# command:# Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/spots/
# command:# ReadVDW initial.radii
# command:Reading spots from dunbrack-925-wet-6.5.spot.  Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes
# command:# reading histogram from smoothed-dunbrack-925-wet-6.5.hist
# command:Reading spots from dunbrack-925-dry-12.spot.  Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes
# command:# reading histogram from smoothed-dunbrack-925-dry-12.hist
# command:Setting costs from histograms
# command:# Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
# command:# reading dunbrack-925.atoms.gz
# After reading dunbrack-925.atoms.gz have 925 chains in training database
# command:# fragment library contains
#    type      	length	num_fragments	num_indexes_used
#    n-terminus	1	849		20 (100%)
#    n-terminus	2	842		253 (63.25%)
#    middle    	1	205367		20 (100%)
#    middle    	2	203845		400 (100%)
#    middle    	3	202366		7929 (99.1125%)
#    middle    	4	200913		88584 (55.365%)
#    c-terminus	1	862		20 (100%)
#    c-terminus	2	216		148 (37%)
#    ss-bonds  		650
# command:# Reading rotamer library from dunbrack-925.rot
# command:# Score parameters set to
# sidechain_weight 1
# clash_penalty 30 nats/clash
# ss_bond_bonus 3
# known_ss_bond_bonus 0
# chain_break_penalty 50 nats/Angstrom
# wet_spot_weight 2
# dry_spot_weight 50
# command:# Prefix for input files set to 
# command:Created new target T0106 from ../T0106.seq
# command:# Will now start reporting scores to t106-6.5w-12d.rdb
# command:# created fragments for T0106 from 1boeA-T0106-local.index
# command:# created fragments for T0106 from 1klo-T0106-local.index
# command:# created fragments for T0106 from T0106-1c4eA-local.index
# command:# created fragments for T0106 from 1by2-T0106-local.index
# command:# created fragments for T0106 from 1qatB-T0106-local.index
# command:# created fragments for T0106 from T0106-1dec-local.index
# command:# created fragments for T0106 from 1c2aA-T0106-local.index
# command:# created fragments for T0106 from T0106-1ayj-local.index
# command:# created fragments for T0106 from T0106-1eaiC-local.index
# command:# created fragments for T0106 from 1c4eA-T0106-local.index
# command:# created fragments for T0106 from T0106-1boeA-local.index
# command:# created fragments for T0106 from T0106-1klo-local.index
# command:# created fragments for T0106 from 1eaiC-T0106-local.index
# command:# created fragments for T0106 from T0106-1c2aA-local.index
# command:# created fragments for T0106 from T0106-1qatB-local.index
# command:# naming current conformation t106-rand
# command:# command:# Will do 10 iterations of optimization

# best score in initial pool at pool[39] 355.678 bits/residue, 202 clashes 5.53366 breaks
# optimizing backbone with 50 conformations in pool
# doing 6 generations, with 300 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 337.686 bits/residue, 56 clashes 5.53366 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	6
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	3
##	ReduceBreak	1

# generation 2: best score 332.496 bits/residue, 55 clashes 5.53367 breaks
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	14
##	CrossOver	4
##	CrossAndInsert	14
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	4
##	ReduceBreak	1

# generation 3: best score 321.049 bits/residue, 64 clashes 5.53367 breaks
# Cumulative usage by method:
##	InsertFragment	45
##	ReduceClash	27
##	CrossOver	6
##	CrossAndInsert	20
##	TwoFragment	22
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	4
##	ReduceBreak	1

# generation 4: best score 319.971 bits/residue, 66 clashes 5.53367 breaks
# Cumulative usage by method:
##	InsertFragment	69
##	ReduceClash	34
##	CrossOver	9
##	CrossAndInsert	28
##	TwoFragment	22
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	4
##	ReduceBreak	1

# generation 5: best score 314.741 bits/residue, 68 clashes 5.53367 breaks
# Cumulative usage by method:
##	InsertFragment	85
##	ReduceClash	39
##	CrossOver	16
##	CrossAndInsert	36
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	5
##	ReduceBreak	1

# generation 6: best score 312.237 bits/residue, 61 clashes 5.53367 breaks
# Cumulative usage by method:
##	InsertFragment	106
##	ReduceClash	41
##	CrossOver	20
##	CrossAndInsert	43
##	TwoFragment	27
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	6
##	ReduceBreak	1

# best score in initial pool at pool[42] 352.101 bits/residue, 101 clashes 26.1572 breaks
# optimizing backbone with 50 conformations in pool
# doing 6 generations, with 300 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 339.799 bits/residue, 50 clashes 25.5664 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	11
##	CrossOver	1
##	CrossAndInsert	11
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	5
##	ReduceBreak	3

# generation 2: best score 332.385 bits/residue, 56 clashes 25.5664 breaks
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	23
##	CrossOver	2
##	CrossAndInsert	23
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	8
##	ReduceBreak	5

# generation 3: best score 321.522 bits/residue, 34 clashes 14.7643 breaks
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	46
##	CrossOver	2
##	CrossAndInsert	28
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	10
##	ReduceBreak	7

# generation 4: best score 321.416 bits/residue, 31 clashes 14.7643 breaks
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	58
##	CrossOver	2
##	CrossAndInsert	37
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	13
##	ReduceBreak	10

# generation 5: best score 317.258 bits/residue, 51 clashes 14.7643 breaks
# Cumulative usage by method:
##	InsertFragment	49
##	ReduceClash	71
##	CrossOver	3
##	CrossAndInsert	43
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	14
##	ReduceBreak	10

# generation 6: best score 316.286 bits/residue, 44 clashes 14.7643 breaks
# Cumulative usage by method:
##	InsertFragment	59
##	ReduceClash	83
##	CrossOver	4
##	CrossAndInsert	49
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	15
##	ReduceBreak	12

# best score in initial pool at pool[14] 365.242 bits/residue, 148 clashes 38.7776 breaks
# optimizing backbone with 50 conformations in pool
# doing 6 generations, with 300 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 349.553 bits/residue, 52 clashes 36.3133 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	8
##	CrossOver	1
##	CrossAndInsert	13
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	3
##	ReduceBreak	5

# generation 2: best score 342.937 bits/residue, 102 clashes 31.4983 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	21
##	CrossOver	1
##	CrossAndInsert	25
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	6
##	ReduceBreak	6

# generation 3: best score 339.194 bits/residue, 86 clashes 21.8176 breaks
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	30
##	CrossOver	1
##	CrossAndInsert	40
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	7
##	ReduceBreak	9

# generation 4: best score 332.753 bits/residue, 129 clashes 21.8176 breaks
# Cumulative usage by method:
##	InsertFragment	27
##	ReduceClash	40
##	CrossOver	2
##	CrossAndInsert	56
##	TwoFragment	22
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	7
##	ReduceBreak	9

# generation 5: best score 320.169 bits/residue, 67 clashes 14.2538 breaks
# Cumulative usage by method:
##	InsertFragment	38
##	ReduceClash	47
##	CrossOver	3
##	CrossAndInsert	70
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	8
##	ReduceBreak	9

# generation 6: best score 318.316 bits/residue, 67 clashes 14.2538 breaks
# Cumulative usage by method:
##	InsertFragment	54
##	ReduceClash	60
##	CrossOver	4
##	CrossAndInsert	81
##	TwoFragment	27
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	8
##	ReduceBreak	9

# best score in initial pool at pool[42] 365.827 bits/residue, 116 clashes 0 breaks
# optimizing backbone with 50 conformations in pool
# doing 6 generations, with 300 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 353.733 bits/residue, 75 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	16
##	CrossOver	0
##	CrossAndInsert	10
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	2
##	ReduceBreak	1