-parser:protocol dock_and_relax.xml -beta -multithreading:total_threads 1 -default_max_cycles 200 -in:file:extra_res_fa 6-chloro-tryptophan.params ARD.fa.params CYY.params FK5.fa.params FKA.fa.params RAD.fa.params RAP.fa.params -parser:script_vars ddg_gate=-14.0214 cms_gate=163.4925