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