I have been using the Phenix-linked Coot to modify a MR solution calculated from a rather poor data set, with high merging Rs and very low absolute intensities. I have observed what I consider bizarre behavior in the real space refinement function. My original observation was that very often RSR would actually make the model look less like the density. I generally use the default matrix weight (60) or reduce it to 20. When I let coot estimate the weight it came up with 65446. With that value the RSR seems to behave normally. How is this weight calculated? What kind of data pathology would produce the results I am seeing? Is it related to the low intensity values in the data?
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