[phenixbb] R/Rfree can not be reproduced

Pavel Afonine pafonine at lbl.gov
Sun Jun 3 05:46:33 PDT 2012

Hi Wenchang,

this should not happen, so I need to debug it. Could you please send me 
new-unique.mtz and model.pdb files off list and I will have a closer look.


On 6/3/12 4:17 AM, 周文昌 wrote:
> Dear all,
> I had a weird case in which I can not reproduce the R/Rfree value for 
> the same refinement. "same" means I run my refinement first and then I 
> rerun with "phenix.refine *.eff --overwrite". The R/Rfree values for 
> the two cases are different (0.2942/0.3190 vs 0.2942/0.3085). Should 
> not they be the same always?
> the command I used:
> 1st.
> phenix.refine new-unique.mtz model.pdb xray_data.high_resolution=2.7 
> fix_rotamers=true strategy=individual_adp+individual_sites+tls 
> ../tls_group_selections.params wxc_scale=0.05 
> refinement.input.xray_data.labels=FP,SIGFP --overwrite
> 2nd
> phenix.refine model_refine_001.eff --overwrite
> thanks,
> Wenchang

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