Hello Jian Wu,
Because the packing does not allow room for your Sub1 and Sub2
domains, I suspect your MR solutions are not correct. It can be
surprisingly difficult to tell from your electron density due to phase
bias. I've found both simulated annealing omit and Resolve prime and
switch maps useful in combating phase bias. I suggest you try to get
experimental phases. It can save you a lot of time struggling with a
difficult MR problem and rebuilding into lousy maps.
I'd love to know how you end up solving the structure!
ho
UC Berkeley
