trefoil_resampling_flags.txt

-shared_output_tag ./trefoil_round2

-my:mode unbound_frag

-adjust_ref_weights A 0.5 W 1.5 G 0.5 H 0.5 D 0.25

-limit_aroma_chi2
-donut_energy_weight 0.5
-centroid_helixseq LEU ILE ASP SER # LIDS
-freeze_centroidseq

-allow_file_stealing

-barrel_mode
-trefoil_mode
-force_helix_capping
-layer_design
-layers_file ./input/basic_layers.txt
-dont_force_first_helix_in

-@resample_bbs input/job26_bbtags.txt
							
-base_repeat 3

-n_refold 5
-n_refold_sspred 40

-freeze_helixseq
-design_cycles 2

-score_filter_acceptance_rate 0.1
-score_filter_pass_early F

-use_softrep_for_design ## unnecessary w/ design_score_function

-score_function input/talaris2014.wts
-design_score_function input/talaris2014.soft.wts
-final_round_design_score_function input/talaris2014.wts

-nstruct 100000

-symmetry_definition stoopid

-ex1
-ex2
#-ex1aro::level 6
#-extrachi_cutoff 15

-mute all

-out::level 550
-ignore_unrecognized_res

-loops::vall_file ./big_input/vall.dat.pc60_2002-12-27_v01.2.trimmed.gz

-unfolded_sasas input/reference_fully_exposed_sasa_values.txt
-database ./big_input/database
-output_virtual T