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Hi Fengyun,
My case is that some part of the model will be refined to large B values (about 100) if the default value of wxu_scale (1.0) is used. The other part of the model will have average B value of about 40, which the wilson B is about 35. The corresponding 2FOFC map has very poor density for the region with large B values.
"large" B-factors for atoms in poor density are expected. Also, the large B-factors is not always something wrong.
If the value of wxu_scale set to be 0.1, that part with large B will be refined to about 80 for B. The corresponding 2FOFC map has some better (but not good enough) density for this region.
My question is that can I keep the wxu_scale at the small value for the refinement?
If it lowers B-factors, improves the R-factors and maps, then yes, keep whatever wxu_scale that does it. wxu_scale is just a number that balances target contributions arising from X-ray data and restrains and its absolute value doesn't have any particular meaning. Pavel.