In i2 if you try the 'Prepare files for deposition' to make the cif's, it seems to do a round of refinement, presumably to get the final stats, etc, but the anisotropic B-factors seem to be ignored and are lost from the output file, as far as I can tell. Hence, the R and R-free rise quite a bit. I can get round it with pdb_extract on the deposition web site, but was wondering if I am missing something in the i2 approach.
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