[phenixbb] problem with high Rfree

Pavel Afonine pafonine at lbl.gov
Mon May 19 23:51:42 PDT 2008

Hi Christina,

I usually observe similar R/Rfree behavior when I use LS target instead 
of maximum-likelihood. In fact, twin refinement in phenix.refine is 
based on LS target function. This is just to share my observations; it's 
not necessarily happening in your case.

- How many of test reflections you have and how they are distributed in 
resolution bins?
- Just out of curiosity: did you try to ignore twinning and run 
refinement with default target?
- What if you don't run SA?
- Did you try to play with target weights (try different values for 
wxc_scale and wxu_scale) to see how this affect the R-factors?
- Are you using the latest (or one of) phenix.refine?
- Did you try to fill in water?

Could you send a log file: may be we could spot something outstanding...


On 5/19/2008 1:32 PM, Christina Bourne wrote:
> Hello BB,
> I am working on a structure that is twinned (merohedral) in P41.  
> Initial estimates of twinning fraction (via xtriage and Yeates server) 
> are around 0.37; in refinement they start around 0.49 and drop to 0.46 
> (so far).  My MR soln is good (Phaser LLG ~550) with 4 mols per AU; 
> this gives good packing with no room for another mol.  I have data 
> from 48-2.8A.
> I should mention that data processing wasn't easy- this crystal form 
> also has an apparent epitaxial twin in the b dimension causing a 
> doubling in that dimension.  During indexing (with SAINT) I applied a 
> transformation of 100 00.50 001 to the reflections, which then gave me 
> the expected cell and from Xprep the data looks OK.  (Yes, I am trying 
> to grow different forms)
> Maps look nice, although I wish my ligand had more/better density.
> I ran phenix.refine with defaults, and included twin_law="h,-k,-l", 
> xray_data.r_free_flags.generate=true, 
> detwin.map_types.aniso_correct=true and also 
> simulated_annealing=true.  My starting R/ Rfree is 0.448/ 0.4385; 
> ending is 0.2962/ 0.4270.  Geometry is somewhat tighter after 
> refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 
> 1.530).  I have not included my ligand, and I can see a few spots 
> where the model needs adjusting, but nothing majorly wrong.
> Why is my Rfree hanging so high?  Is it becaues I have bad karma?  Is 
> it to do with the twinning?  I am pretty sure my space group is right 
> (based on the above info and the maps look fine; Phaser could not find 
> a solution in P43).  There isn't room for anything else in the cell.
> Any opinions or suggestions are most welcome as I wait for better 
> xtals to grow...
> Thanks in advance,
> Christina
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