How many cycles are
required to remove the Rfree bias for different R-free
data set. I usually do annealing at CNS.
- slightly shake coordinates and ADPs;
- remove water (if present);
- run phenix.refine with or without SA, refine coordinates,
B-factors, use automated water update option, as many macro-cycles
as necessary to achieve convergence (for example, R-factors stop
changing).
Alternatively, you may consider running your model through
phenix.autobuild (which will be more thorough but time consuming
option).
The above strategy may (significantly) vary depending on the data
resolution.