[phenixbb] Stalled refinement

Yarrow Madrona amadrona at uci.edu
Thu Apr 17 20:37:57 PDT 2014


I will try this but I performed molecular replacment with the
same structure that has a simillar size ligand (Orthorhombic unit cell
instead of monoclinic with different lengths and angles). I would be
surprised if the changes were this large without any visible fo-fc density
showing up.

On Thursday, April 17, 2014, Paul Adams <pdadams at lbl.gov> wrote:

>
> Given the resolution you might want to try auto(re)building or morphing to
> see if there are any unexpected structural changes which explain the high
> R-factor.
>
> On Apr 17, 2014, at 6:05 PM, Yarrow Madrona <amadrona at UCI.EDU> wrote:
>
> > There is no significant peaks for translational NCS. I also didn't see
> anything in the patterson map.
> >
> > However, the Multivariate Z score L-test gives 6.218. Also the observed
> Centric reflections are more intense than they should be but I don't
> suspect twinning in a monoclinic space group.
> >
> > -Yarrow
> >
> >
> > On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams at lbl.gov> wrote:
> >
> > What does triage say about translation NCS?
> >
> >
> > On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona <amadrona at uci.edu>
> wrote:
> > Hello,
> >
> > I using the latest stable build of phenx.refine (1.8.4) I recently
> collected data, processed and obtained an MR solution using phaser. I am
> stuck trying to refine with an Rfree sitting at 40%
> >
> > I really want to know if the high Rfree is due to poor data quality or
> if non-crystallographic symmetry involving a near perfect two fold rotation
> between the two molecules in the ASU could somehow impede refinement. Stats
> and other information is below. Thank you for any help you can give.
> >
> > -Yarrow
> >
> >
> > Visually, the quality of the data is marginal at best (streaky/ice rings
> in many frames) despite good processing stats from XDS. Processing with
> mosflm or HKL2000 managed to index but failed pretty bad in integration and
> scaling.
> >
> > Phaser gave high TFZ scores for 2 molecules in the asu (see below).
> >
> > Density for a cholesterol like ligand shows up even though not present
> in the search model.
> >
> > MolRep Self rotation shows rotational symmetry.
> >
> https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf
> >
> > The 2 molecules in the ASU are related by almost a 2 fold rotation:
> >
> > Rotation matrix for chain A to chain B:
> >
> > new_ncs_group
> > rota_matrix    1.0000    0.0000    0.0000
> > rota_matrix    0.0000    1.0000    0.0000
> > rota_matrix    0.0000    0.0000    1.0000
> > tran_orth     0.0000    0.0000    0.0000
> >
> > center_orth   15.2016    0.5245   33.7070
> >
> > rota_matrix   -0.9860   -0.1636   -0.0309
> > rota_matrix   -0.1659    0.9511    0.2605
> > rota_matrix   -0.0132    0.2620   -0.9650
> > tran_orth      34.3310  -24.0033  107.0457
> >
> > center_orth   15.7607    7.2426   77.7512
> >
> > RMSD, B onto A = 0.0007 after phaser
> > RMSD, B onto A = 0.347 after one round of refinement in phenix
> >
> >
> > Refinement using aniostropically corrected data (ucla web server:
> Services.mbi.ucla.edu/anisoscale) did not improve the Rfree in refinement.
> >
> >
> > Statistics are listed below:
> >
> > UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21
> >
> > RESOLUTION     NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR
> COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno   Nano
> >    LIMIT     OBSERVED  UNIQUE  POSSIBLE     OF DATA   observed  expected
>                                      Corr
> >
> >      5.99        8280    1927      2087       92.3%       3.1%      3.3%
>     8246   35.09      3.5%    99.8*    20*   0.909    1296
> >      4.30       14606    3401      3487       97.5%       3.3%      3.5%
>    14580   33.37      3.8%    99.9*    11*   0.843    2273
> >      3.53       17961    4244      4445       95.5%       3.8%      3.9%
>    17944   31.11     Building 80, Room 247
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> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
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>
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> --
>
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