[phenixbb] Simulated anneal

[Qiang Chen]

Hi all,

I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use
Molprobity to check the structure. The clash score is 100th and Molprobity
score is 99th.  I was suggested to run simulated anneal to help reduce
Rwork and Rfree. I tried Cartesian and Torsion and different seed. The
best result I got is: torsion anneal, start_temp=2500,final_temp=300,
random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model
and found that some places in a domain were not correctly traced. The
density for that domain is not good and have several flexible loops.  My
question is: does simulated anneal always work and reduce Rwork/Rfree?  At
the final stage of refinement, does it necessary to use simulated anneal
again?

Thanks!

yamei



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