Hi,
I do have a data is at very low resolution, so only possible to do rigid body refinement.
it depends what you call "low resolution". In small molecule crystallography ~1A resolution is "low resolution" (Acta Cryst. (2007). D63, 160-170). So, without knowing what the resolution of your data is I can't really tell whether you need to refine individual anisotropic B-factors or the whole model as just one TLS group. Anyway, if by "low resolution" you mean what comes to my mind this very minute, you can still try: Coordinates: - Simulated Annealing refinement in torsion angle space; - Highly restrained refinement of individual coordinates; - Optimize weights against Rfree. - You may need to use secondary-structure restrains (available in recent PHENIX versions). ADP: - combined refinement of TLS+individual or group B-factors; - Highly restrained individual ADP refinement; - Simple group ADP refinement (where the size of groups depends on resolution or/and data-to-parameters ratio) - Optimize target weights. NCS: - use if available. Bulk-solvent: - optimize mask parameters (r_solvent and r_shrink) using optimize_mask=true (this is will done automatically in future versions of phenix.refine). Multi-Start SA: - people find it useful (Andrei Korostelev, Martin Laurberg, and Harry F. Noller "Multistart simulated annealing refinement of the crystal structure of the 70S ribosome". PNAS 2009 106:18195-18200). Good luck! Pavel.