[phenixbb] Phenix.refine on coordinate-optimised structures

[Joey Farrell]

Hello,

I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures
that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol.
I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors
of such structures while preserving their earlier optimisation in real space.

I have been having some success using “strategy =  tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as
well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities
that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software
that I am not yet aware of.

Thank you for your help!

Best,
Joey
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