On Fri, Mar 18, 2011 at 2:39 PM, Pavel Afonine
I have no idea where you read this ("Phenix suggested "Individual site" refinement is only suitable for high or midi resolution data (<3.5A)") - I would never say this.
With proper set of restraints (Ramachandran plot restraints, secondary structure restraints, reference model (if available) restraints) and weights (tight enough geometry) you can refine individual coordinates (as well as B-factors) at this resolution.
The documentation for the GUI says that individual_sites "is almost always appropriate except at low-resolution (typically 3.5A or worse), unless additional restraints (NCS, reference model, etc.) are used." Which, in retrospect, was not the clearest way to state it, so I've modified that sentence to sound less negative. The intended message was the same as Pavel's - you usually need to add more restraints to make coordinate refinement behave well at low resolution. However, I would recommend trying them in the opposite order: a high-resolution reference model is ideal if available. (You should also use NCS restraints if NCS is present.) The Ramachandran restraints should only be used as a last resort, at the end of refinement, and after you've fixed as many problems as possible manually in Coot (with real-space refinement). -Nat