The default value of the starting temperature of Phenix refine
simulated annealing is 5000. At this temperature all
the protein structure will be destroyed.
it depends on parametrization. In phenix.refine you can use
10000-15000K and the model will not explode. Simply try it - that's
the best way to find out.
Will you please explain
why we start the simulated annealing at 5000?
As with ~500-600 parameters in phenix.refine, the defaults are set
to the values that are "good in average, most of the time". If you
want to do aggressive SA refinement (eg.: Korostelev et al, PNAS
2009), then 5000K is too low, and 10000 may be way better. If you
want to get multi-start SA averaged map for a 1A resolution model,
then 5000 is too high, and 500-1000K is a better start.