[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
> Building 978, Room 4126
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
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> BLDG 64R0121
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov <javascript:;>][ 1-510-495-2506 ]
> --
>
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