[phenixbb] Twin_law in GUI Phenix Refinement
pafonine at lbl.gov
Wed Jan 25 07:32:48 PST 2012
> 2. I used phenix refinement in Windows to refine a 2.3A structure. My
> problem is the Rfree is quite high.
> - I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1)
> Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988
> Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448
> - Then I use auto-weight to optimize the Rfree.
> optimize_xyz_weight = True
> optimize_adp_weight = True
> wxc_scale = 0.5
> wxu_scale = 1
> Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322
> Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848
> I think the bond rmsd and angle rmsd were too small in this final
> refinement. Do you think it's normal or I need to try more? Thank you
> very much for your helpful input.
Numbers after weight optimization look ok to me. Data of 2.3A resolution
may not be able to tell you the difference between bond lengths varying
by a tiny fraction of angstrom. So what you get is dictated by the Fobs
For more details about weight optimization see "Improved target weight
optimization in phenix.refine" here: http://phenix-online.org/newsletter/
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