I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing. 

autosol gave me many different output MTZ files . 

for building further in coot which MTZ file i should use and for refinement in phenix refinement which MTZ file i should use . I tried doing refinement with .sca file it gave me increase Rfree afte single cycle of refinement . 

thanks for your suggestions.