Hi Scott,

As the TLS refinement can take a significant amount of time, I'm wondering if I can turn it off after a few rounds with it on?

technically, you can (=program will not crash). But in this case phenix.refine will automatically convert all anisotropic ADP into isotropic which will in turn invalidate previous TLS refinement. To stop this you will need to turn off the B-factor refinement completely, which is unlikely to be a good idea.

or will phenix.refine "see" the ANISOU records and assume I am doing anisotropic ADP?

This was the behavior in earlier versions. We fixed it sometime ago. Now if phenix.refine "sees" ANISOU and these atoms do not participate in TLS group and the resolution is "low enough", then it automatically converts ADPs to isotropic. If resolution is "high enough" then these atoms will be refined with individual anisotropic B-factors. The parameter used to decide about "low/high enough" resolution is: switch_to_isotropic_high_res_limit = 1.7 So once you started using TLS then it is the best to keep using it. Pavel.