##### ##### ##### Parameter File for DireX 0.7.1 ##### ##### # Number of structures to generate nsteps = 100 # Annealing steps # (set to zero for no annealing) annealing = 0 # Sampling mode (concoord/gradient) sampling_mode = concoord # Damp sampling moves # for concoord method concoord_damp = 1.000000 # for gradient method gradient_damp = 0.100000 # Frequency of xtc output nsxtcout = 1 # Frequency of pdb output nspdbout = 1 # Frequency of current model (pdb) output nscur = 1 # Frequency of message output nsmessout = 1 # Maximally allowed number of restraint violations nviol = 0 # Perturbation factor in (Ang) pert_fac = 0.000000 ##### ##### ##### Tirion mode enhanced sampling ##### ##### # Use tirion modes for enhanced sampling tirion_use = no # Perturbation factor for Tirion mode # calculation in (Ang) tirion_pert_fac = 1.000000 # Distance bounds in (Ang) tirion_lb = 0.500000 tirion_ub = 0.500000 # Stepsize for Tirion mode tirion_fac = 1.000000 ##### ##### ##### Adaptive Perturbation ##### ##### # Use Adaptive Perturbation use_ap = no # Perturbation factor in (Ang) ap_pert_fac = 0.100000 # Stepsize ap_fac = 20.000000 ##### ##### ##### DEFORMABLE ELASTIC NETWORK (DEN) ##### ##### # Use DEN (yes/no) use_den = yes # Generate DEN restraints only between CA atoms. den_ca = no # Number of (randomly chosen) elastic restraints # as multiple of number of atoms. (Default: 2.0) den_no_ratio = 2.000000 # Strength of elastic potential (0.0-1.0) den_strength = 0.400000 # Upper distance bound in (Ang) den_upper = 15.000000 # Lower distance bound in (Ang) den_lower = 3.000000 # DEN restraints only between atoms within # given residue range. # A negative value switches off the range # limitation. den_resid_range = -1 # Number of steps during which the DEN restraints are # scaled down from 1 to 0 den_damp_restraints = 40 # Weight initial structure and experimental data # 0 means the network moves only towards the reference model. # 1 means the network does not use reference information at all. # (0.0-1.0) den_gamma = 0.000000 # Damping of the deformation of the elastic # network (0.0-1.0) # low/high value means high/low damping den_kappa = 0.200000 # Beyond this distance difference the force # is constant (in Ang) den_const_dist = 2.000000 # DEN restraint breaks if distance difference is larger # than this value (in Ang) den_break_dist = 4.000000 # DEN strength depends on secondary structure # if not defined, then this will be used when a # secondary structure file is read with -secstr # den_strength will be scaled by this factor for loop # residues. Secondary structure must be read with # -secstr option. den_secstr_loop = 1.000000 # den_strength will be scaled by this factor for # sidechains den_sidechain = 1.000000 ##### ##### ##### ELECTRON DENSITY MAP ##### ##### # Strength of electron density map restraints map_strength = 0.030000 # Model map is updated only every map_update_freq steps # only if 'use_difference_map = yes' map_update_freq = 1 # Probe sigma in (Ang) map_probe_sig = 0.500000 # Set maximum and minimum values [999999.99] and [-999999.99] map_cap = 999999.990000 map_cap_lower = -999999.990000 # Move residues instead of individual atoms. map_move_resid = no # Number of steps during which forces from the density map are # scaled down from 1 to 0 map_damp_restraints = 40 ### ### Compute Model Map ### # Resolution interval (in Ang) used for model refinement # !!! Meaning of cur_map_dmin has changed from previous versions !!! cur_map_dmin = 5.000000 cur_map_dmax = 99999.900000 # Resolution interval (in Ang) used for cross-validation # (If map_cv_dmax <=0, it is automatically set to cur_map_dmin) map_cv_dmin = 4.000000 map_cv_dmax = -1 # Use random choice of structure factors for the free set. # The map_cv_dmax value is ignored in this case. use_cv_random = no cv_random_frac = 0.1 ### Bulk solvent correction ksol = 0.000000 Bsol = 0.000000 # Apply overall B-factor Boverall = 0.000000 # Optimize parameters ksol, Bsol, and Boverall. opt_solvent_bfactor = no map_match_sf = no # Write free and work input and model maps # (only when using cross-validation). output_cvmaps = no # Use bootstrapping to estimate error of # the density map correlation coefficient. bootstrap_error = no # Use only CA atoms to compute model map cur_map_ca = no # Density forces are scaled by occupancy map_use_occ = no # Mass of atoms is scaled by occupancy for # model map computation compute_map_use_occ = no # Use secondary structure information for # model map map_use_secstr = no # Relative mass of loops map_mass_loop = 1.000000 ### ### Refine occupancy ### map_refine_occ = no # Group occupancy refinement (residue-wise) map_group_refine_occ = yes # Refine occupancy damp map_refine_occ_damp = 0.000100 # Write 100*(1-occupancy value) into # PDB B-factor column map_bfac_as_occ = no # Occupancy restraints between bonded atoms. # Values between 0 and 1. # No restraints are used if set to 0. map_occ_restraint_lambda = 0.100000 # Number of iterations the neighboring occupancies # are averaged. The more cycles, the stronger the restraints. map_occ_restraint_cycles = 1 # Exclude atoms using a threshold definition map_use_threshold = no # Atoms that are # above model density threshold and map_model_threshold = 5.000000 # below target density threshold map_target_threshold = 0.000000 # are excluded. # Exclude those atoms also from model map computation # !! Becomes effective only at step 2 !! compute_map_use_threshold = no # Frequency of map output # Current model map nscurmapout = 1 nscurdifmapout = 1 ##### ##### ##### EXPERIMENTAL (OR OTHER) DISTANCE RESTRAINTS ##### (read by -expd option) ##### ##### # Strength of distance # restraints (0.0-1.0) expd_strength = 0.100000 # Beyond this distance the force is # constant (in Ang) expd_const_dist = 2.000000 # Deformable restraints expd_deformable = no # Deformability expd_deform_strength = 1.000000 # Weak restoring force to counterbalance diffusion expd_deform_back = 0.100000 # Restoring force linear ? (or harmonic otherwise) expd_deform_linear = no # Number of steps during which restraints are # scaled down from 1 to 0 expd_damp_restraints = 40 ##### ##### ##### POSITION RESTRAINTS ##### (read by -posre option) ##### ##### # Strength of position restraints (0.0-1.0) posre_strength = 0.100000 # Beyond this distance the force is # constant (in Ang) posre_const_dist = 2.000000 # Number of steps during which restraints are # scaled down from 1 to 0 posre_damp_restraints = 40 ##### ##### ##### NCS Restraints ##### (read by -ncs option) ##### ##### # Number of Restraints per Group # (will be set equal to number of atoms in that group # if set to -1) n_ncs = -1 # Strength of NCS restraints (0.0-1.0) ncs_strength = 0.500000 # Number of steps during which restraints are # scaled down from 1 to 0 ncs_damp_restraints = 40 # Beyond this distance the force is # constant (in Ang) ncs_const_dist = 2.000000 # Upper distance bound in (Ang) ncs_upper = 15.000000 # Lower distance bound in (Ang) ncs_lower = 3.000000 ##### ##### ##### Pair Distance Distribution Restraints ##### For use with SAXS data ##### ##### # Number of atom pairs to be used # for histogram calculation. If -1 it is set automatically. pr_n_pairs = -1 pr_strength = 0.400000 pr_damp = 40 ##### ##### ##### H-BONDS ##### ##### # Optimize hbonds opt_hb = no # Strength of hbond optimization opt_hb_fac = 1.000000 # Hbond cutoff in (Ang) hb_cutoff = 2.500000 # Hbond angle cutoff hb_angle_cutoff = 30.000000 # Search distance for potential # h-bond (cut-off) in (Ang) pot_hb_cutoff = 5.000000 # Use implicit solvent # (no optimization for surface hb-bonds) implicit_solvent = yes # Try to keep existing h-bonds by # defining a restraint keep_existing_hb = no # Output list of currently detected Hbonds output_hb_list = no # Output list of backbone N-O pairs that are # closer than 'hb_list_no_d' Ang. output_hb_list_no = no # Cut-off in (Ang) hb_list_no_d = 3.100000 ##### ##### ##### NEIGHBOR GRID OPTIONS ##### ##### max_atoms_per_grid = 100 # in (Ang) neighbor_grid_constant = 5.000000 # Maximum grid points of the neighbor grid. Estimated automatically if set to -1. max_n_grid = -1 ##### ##### Memory allocation ##### # Maximum number of atoms. max_n_atoms = 200000 # Maximum number of distance restraints. Estimated automatically if set to -1. max_n_disre = -1 # Maximum number of potential hbonds. Estimated automatically if set to -1. max_n_pothb = -1 # Maximum number of bonds, calculated as (max_n_bonds_fac * natoms). max_n_bonds_fac = 2.000000 # Maximum number of angles, calculated as (max_n_angles_fac * natoms). max_n_angles_fac = 3.000000 ##### ##### ##### Misc options ##### ##### # Maximal number of attempts to generate # a structure before a new attempt is started max_cycles = 500 min_cycles = 0 # VdW cutoff in (Ang) vdw_cutoff = 5.500000 # Bead mode: no chemical bonds, no stereochemistry. # Used for a general bead model bead_mode = no no_bonds = no # Use interchain concoord # if "no", chains are allowed to overlap. interchain_concoord = yes # Forces to repel chains. This is ony used if # interchain_concoord is set to "no". # >0 means atoms repel each other. # <0 means atoms attract each other. # Example: repel_shift = 0.01 repel_shift = 0.000000 # Number of steps during which restraints are # scaled down from 1 to 0 repel_damp = 40 repel_all_atoms = 0.000000 # Set interval for vdw restraints. This gives the distance from the actual distance # to the upper/lower bound, respectively. # to lower bound in (Ang) vdw_lb_dif = 1.140000 # to upper bound in (Ang) vdw_ub_dif = 1.140000 # relative strength of hbonds. Change only if you know what you are doing! hb_NH_O = 2.000000 hb_OH_O = 5.000000 hb_NH_N = 3.000000 hb_OH_N = 7.000000 hb_ELSE = 1.000000 bound_factor = 1.000000 # Output structures that are not converged. Only for debugging. output_unconverged = no # Output structures every n-th correction-cycle. output_unconverged_freq = 10 # Write list of violated concoord restraints after max_cycles # into a file "violations.dat" output_violations = no fix_com = no # Use planarity constraints use_planar_constraints = yes use_improper_constraints = yes fft_optimize = no