[phenixbb] R-free problem with phenix.refine

Pavel Afonine pafonine at lbl.gov
Fri Oct 22 08:53:05 PDT 2010


  Hi Shya,

> I have a related question, when you run phenix.model_vs_data you get
> recomputed R and R free values, what does this mean? I ran my data and got
> the following:
>    Model_vs_Data:
>      r_work(re-computed)                : 0.1823
>      r_free(re-computed)                : 0.2076
>      bulk_solvent_(k_sol,b_sol)         : 0.36  44.79
>      overall_anisotropic_scale_(b_cart) : 21.60 -11.34 -9.52 -0.00 -0.00 -0.00
>      solvent_content_estimated_via_mask : 41.5 %

these are the value computed using your all input data (no resolution or 
sigma cutoffs) and input model. The other values are those extracted 
from PDB file header, and those computed using resolution and sigma 
cutoffs (if any were used).

Pavel.




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