Hi Chen, my apologies for the late reply, somehow I managed to overlook your email.. Ok, here it is (better late than never!):
I have a question about the occupancy refinement of the anomalous scatters. This is because when I went through all the HA sites, I found that some of them has too high B factor and too high occ. I manually adjusted the occ and fed the model into refinement, but the B factor and occ came back to around their original level again. It seems that those have a stronger peak in the anomalous difference Fourier map has a higher occupancy after refinement, but this does not necessarily equals to a strong density peak in 2Fo-Fc map (some of them even disappear after refinement), and this might be related to their high B factor. Am I doing something wrong in the refinement? I am basically using phenix.refine default setting, but with TLS+isotropic B factor refinement and occupancy refinement of a small region (5-8 residues). The resolution is 3 A, and the refinement is already at the final stage. I am still at the learning stage and your input will be greatly appreciated.
HA sites may be partially occupied. Try this for HA with high B: set occupancy of HA to some number less than 1 and reset B to mean B, then run phenix.refine (make sure occupancy refinement is enables, which is the default). If this does not help then please send me files and I will have a closer look. Pavel