# 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 5 nats/clash
# ss_bond_bonus 50
# known_ss_bond_bonus 1
# chain_break_penalty 5 nats/Angstrom
# wet_spot_weight 1
# dry_spot_weight 3
# command:# Prefix for input files set to 
# command:Created new target T0111 from ../T0111.seq
# command:# Will now start reporting scores to t111-6.5-12+rot.rdb
# command:# naming current conformation t111-rand
# command:# created fragments for T0111 from T0111-2oneA-karplus.index
# command:# created conformation for T0111 by applying fragments
# command:# naming current conformation t111-2oneA
# command:# ScoreConform
t111-rand 25.5591 bits/residue, 435 clashes 
t111-2oneA at pool[1] 56.844 bits/residue, 97 clashes 53.2496 breaks
# command:# Will do 10 iterations of optimization

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.1206 bits/residue, 95 clashes 48.8701 breaks
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	1
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	31
##	ReduceBreak	2

# generation 2: best score 20.1206 bits/residue, 95 clashes 48.8701 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	2
##	CrossOver	0
##	CrossAndInsert	4
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	70
##	ReduceBreak	2

# generation 3: best score 19.8283 bits/residue, 86 clashes 48.2323 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	3
##	CrossOver	0
##	CrossAndInsert	6
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	100
##	ReduceBreak	2

# generation 4: best score 19.6476 bits/residue, 60 clashes 50.1988 breaks
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	4
##	CrossOver	2
##	CrossAndInsert	6
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	130
##	ReduceBreak	2

# generation 5: best score 19.6476 bits/residue, 60 clashes 50.1988 breaks
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	5
##	CrossOver	5
##	CrossAndInsert	6
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	157
##	ReduceBreak	2

# generation 6: best score 19.4401 bits/residue, 59 clashes 45.1098 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	9
##	CrossOver	7
##	CrossAndInsert	8
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	175
##	ReduceBreak	2

# generation 7: best score 19.4401 bits/residue, 59 clashes 45.1098 breaks
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	12
##	CrossOver	14
##	CrossAndInsert	9
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	190
##	ReduceBreak	3

# generation 8: best score 19.3568 bits/residue, 48 clashes 47.389 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	14
##	CrossOver	19
##	CrossAndInsert	10
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	210
##	ReduceBreak	3

# generation 9: best score 19.3188 bits/residue, 58 clashes 46.9331 breaks
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	19
##	CrossOver	24
##	CrossAndInsert	11
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	226
##	ReduceBreak	3

# generation 10: best score 19.1603 bits/residue, 57 clashes 43.2838 breaks
# Cumulative usage by method:
##	InsertFragment	22
##	ReduceClash	20
##	CrossOver	37
##	CrossAndInsert	12
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	239
##	ReduceBreak	3

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.1263 bits/residue, 82 clashes 48.3107 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	4
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	22
##	ReduceBreak	1

# generation 2: best score 19.9957 bits/residue, 77 clashes 47.8707 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	12
##	CrossOver	0
##	CrossAndInsert	5
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	50
##	ReduceBreak	1

# generation 3: best score 19.6719 bits/residue, 55 clashes 47.8729 breaks
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	19
##	CrossOver	0
##	CrossAndInsert	6
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	71
##	ReduceBreak	1

# generation 4: best score 19.6719 bits/residue, 55 clashes 47.8729 breaks
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	25
##	CrossOver	0
##	CrossAndInsert	9
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	90
##	ReduceBreak	1

# generation 5: best score 19.4129 bits/residue, 32 clashes 50.7697 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	32
##	CrossOver	0
##	CrossAndInsert	11
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	108
##	ReduceBreak	1

# generation 6: best score 19.3852 bits/residue, 32 clashes 48.9397 breaks
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	38
##	CrossOver	2
##	CrossAndInsert	13
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	125
##	ReduceBreak	2

# generation 7: best score 19.1909 bits/residue, 31 clashes 59.9637 breaks
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	42
##	CrossOver	3
##	CrossAndInsert	19
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	139
##	ReduceBreak	2

# generation 8: best score 19.1909 bits/residue, 31 clashes 59.9637 breaks
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	49
##	CrossOver	3
##	CrossAndInsert	25
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	150
##	ReduceBreak	2

# generation 9: best score 19.1353 bits/residue, 20 clashes 61.012 breaks
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	56
##	CrossOver	5
##	CrossAndInsert	30
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	162
##	ReduceBreak	3

# generation 10: best score 19.0682 bits/residue, 42 clashes 49.3711 breaks
# Cumulative usage by method:
##	InsertFragment	37
##	ReduceClash	67
##	CrossOver	6
##	CrossAndInsert	33
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	172
##	ReduceBreak	3

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.2504 bits/residue, 93 clashes 53.6633 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	8
##	CrossOver	0
##	CrossAndInsert	7
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	15
##	ReduceBreak	2

# generation 2: best score 19.9323 bits/residue, 75 clashes 53.5661 breaks
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	15
##	CrossOver	1
##	CrossAndInsert	8
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	36
##	ReduceBreak	2

# generation 3: best score 19.7862 bits/residue, 64 clashes 54.3362 breaks
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	22
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	60
##	ReduceBreak	2

# generation 4: best score 19.6705 bits/residue, 64 clashes 50.4741 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	30
##	CrossOver	3
##	CrossAndInsert	10
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	77
##	ReduceBreak	2

# generation 5: best score 19.4545 bits/residue, 40 clashes 54.9936 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	38
##	CrossOver	4
##	CrossAndInsert	14
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	96
##	ReduceBreak	2

# generation 6: best score 19.2411 bits/residue, 25 clashes 50.0547 breaks
# Cumulative usage by method:
##	InsertFragment	28
##	ReduceClash	46
##	CrossOver	5
##	CrossAndInsert	16
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	110
##	ReduceBreak	2

# generation 7: best score 19.1363 bits/residue, 30 clashes 45.0236 breaks
# Cumulative usage by method:
##	InsertFragment	31
##	ReduceClash	55
##	CrossOver	9
##	CrossAndInsert	19
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	121
##	ReduceBreak	2

# generation 8: best score 19.1363 bits/residue, 30 clashes 45.0236 breaks
# Cumulative usage by method:
##	InsertFragment	37
##	ReduceClash	63
##	CrossOver	12
##	CrossAndInsert	21
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	131
##	ReduceBreak	3

# generation 9: best score 19.1363 bits/residue, 30 clashes 45.0236 breaks
# Cumulative usage by method:
##	InsertFragment	40
##	ReduceClash	70
##	CrossOver	15
##	CrossAndInsert	23
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	145
##	ReduceBreak	3

# generation 10: best score 19.1278 bits/residue, 18 clashes 49.3328 breaks
# Cumulative usage by method:
##	InsertFragment	47
##	ReduceClash	74
##	CrossOver	19
##	CrossAndInsert	26
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	157
##	ReduceBreak	3

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.0381 bits/residue, 76 clashes 54.3715 breaks
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	4
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	16
##	ReduceBreak	9

# generation 2: best score 20.0381 bits/residue, 76 clashes 54.3715 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	8
##	CrossOver	0
##	CrossAndInsert	11
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	46
##	ReduceBreak	9

# generation 3: best score 20.0381 bits/residue, 76 clashes 54.3715 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	17
##	CrossOver	1
##	CrossAndInsert	11
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	69
##	ReduceBreak	9

# generation 4: best score 19.9176 bits/residue, 68 clashes 55.7492 breaks
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	26
##	CrossOver	1
##	CrossAndInsert	15
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	83
##	ReduceBreak	9

# generation 5: best score 19.7913 bits/residue, 77 clashes 45.6535 breaks
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	30
##	CrossOver	1
##	CrossAndInsert	20
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	101
##	ReduceBreak	9

# generation 6: best score 19.6857 bits/residue, 62 clashes 52.9751 breaks
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	34
##	CrossOver	4
##	CrossAndInsert	21
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	123
##	ReduceBreak	9

# generation 7: best score 19.5359 bits/residue, 57 clashes 49.0209 breaks
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	43
##	CrossOver	5
##	CrossAndInsert	21
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	141
##	ReduceBreak	10

# generation 8: best score 19.2801 bits/residue, 54 clashes 38.7571 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	45
##	CrossOver	8
##	CrossAndInsert	21
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	168
##	ReduceBreak	10

# generation 9: best score 19.2801 bits/residue, 54 clashes 38.7571 breaks
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	49
##	CrossOver	10
##	CrossAndInsert	22
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	193
##	ReduceBreak	10

# generation 10: best score 19.268 bits/residue, 56 clashes 38.7571 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	54
##	CrossOver	12
##	CrossAndInsert	24
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	214
##	ReduceBreak	10

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.3397 bits/residue, 97 clashes 53.2496 breaks
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	1
##	CrossOver	0
##	CrossAndInsert	11
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	20
##	ReduceBreak	6

# generation 2: best score 20.269 bits/residue, 95 clashes 53.4161 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	4
##	CrossOver	0
##	CrossAndInsert	15
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	52
##	ReduceBreak	7

# generation 3: best score 19.9242 bits/residue, 43 clashes 71.9133 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	6
##	CrossOver	0
##	CrossAndInsert	22
##	TwoFragment	5
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	79
##	ReduceBreak	7

# generation 4: best score 19.8521 bits/residue, 43 clashes 67.9749 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	9
##	CrossOver	2
##	CrossAndInsert	23
##	TwoFragment	5
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	101
##	ReduceBreak	7

# generation 5: best score 19.5283 bits/residue, 29 clashes 52.3954 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	11
##	CrossOver	2
##	CrossAndInsert	25
##	TwoFragment	5
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	132
##	ReduceBreak	7

# generation 6: best score 19.5256 bits/residue, 36 clashes 59.6499 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	12
##	CrossOver	2
##	CrossAndInsert	30
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	161
##	ReduceBreak	7

# generation 7: best score 19.4002 bits/residue, 34 clashes 58.5732 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	16
##	CrossOver	6
##	CrossAndInsert	32
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	183
##	ReduceBreak	7

# generation 8: best score 19.3216 bits/residue, 31 clashes 57.4964 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	18
##	CrossOver	12
##	CrossAndInsert	35
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	199
##	ReduceBreak	7

# generation 9: best score 19.2441 bits/residue, 29 clashes 57.1437 breaks
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	21
##	CrossOver	18
##	CrossAndInsert	39
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	215
##	ReduceBreak	7

# generation 10: best score 19.1014 bits/residue, 23 clashes 62.1585 breaks
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	23
##	CrossOver	26
##	CrossAndInsert	40
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	233
##	ReduceBreak	7

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.0957 bits/residue, 57 clashes 63.4983 breaks
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	5
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	14
##	ReduceBreak	6

# generation 2: best score 19.9157 bits/residue, 61 clashes 55.2901 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	9
##	CrossOver	0
##	CrossAndInsert	10
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	39
##	ReduceBreak	8

# generation 3: best score 19.6381 bits/residue, 57 clashes 53.927 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	14
##	CrossOver	0
##	CrossAndInsert	13
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	63
##	ReduceBreak	8

# generation 4: best score 19.5023 bits/residue, 51 clashes 54.6486 breaks
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	18
##	CrossOver	0
##	CrossAndInsert	15
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	91
##	ReduceBreak	8

# generation 5: best score 19.4467 bits/residue, 51 clashes 54.193 breaks
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	18
##	CrossOver	1
##	CrossAndInsert	17
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	113
##	ReduceBreak	9

# generation 6: best score 19.4467 bits/residue, 51 clashes 54.193 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	23
##	CrossOver	2
##	CrossAndInsert	19
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	133
##	ReduceBreak	9

# generation 7: best score 19.4402 bits/residue, 54 clashes 52.419 breaks
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	29
##	CrossOver	5
##	CrossAndInsert	22
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	147
##	ReduceBreak	9

# generation 8: best score 19.3871 bits/residue, 44 clashes 59.0728 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	32
##	CrossOver	10
##	CrossAndInsert	25
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	162
##	ReduceBreak	10

# generation 9: best score 19.3871 bits/residue, 44 clashes 59.0728 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	38
##	CrossOver	17
##	CrossAndInsert	27
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	173
##	ReduceBreak	10

# generation 10: best score 19.3791 bits/residue, 43 clashes 59.3179 breaks
# Cumulative usage by method:
##	InsertFragment	26
##	ReduceClash	46
##	CrossOver	21
##	CrossAndInsert	28
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	187
##	ReduceBreak	10

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 20.3397 bits/residue, 97 clashes 53.2496 breaks
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	2
##	CrossOver	1
##	CrossAndInsert	8
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	25
##	ReduceBreak	3

# generation 2: best score 20.3029 bits/residue, 98 clashes 53.2483 breaks
# Cumulative usage by method:
##	InsertFragment	4
##	ReduceClash	4
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	61
##	ReduceBreak	3

# generation 3: best score 20.3029 bits/residue, 98 clashes 53.2483 breaks
# Cumulative usage by method:
##	InsertFragment	4
##	ReduceClash	6
##	CrossOver	1
##	CrossAndInsert	12
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	91
##	ReduceBreak	3

# generation 4: best score 19.6868 bits/residue, 69 clashes 47.4248 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	8
##	CrossOver	2
##	CrossAndInsert	15
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	114
##	ReduceBreak	3

# generation 5: best score 19.6866 bits/residue, 69 clashes 47.4142 breaks
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	16
##	CrossOver	3
##	CrossAndInsert	16
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	134
##	ReduceBreak	3

# generation 6: best score 19.5718 bits/residue, 46 clashes 52.0763 breaks
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	22
##	CrossOver	4
##	CrossAndInsert	17
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	154
##	ReduceBreak	3

# generation 7: best score 19.4328 bits/residue, 66 clashes 42.9798 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	28
##	CrossOver	8
##	CrossAndInsert	19
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	169
##	ReduceBreak	4

# generation 8: best score 19.4328 bits/residue, 66 clashes 42.9798 breaks
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	30
##	CrossOver	14
##	CrossAndInsert	22
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	184
##	ReduceBreak	4

# generation 9: best score 19.3082 bits/residue, 30 clashes 49.7302 breaks
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	37
##	CrossOver	18
##	CrossAndInsert	28
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	193
##	ReduceBreak	4

# generation 10: best score 19.2608 bits/residue, 65 clashes 32.0194 breaks
# Cumulative usage by method:
##	InsertFragment	18
##	ReduceClash	47
##	CrossOver	24
##	CrossAndInsert	32
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	201
##	ReduceBreak	4

# best score in initial pool 20.3397 bits/residue, 97 clashes 53.2496 breaks
# optimizing backbone with 50 conformations in pool
# doing 10 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool