Dear Mohamed,
Have you tried using other software packages? For some S-SAD data I collected the signal was good but we were unable to solve it via the use of any one package. In the end we used a number of exhaustive searches over a number of sites/disulphides in SHELXD until something with a reasonable-looking substructure solution was found. We couldn't go any further with this using just SHELXE or Phenix AutoSol but using the experimental data alongside the SHELXD sites file we were eventually able to solve the structure using successive AutoBuild/AutoSol cycles.
Just a thought!
Regards,
Sam
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