[phenixbb] Stalled refinement

Thu Apr 17 21:52:14 PDT 2014

Given the high TFZ scores in Phaser is does seem unlikely that the search model is dramatically different from the structure in the crystal, however it would be sensible to rule that out. In the absence of other explanations it is possible that there is some issue with the data, but it must have some correctness to it for you to see the difference density for ligands. 

On Apr 17, 2014, at 8:37 PM, Yarrow Madrona <amadrona at UCI.EDU> wrote:

> 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
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> http://cci.lbl.gov/paul
> 
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-- 
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 64, Room 248
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 ][ 1-510-495-2506 ]
--