refinement { main { nproc = 4 } refine { strategy = individual_sites rigid_body individual_adp \ group_adp tls occupancies group_anomalous *den } den { reference_file = none gamma = 0.0 kappa = 0.1 weight = 300 sigma = 0.44 optimize = true opt_gamma_values = 0 0.2 opt_weight_values = 100 300 num_cycles = 2 kappa_burn_in_cycles = 2 bulk_solvent_and_scale = True refine_adp = False final_refinement_cycle = False verbose = True annealing_type = *torsion cartesian output_kinemage = False restraint_network { lower_distance_cutoff = 5 upper_distance_cutoff = 20 sequence_separation_low = 0 sequence_separation_limit = 10 exclude_hydrogens = True ndistance_ratio = 1 export_den_pairs = False den_network_file = None } } tardy { mode = every_macro_cycle second_and_before_last *once first first_half start_temperature_kelvin = 3300 final_temperature_kelvin = 300 number_of_cooling_steps = 1440 number_of_time_steps = 1 time_step_pico_seconds = 0.001 prolsq_repulsion_function_changes { c_rep = 100 k_rep = 1 } } simulated_annealing { start_temperature = 3300 final_temperature = 300 cool_rate = 50 number_of_steps = 24 time_step = 0.001 } }