I am new to low resolution refinement parametrization and regularization. Crystal diffracted with high anisotropy reaching to 3.5A in one direction and 4.5A other direction. I am refining a structure at 3.9A resolution. Protein has two domain connected trhough a linker and is packed as tetramer in ASU. Refinement in phenix as well as in refmac leads to wipe away of electron density in helical domain of protein leaving only blobs of electron density while other domain have good amount of density after refinement. I need your precious and valuable suggestion for proceeding with refinement.

Thanks in advance for your suggestion.