-in
	-file
		-s 2eu2_A_0001.pdb
		-load_PDB_components true
		#-fullatom true
		#-centroid_input true
		#-residue_type_set centroid
	#-ignore_unrecognized_res true
		#-extra_res_fa ~/rosetta_src_2021.16.61629_bundle/main/database/chemical/residue_type_sets/centroid/residue_types/metal_ions/ZN.params
	#-auto_setup_metals true
	#-prevent_auto_setup_metal_bb_variants true
	#-metals_detection_LJ_multiplier 1.0
	#-metals_distance_constraint_multiplier 1.0
	-metals_angle_constraint_multiplier 1.0
	-detect_disulf true
	-detect_disulf_tolerance 1.0

		
-inout
	-write_all_connect_info true
	
-overwrite

-corrections
	-beta_nov16 true

-database ~/rosetta_src_2021.16.61629_bundle/main/database/
-database ~/rosetta.ncaa.rotamer.libraries/

-chemical
	-override_rsd_type_limit true

-parser
	-protocol Remodel.xml
	
-remodel
	-blueprint Blueprint.2EU2.denovo
	-use_blueprint_sequence true
	-num_trajectory 1
	-quick_and_dirty true
	-build_disulf false
	-run_confirmation true
	-swap_refine_confirm_protocols true
#	-match_rt_limit 0.4
	-two_chain_tree 258
	-no_jumps false
	-hb_srbb 1.0
	-hb_lrbb 1.0
	-rsigma 1.0
	-ss_pair 1.0
	-use_clusters false
#	-domainFusion
#		-insert_segment_from_pdb ZN.pdb
#	-RemodelLoopMover
#		-max_linear_chainbreak 2.5
#		-randomize_loops true
#		-allowed_closure_attempts 1
#		-temperature 0.616
#	-design
		#-design_all
#		-allow_rare_aro_chi true
		#-find_neighbors true

#-loops
#	-loop_file Insert.txt
#	-remodel kic
#	-refine kic
#	-remodel_init_temp 2.0
#	-remodel_final_temp 0.616
#	-refine_init_temp 2.0
#	-refine_final_temp 0.616
	
-packing
	-ex1
		-level 7
	-ex2
		-level 7
	-ex3
		-level 7
	-ex4
		-level 7
	-ex1aro
		-level 7
	-ex2aro
		-level 7
	-ex1aro_exposed
		-level 7
	-ex2aro_exposed
		-level 7
	-no_optH false
	-optH_MCA true
#	-multi_cool_annealer 10
	-extrachi_cutoff 18
#	-use_input_sc
	
-run
	-chain _
	-preserve_header true
			
-out
	-suffix _remodel
	-nstruct 1