verbose = False dry_run = False show_script = False show_defaults = False test_mode = False phaser { mode = ANO EP_AUTO EP_SAD *MR_AUTO MR_BRF MR_BTF MR_FRF MR_FTF MR_LLG \ MR_PAK MR_RNP NMA sad_mode = *SAD MR_SAD hklin = beta_blip_P3221.mtz labin = Fobs,Sigma model = None seq_file = None mol_weight = None model_rmsd = None model_identity = None search_copies = 1 chain_type = *protein dna rna crystal { xtal_id = None pdb_file = None ha_file = None dataset { wave_id = None hklin = None labin = None wavelength = None energy = None } } crystal_symmetry { unit_cell = 75.11 75.11 133.31 90 90 120 space_group = P 32 2 1 } composition { solvent = None chain { chain_type = *protein na sequence_file = None sequence = None nres = None mw = 28853 num = 1 } chain { chain_type = *protein na sequence_file = None sequence = None nres = None mw = 17522 num = 1 } atom { element = None num = None } } ensemble { model_id = "beta" disable_check = False solution_at_origin = False coordinates { pdb = "beta.pdb" rmsd = None identity = 1.0000 read_variance_from_pdb_remarks = False } map_hklin = None map_labels = None map_extent = None map_rms = 1.0 map_centre = None map_protein_mw = 0 map_nucleic_mw = 0 fractional_comp = none } ensemble { model_id = "blip" disable_check = False solution_at_origin = False coordinates { pdb = "blip.pdb" rmsd = None identity = 1.0000 read_variance_from_pdb_remarks = False } map_hklin = None map_labels = None map_extent = None map_rms = 1.0 map_centre = None map_protein_mw = 0 map_nucleic_mw = 0 fractional_comp = none } search { ensembles = beta copies = 1 } search { ensembles = blip copies = 1 } solution = None output_dir = None keywords { general { root = "beta-blip_phaser" title = None verbose = None debug = None mute = None xyzout = None xyzout_ensemble = None hklout = None jobs = 2 keywords = False } atoms { change_scatterer = False change_scatterer_type = "" change_bfac_wilson = True } bfactor_wilson { restraint = True sigma = 5 } bfactor_sphericity { restraint = True sigma = 5 } bfactor_refine { restraint = True sigma = 40.0 } bins { minimum = 6 maximum = 50 width = 500 cubic = 0 1 0 } boxscale = 4.0 clmn { sphere = 0.0 lmin = 4 lmax = 100 } cluster_pdb = None eigen { read = None write = True } ellg { use = True target = 120.0 } ffts { minimum = 20 maximum = 80 } hand = off on *both integration { fixed = False step = None } llgcompletion { complete = True scatterer = None clash = 0 sigma = 6 ncycle = 50 maps = False } macano { protocol = *default off custom macrocycle { ref_anis = None ref_bins = None ref_solk = None ref_solb = None ncycle = None minimiser = *BFGS NEWTON DESCENT } } macmr { protocol = *default off custom macrocycle { ref_rota = None ref_tran = None ref_bfac = None ref_vrms = None ncyc = None minimizer = *BFGS NEWTON DESCENT } } macsad { protocol = *default off custom macrocycle { ref_k = None ref_b = None ref_sigma = None ref_xyz = None ref_occ = None ref_bfac = None ref_fdp = None ref_sa = None ref_sb = None ref_sp = None ref_sd = None ncycle = None minimizer = *bfgs newton descent } } nmamethod { oscillators = *rtb ca all rtb_maxblocks = 125 rtb_nresidues = 0 radius = 5 force = 1 } nmapdb { mode = None combination = None perturb = *rms dq rms { step = None stretch = None clash = None maxrms = None direction = *forward backward tofro } dq = None } normalization { bins = None aniso = None solk = None solb = None } outlier { reject = True probability = 1e-06 } pack { select = *percent best allow all cutoff = 5 quick = True compact = True distance = 3.0 trace = True } partial { pdb = None hklin = None variance = rms *id deviation = None } peaks_rotation { select = *percent sigma number all cutoff = 75.0 cluster = True } peaks_translation { select = *percent sigma number all cutoff = 75.0 cluster = True } permutations = False ptgroup { coverage = 0.90 identity = 0.95 rmsd = 1.00 tolerance_angular = 0.035 tolerance_spatial = 0.5 } purge_rotation { enable = True percent = 75 number = 0 } purge_translation { enable = True percent = 75 number = 0 } rescore_rotation = True rescore_translation = True resharpen_percent = 100.0 resolution { high = 4.0 low = None auto { high = 4.0 low = None } } rotate { volume = *full around euler = None range = None } sampling_rotation = None sampling_translation = None scattering { scatterer { type = None fp = None fdp = None fixfdp = *EDGE ON OFF } restraint = True sigma = 0.2 } search { order_auto = True method = *fast full deep = True down_percent = 25.0 } sgalternative { select = *all hand list none test = None sort = True } solparameters { fsol = 0.95 bsol = 300.0 } solution_origin_ensemble = None target_frf = *lerf1 lerf2 crowther target_ftf = *letf1 letf2 correlation tncs { use = True nmol = 2 refine_rotation = False pair_only = False translation_vector = 0 0 0 rotation_angle = 0 0 0 rotation_grid = True patterson_hires = 5.0 patterson_lores = 10.0 patterson_percent = 20.0 patterson_distance = 15.0 variance_rmsd = 0.4 variance_frac = 1.0 link_restraint = True link_sigma = 0.1 gfunction_radius = 0.0 rotation_sampling = None rotation_range = 0.0 } topfiles = 1 translate { volume = *full line region around fractional = None start = None end = None range = None } zscore { use = True solved = 8.0 half = True } } run_control { gui_run = False } } density_modification { dm = False solvent_fraction = None initial_steps = 10 shrink_steps = 20 final_steps = 10 grid_resolution_factor = 1/4 d_min = None initial_d_min = None phase_extension = False verbose = True change_basis_to_niggli_cell = True ncs_averaging = False protein_solvent_ratio = 1.31 density_truncation { fraction_min = 0.35 fraction_max = None } solvent_modification { method = *flipping flattening scale_flip = True } solvent_adjust = True solvent_mask { averaging_radius { initial = None final = None } } anisotropic_correction = True asu_contents { n_residues = None n_bases = None n_copies_per_asu = None } }