#####
#####
##### Parameter File for DireX v0.4
#####
#####
# Number of structures to generate
nsteps = 100
# 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 output nscur = 1
# Frequency of message output
nsmessout = 1
# Maximally allowed number of restraint violations
nviol = 0
# Perturbation factor in (Ang)
pert_fac = 0.100000
#####
#####
##### 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
# negative value sets equal to the number of atoms
den_no = -1
# Strength of elastic potential (0.0-1.0)
den_strength = 0.200000
# 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
# Beyond this distance difference the force
# is constant (in Ang)
den_const_dist = 2.000000
# 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
# No back relaxation 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 = 0.020000
# Model map is updated only every map_update_freq steps
# only if 'use_difference_map = yes'
map_update_freq = 1
# Number of probe points to determine stochastic gradient
map_probe_n = 12
# Probe sigma in (Ang)
map_probe_sig = 2.000000
# Probe mode 1 : probability based
# 2 : average direction weighted with density (default)
# 3 : walk in direction with max density
map_probe_mode = 2
# Set maximum and minimum values [999999.99] and [-999999.99]
map_cap = 1000000.000000
map_cap_lower = -1000000.000000
# Scale input map (yes/no)
map_scale = yes
# 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 = 10
###
### Compute Model Map
###
# Choose kernel for current model map computation
# (gaussian/chapman)
cur_map_kernel = chapman
# Resolution range in (Ang)
# only for 'chapman'
cur_map_dmin = 3.000000
cur_map_dmax = 40.000000
# Sigma of gaussian kernel in (Ang)
# only for 'gaussian'
# Use 0.2944 * Resolution
cur_map_sig = 2.000000
# Use kernel within this radius to compute model map (Ang)
cur_map_kernel_rad = 10.000000
# Use only CA atoms to compute model map
cur_map_ca = no
# difference map = ( exp_map - scale_difmap * current_map )
# use difference map
# if 'no', then no model map is generated
use_difference_map = yes
# scaling factor of current density estimate
scale_difmap = 1.000000
# Histogram matching
map_match_hist = no
# Number of bins for histogram matching
map_n_hist = 20
# 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 = 0.010000
# 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
# 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
# Output scaled input and model map values
output_map_values = no
# Frequency of map output
# Current model map
nscurmapout = 1
nscurdifmapout = 1
#####
#####
##### EXPERIMENTAL DISTANCE RESTRAINTS
##### (read by -expd option)
#####
#####
# Strength of experimental 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 = 0
#####
#####
##### 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 = 10
#####
#####
##### 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 = 0
# Strength of NCS restraints (0.0-1.0)
ncs_strength = 0.100000
# Number of steps during which restraints are
# scaled down from 1 to 0
ncs_damp_restraints = 10
# 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
#####
#####
##### 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
#####
#####
##### RAMACHANDRAN BIAS
#####
#####
# ! EXPERIMENTAL FEATURE !
# ! LIKELY NOT TO WORK CORRECTLY !
# Optimize backbone dihedrals
use_rama_bias = no
rama_bias_strength = 1.000000
#####
#####
##### 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 = 2.000000
#####
#####
##### Misc options
#####
#####
# Maximal number of attempts to generate
# a structure before a new attempt is started
max_cycles = 500
# VdW cutoff in (Ang)
vdw_cutoff = 5.500000
# 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.
repel_shift = 0.010000
# Number of steps during which restraints are
# scaled down from 1 to 0
repel_damp = 20
# 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
# 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
# Use planarity constraints
use_planar_constraints = yes