[domino]
max_value_threshold = 10000.
max_num_states_for_subset = 1000
; Allowed percentage of beads assigned to the same anchor point, used for
; coarse protein representation
max_anchor_penetration = 0.
; The size of the domino heap
heap_size = 500000
; The size of the domino restraint score cache, set per restraint set
cache_size = 50000
 
[fragments]
; The length of the fragment
length = 1
; Scale of approximated radius of the fragment
radius_scale = 1.
; 1 means that the subunits will have atomic representation
atomic = 1
; 1 means that the subunits are rigid
rigid = 1

[fitting]
pca_max_angle_diff = 15.
pca_max_size_diff = 10.
pca_max_cent_dist_diff = 10.
max_asmb_fit_score = 0.5

[connectivity]
upper_bound = 10
k = 0.0236
; Maximum value for the restraint, used for filters
; 0.0236 corresponds to 5A std, 0.3 corresponds to 1 STD, 1.18 to 2 STD
max_value = 0.3

[xlink]
upper_bound = 20
k = 0.0236
max_value = 0.3
; If set to 1 the restraint is between the residues; if set to 0 the restraint
; is between the proteins, like a connectivity restraint
between_residues = 0

[radius_of_gyration]
; Note: these restraints are only relevant if a coarse representation of a
; protein is used
; Allow the radius of gyration of the particles to be at most scale times the
; predicted one
scale = 1.5
; Maximum value allowed for a radius of gyration restraint applied on each
; protein separately
max_score = 10

[filters]
; If more than X connectivity restraints exceed their maximum score the
; solution is removed
conn_max_violations = 4
; If more than X xlink restraints exceed their maximum score the solution is
; removed
xlink_max_violations = 4
; If more than X pairwise excluded volume restraints exceed their maximum score
; the solution is removed
ev_max_violations = 3 

[excluded_volume]
; Restraint works on a pairs container that includes all pairs within
; this distance
distance = 3
; The container will be recalculated if the distance between one of the pairs
; changes more than slack
slack = 1
; Use harmonic lower bound, meaning that if the distance between a pair is
; lower than lower_bound the score is 0
lower_bound = 2
; For the harmonic calculation on each pair
; (0.5*k*(d-lower_bound)*(d-lower_bound))
; k of 0.59 means 1 STD
k = 0.59
; The EV score is divided by the number of pairs BETWEEN the two proteins 
; (0.3 means 1 STD is allowed, which in our case means that penetration of
; up to 1 A is ok).
max_score_for_pair = 0.295
; The max score allowed will be max_score_for_pair*
; total_num_of_pairs*allowed_percentage_of_bad_pairs
allowed_percentage_of_bad_pairs = 0.01
; 0: no ev will be calculated
; 1: ev between all pairs will be calculated
; 2: ev only between selected pairs (as noted in the proteomics file) will be
; calculated
scoring_mode = 2

[complementarity]
; The score is defined as: penetration_coef_*penetration_score
;                          + comp_coef_*complementarity_score
;                          + boundary_coef_*boundary_score;
max_score = 100000
; Maximum penetration score allowed. The score is roughly the number of cubic
; angstroms that the two molecules overlap (assuming only one internal layer)
max_penetration = 200
; The thickness of the interior layers. The higher the number, the more
; penetration that is allowed
interior_layer_thickness = 2
; The boundary score is roughly the number of cubic angstroms that the outer
; surfaces of the two molecules overlap. The coefficient determines how much
; to account for this score
boundary_coef = -3
comp_coef = 1
penetration_coef = 2