# io -database ./database/ -in:file:fasta inputs/3PDM_.fasta -in:file:native inputs/3pdmP.pdb -in:file:native_exclude_res 163 164 165 -parser:protocol inputs/rosetta_cm.xml -out:file:silent_struct_type binary # relax options -relax:minimize_bond_angles -relax:minimize_bond_lengths -relax:jump_move true -default_max_cycles 100 -relax:min_type lbfgs_armijo_nonmonotone -score:weights inputs/stage3_rlx.wts -symmetry:symmetry_definition inputs/helix_denovo.sdef -score:patch inputs/fiberdiff_patch -hybridize:stage1_probability 1.0 -use_bicubic_interpolation -sog_upper_bound 15 -fiber_diffraction:layer_lines inputs/3PDM.work.fiber.dat -fiber_diffraction:a 49 -fiber_diffraction:b 3 -fiber_diffraction:p 1.44 -fiber_diffraction:resolution_cutoff_low 0.1 -fiber_diffraction:resolution_cutoff_high 0.286 -fiber_diffraction:max_bessel_order 70 -fiber_diffraction::b_factor 20.0 -fiber_diffraction::b_factor_solv 400 -fiber_diffraction::b_factor_solv_K 0.4 -fiber_diffraction:qfht_K1 2.0 -fiber_diffraction:qfht_K2 2.2 -edensity:sc_scaling 0.92 -fiber_diffraction:grid_r 512 -fiber_diffraction:grid_z 128 -fiber_diffraction:grid_phi 256