pentafoil_flags.txt

-shared_output_tag ./penta_round1

-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

-allow_file_stealing

-barrel_mode
-pentafoil_mode
-old_sym_min

-n_refold 5
-n_refold_sspred 40

-nrepeats 7 ## actually 5-repeat
-base_repeat 3 ## until fullatom, then should switch to 2

## default now is to do fragment sequence insertions during centroid sim
#-fastrelax_before_design
-freeze_helixseq
-freeze_centroidseq ### NO SEQMOVES AT ALL DURING CENTROID, SHOULD SPEED THINGS UP A BIT

-design_cycles 2
-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


#-sometimes_break_longer_helix 0.33

-repeatlens 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57

-helix1_len_range 0.25 0.5

-force_helix_capping
-layer_design
-layers_file ./input/basic_layers.txt

-turns GBB GBB GBB E BB BAB

-score_filter_acceptance_rate 0.1
-score_filter_pass_early F

-nstruct 100000

-symmetry_definition stoopid

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

-mute all
#-run:dry_run

-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
-output_virtual F


-database ./big_input/database/