0.562
  B-factor distribution          :   0.548
  Inside/Outside distribution    :   0.994
==============

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.