WHAT IF Check report

This file was created 2012-10-23 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 pdb4apj.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.

 599 PE4   (1629-)  A  -
 600 PE4   (1630-)  A  -
 602 ACT   (1635-)  A  -
 603 BMA   (1634-)  A  -
 604 PE4   (1631-)  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.

 593 NAG   (1632-)  A  -   O4  bound to  594 NAG   (1633-)  A  -   C1
 594 NAG   (1633-)  A  -   O4  bound to  603 BMA   (1634-)  A  -   C1

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: P

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: 1

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: P

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

 |  0.997494  0.000203 -0.000175|
 |  0.000203  0.997861  0.000291|
 | -0.000175  0.000291  0.997110|
Proposed new scale matrix

 |  0.017628 -0.000004  0.000003|
 | -0.000002  0.011751 -0.000003|
 |  0.000001 -0.000002  0.007528|
With corresponding cell

    A    =  56.727  B   =  85.098  C    = 132.842
    Alpha=  89.967  Beta=  90.020  Gamma=  89.977

The CRYST1 cell dimensions

    A    =  56.870  B   =  85.280  C    = 133.220
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 131.233
(Under-)estimated Z-score: 8.443

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 425 ARG   ( 468-)  A      CB   CG   CD  105.76   -4.2

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.

 542 PRO   ( 585-)  A    -2.7
 124 PRO   ( 163-)  A    -2.6
 509 ILE   ( 552-)  A    -2.6
 355 TYR   ( 394-)  A    -2.4
 321 TYR   ( 360-)  A    -2.3
 438 TYR   ( 481-)  A    -2.3
 247 ILE   ( 286-)  A    -2.2
  84 GLU   ( 123-)  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.

  84 GLU   ( 123-)  A  Poor phi/psi
 123 GLU   ( 162-)  A  PRO omega poor
 131 ALA   ( 170-)  A  omega poor
 309 ARG   ( 348-)  A  Poor phi/psi
 310 GLU   ( 349-)  A  Poor phi/psi
 366 ALA   ( 405-)  A  omega poor
 392 ASN   ( 431-)  A  Poor phi/psi
 474 SER   ( 517-)  A  Poor phi/psi
 511 GLN   ( 554-)  A  Poor phi/psi
 543 ASN   ( 586-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -1.575

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!

  32 THR   (  71-)  A      0
  33 ASN   (  72-)  A      0
  69 GLN   ( 108-)  A      0
  84 GLU   ( 123-)  A      0
  85 ARG   ( 124-)  A      0
 115 PRO   ( 154-)  A      0
 116 ASN   ( 155-)  A      0
 122 LEU   ( 161-)  A      0
 123 GLU   ( 162-)  A      0
 133 SER   ( 172-)  A      0
 175 VAL   ( 214-)  A      0
 220 TYR   ( 259-)  A      0
 224 HIS   ( 263-)  A      0
 234 HIS   ( 273-)  A      0
 235 LEU   ( 274-)  A      0
 236 LEU   ( 275-)  A      0
 240 TRP   ( 279-)  A      0
 242 GLN   ( 281-)  A      0
 243 THR   ( 282-)  A      0
 244 TRP   ( 283-)  A      0
 245 SER   ( 284-)  A      0
 247 ILE   ( 286-)  A      0
 254 PHE   ( 293-)  A      0
 257 ALA   ( 296-)  A      0
 260 MET   ( 299-)  A      0
And so on for a total of 167 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].

 124 PRO   ( 163-)  A   -53.4 half-chair C-beta/C-alpha (-54 degrees)
 203 PRO   ( 242-)  A  -113.5 envelop C-gamma (-108 degrees)
 258 PRO   ( 297-)  A   -65.9 envelop C-beta (-72 degrees)
 294 PRO   ( 333-)  A  -113.0 envelop C-gamma (-108 degrees)
 457 PRO   ( 500-)  A  -131.5 half-chair C-delta/C-gamma (-126 degrees)
 542 PRO   ( 585-)  A   -48.7 half-chair C-beta/C-alpha (-54 degrees)
 586 PRO   (   5-)  P  -120.8 half-chair C-delta/C-gamma (-126 degrees)
 588 PRO   (   7-)  P  -130.4 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 594 NAG   (1633-)  A      O4  <->  603 BMA   (1634-)  A      C1     0.95    1.45  INTRA B3
 594 NAG   (1633-)  A      C4  <->  603 BMA   (1634-)  A      C1     0.85    2.35  INTRA
  85 ARG   ( 124-)  A      NH2 <->  605 HOH   (2018 )  A      O      0.25    2.45  INTRA
 425 ARG   ( 468-)  A      NH2 <->  470 HIS   ( 513-)  A      O      0.21    2.49  INTRA BL
 464 ASP   ( 507-)  A      N   <->  465 PRO   ( 508-)  A      CD     0.15    2.85  INTRA BL
 193 ASP   ( 232-)  A      OD1 <->  196 ARG   ( 235-)  A      NH2    0.13    2.57  INTRA
 218 ARG   ( 257-)  A      NH2 <->  604 PE4   (1631-)  A      O4     0.13    2.57  INTRA
 531 TRP   ( 574-)  A      N   <->  532 PRO   ( 575-)  A      CD     0.13    2.87  INTRA BL
 348 HIS   ( 387-)  A      ND1 <->  371 HIS   ( 410-)  A      ND1    0.12    2.88  INTRA
 314 HIS   ( 353-)  A      NE2 <->  605 HOH   (2081 )  A      O      0.10    2.60  INTRA
 168 ALA   ( 207-)  A      O   <->  172 ASN   ( 211-)  A      ND2    0.09    2.61  INTRA BL
 364 GLU   ( 403-)  A      OE2 <->  589 LYS   (   8-)  P      NZ     0.08    2.62  INTRA
 147 ARG   ( 186-)  A      NH1 <->  239 MET   ( 278-)  A      SD     0.07    3.23  INTRA BL
 426 TRP   ( 469-)  A      NE1 <->  605 HOH   (2095 )  A      O      0.07    2.63  INTRA BL
 203 PRO   ( 242-)  A      O   <->  207 ASN   ( 246-)  A      ND2    0.06    2.64  INTRA BL
 192 GLN   ( 231-)  A      NE2 <->  605 HOH   (2050 )  A      O      0.06    2.64  INTRA
 218 ARG   ( 257-)  A      NH2 <->  604 PE4   (1631-)  A      O3     0.05    2.65  INTRA
 474 SER   ( 517-)  A      O   <->  587 ARG   (   6-)  P      NH2    0.04    2.66  INTRA BL
 458 ARG   ( 501-)  A      NE  <->  464 ASP   ( 507-)  A      OD2    0.04    2.66  INTRA BL
  24 ALA   (  63-)  A      O   <->   28 TRP   (  67-)  A      N      0.03    2.67  INTRA
 237 GLY   ( 276-)  A      N   <->  605 HOH   (2029 )  A      O      0.02    2.68  INTRA BL
 240 TRP   ( 279-)  A      NE1 <->  467 ALA   ( 510-)  A      O      0.01    2.69  INTRA BL
 255 PRO   ( 294-)  A      N   <->  256 SER   ( 295-)  A      N      0.01    2.59  INTRA B3
 266 MET   ( 305-)  A      SD  <->  335 ASN   ( 374-)  A      C      0.01    3.39  INTRA
 358 LEU   ( 397-)  A      O   <->  363 ARG   ( 402-)  A      NE     0.01    2.69  INTRA
 379 ALA   ( 418-)  A      O   <->  383 SER   ( 422-)  A      N      0.01    2.69  INTRA BL

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.

 309 ARG   ( 348-)  A      -7.48
 567 HIS   ( 610-)  A      -6.17
 460 GLN   ( 503-)  A      -6.07
 570 LYS   ( 613-)  A      -5.98
 223 GLN   ( 262-)  A      -5.75
 219 HIS   ( 258-)  A      -5.66
 587 ARG   (   6-)  P      -5.61
  67 GLN   ( 106-)  A      -5.58
 576 TYR   ( 619-)  A      -5.51
 116 ASN   ( 155-)  A      -5.47
 304 LYS   ( 343-)  A      -5.21
 450 GLN   ( 493-)  A      -5.13
 227 LEU   ( 266-)  A      -5.08
 584 LEU   (   3-)  P      -5.06
 458 ARG   ( 501-)  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.

 218 ARG   ( 257-)  A       220 - TYR    259- ( A)         -4.79

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.

  83 LEU   ( 122-)  A   -2.88
 541 GLN   ( 584-)  A   -2.59
 184 MET   ( 223-)  A   -2.51

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: 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.

 605 HOH   (2010 )  A      O
 605 HOH   (2018 )  A      O
 605 HOH   (2062 )  A      O
 605 HOH   (2086 )  A      O
Bound group on Asn; dont flip   70 ASN  ( 109-) A
Bound to:  593 NAG  (1632-) A
Marked this atom as acceptor  596  CL  (1625-) A     CL
Marked this atom as acceptor  597  CL  (1627-) A     CL
Marked this atom as acceptor  598  CL  (1628-) A     CL

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.

  48 GLN   (  87-)  A
 114 HIS   ( 153-)  A
 224 HIS   ( 263-)  A
 344 HIS   ( 383-)  A
 575 GLN   ( 618-)  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.

  20 TRP   (  59-)  A      NE1
  65 VAL   ( 104-)  A      N
 125 ASP   ( 164-)  A      N
 166 ASN   ( 205-)  A      ND2
 176 ASP   ( 215-)  A      N
 218 ARG   ( 257-)  A      NH2
 225 ILE   ( 264-)  A      N
 226 ASN   ( 265-)  A      ND2
 234 HIS   ( 273-)  A      NE2
 238 ASN   ( 277-)  A      N
 243 THR   ( 282-)  A      N
 260 MET   ( 299-)  A      N
 322 ASN   ( 361-)  A      N
 324 LYS   ( 363-)  A      N
 325 ASP   ( 364-)  A      N
 356 LYS   ( 395-)  A      N
 357 ASP   ( 396-)  A      N
 361 ALA   ( 400-)  A      N
 367 ASN   ( 406-)  A      N
 372 GLU   ( 411-)  A      N
 375 GLY   ( 414-)  A      N
 378 LEU   ( 417-)  A      N
 394 LEU   ( 433-)  A      N
 398 GLU   ( 441-)  A      N
 399 HIS   ( 442-)  A      N
 406 LYS   ( 449-)  A      NZ
 414 PHE   ( 457-)  A      N
 417 PHE   ( 460-)  A      N
 422 ASP   ( 465-)  A      N
 434 THR   ( 477-)  A      N
 435 LYS   ( 478-)  A      N
 446 ARG   ( 489-)  A      NE
 456 VAL   ( 499-)  A      N
 458 ARG   ( 501-)  A      NH2
 479 ARG   ( 522-)  A      N
 483 SER   ( 526-)  A      OG
 489 GLN   ( 532-)  A      NE2
 505 HIS   ( 548-)  A      N
 513 LYS   ( 556-)  A      NZ
 534 ALA   ( 577-)  A      N
 543 ASN   ( 586-)  A      N
 575 GLN   ( 618-)  A      NE2
 581 ASN   ( 624-)  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.

 148 ASP   ( 187-)  A      OD1
 343 HIS   ( 382-)  A      NE2
 345 GLU   ( 384-)  A      OE1
 345 GLU   ( 384-)  A      OE2
 387 HIS   ( 426-)  A      NE2
 462 ASP   ( 505-)  A      OD1
 508 ASP   ( 551-)  A      OD2

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.

 605 HOH   (2077 )  A      O  0.87  K  4 ION-B

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.

 310 GLU   ( 349-)  A   H-bonding suggests Gln; but Alt-Rotamer
 338 ASP   ( 377-)  A   H-bonding suggests Asn
 376 ASP   ( 415-)  A   H-bonding suggests Asn; Ligand-contact
 430 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 :  -0.439
  2nd generation packing quality :  -1.323
  Ramachandran plot appearance   :  -0.418
  chi-1/chi-2 rotamer normality  :  -1.575
  Backbone conformation          :  -0.325

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.329 (tight)
  Bond angles                    :   0.532 (tight)
  Omega angle restraints         :   0.866
  Side chain planarity           :   0.254 (tight)
  Improper dihedral distribution :   0.439
  B-factor distribution          :   0.358
  Inside/Outside distribution    :   1.006

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 : 2.60

Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.329 (tight)
  Bond angles                    :   0.532 (tight)
  Omega angle restraints         :   0.866
  Side chain planarity           :   0.254 (tight)
  Improper dihedral distribution :   0.439
  B-factor distribution          :   0.358
  Inside/Outside distribution    :   1.006

      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
    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).

    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
      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
    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.