# 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 4 nats/clash
# ss_bond_bonus 50
# known_ss_bond_bonus 25
# chain_break_penalty 5 nats/Angstrom
# wet_spot_weight 0.7
# dry_spot_weight 4
# command:# Prefix for input files set to 
# command:Created new target T0125 from ../T0125.seq
# command:# SSbond between 59 and 133
# command:# Will now start reporting scores to t125-6.5-12+rot.rdb
# command:# naming current conformation t125-rand
# command:# created fragments for T0125 from 2lisA-T0125-karplus1.index
# command:# created conformation for T0125 by applying fragments
# command:# naming current conformation t125-2lisA
# command:# command:# created fragments for T0125 from T0125-3lynA-karplus1.index
# command:# created fragments for T0125 from T0125-3lynA-karplus2.index
# command:# created fragments for T0125 from T0125-3lynA-karplus3.index
# command:# created conformation for T0125 by applying fragments
# command:# naming current conformation t125-3lynA
# command:# command:# ScoreConform
t125-rand 589.533 bits/residue, 191 clashes 
t125-2lisA at pool[1] 74.2495 bits/residue, 160 clashes 26.1115 breaks
t125-3lynA at pool[2] 77.2752 bits/residue, 239 clashes 28.3199 breaks
# command:# Will do 10 iterations of optimization

# best score in initial pool at pool[20] 26.1386 bits/residue, 80 clashes 9.6263 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 25.297 bits/residue, 32 clashes 11.9426 breaks
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	8
##	CrossOver	0
##	CrossAndInsert	5
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	9
##	ReduceBreak	2

# generation 2: best score 25.267 bits/residue, 16 clashes 11.9426 breaks
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	12
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	13
##	ReduceBreak	2

# generation 3: best score 24.7274 bits/residue, 32 clashes 9.08985 breaks
# Cumulative usage by method:
##	InsertFragment	24
##	ReduceClash	15
##	CrossOver	1
##	CrossAndInsert	17
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	15
##	ReduceBreak	2

# generation 4: best score 24.6347 bits/residue, 36 clashes 9.08999 breaks
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	22
##	CrossOver	2
##	CrossAndInsert	21
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	13
##	InsertAlignment	22
##	ReduceBreak	2

# generation 5: best score 24.2021 bits/residue, 9 clashes 13.3532 breaks
# Cumulative usage by method:
##	InsertFragment	44
##	ReduceClash	29
##	CrossOver	4
##	CrossAndInsert	25
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	26
##	ReduceBreak	2

# generation 6: best score 23.7804 bits/residue, 11 clashes 6.24551 breaks
# Cumulative usage by method:
##	InsertFragment	54
##	ReduceClash	32
##	CrossOver	7
##	CrossAndInsert	28
##	TwoFragment	22
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	33
##	ReduceBreak	2

# generation 7: best score 23.548 bits/residue, 12 clashes 6.24551 breaks
# Cumulative usage by method:
##	InsertFragment	66
##	ReduceClash	37
##	CrossOver	9
##	CrossAndInsert	32
##	TwoFragment	23
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	38
##	ReduceBreak	3

# generation 8: best score 23.4546 bits/residue, 14 clashes 6.24551 breaks
# Cumulative usage by method:
##	InsertFragment	80
##	ReduceClash	38
##	CrossOver	15
##	CrossAndInsert	37
##	TwoFragment	23
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	42
##	ReduceBreak	3

# generation 9: best score 23.4546 bits/residue, 14 clashes 6.24551 breaks
# Cumulative usage by method:
##	InsertFragment	91
##	ReduceClash	42
##	CrossOver	23
##	CrossAndInsert	43
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	42
##	ReduceBreak	3

# generation 10: best score 23.2798 bits/residue, 6 clashes 7.49616 breaks
# Cumulative usage by method:
##	InsertFragment	98
##	ReduceClash	44
##	CrossOver	37
##	CrossAndInsert	47
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	45
##	ReduceBreak	3

# best score in initial pool at pool[18] 25.6303 bits/residue, 54 clashes 11.7033 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 25.0071 bits/residue, 45 clashes 9.43885 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	5
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	8
##	ReduceBreak	3

# generation 2: best score 24.7946 bits/residue, 39 clashes 9.43885 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	10
##	CrossOver	0
##	CrossAndInsert	6
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	15
##	ReduceBreak	8

# generation 3: best score 24.3497 bits/residue, 30 clashes 8.90449 breaks
# Cumulative usage by method:
##	InsertFragment	27
##	ReduceClash	18
##	CrossOver	0
##	CrossAndInsert	9
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	20
##	ReduceBreak	9

# generation 4: best score 24.3497 bits/residue, 30 clashes 8.90449 breaks
# Cumulative usage by method:
##	InsertFragment	36
##	ReduceClash	23
##	CrossOver	2
##	CrossAndInsert	10
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	24
##	InsertAlignment	24
##	ReduceBreak	11

# generation 5: best score 24.0825 bits/residue, 15 clashes 9.53837 breaks
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	24
##	CrossOver	2
##	CrossAndInsert	16
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	29
##	InsertAlignment	30
##	ReduceBreak	14

# generation 6: best score 23.8306 bits/residue, 19 clashes 8.76591 breaks
# Cumulative usage by method:
##	InsertFragment	51
##	ReduceClash	27
##	CrossOver	4
##	CrossAndInsert	17
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	37
##	InsertAlignment	37
##	ReduceBreak	15

# generation 7: best score 23.8306 bits/residue, 19 clashes 8.76591 breaks
# Cumulative usage by method:
##	InsertFragment	58
##	ReduceClash	30
##	CrossOver	6
##	CrossAndInsert	26
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	41
##	InsertAlignment	40
##	ReduceBreak	17

# generation 8: best score 23.7851 bits/residue, 19 clashes 8.76591 breaks
# Cumulative usage by method:
##	InsertFragment	64
##	ReduceClash	35
##	CrossOver	8
##	CrossAndInsert	30
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	43
##	InsertAlignment	48
##	ReduceBreak	19

# generation 9: best score 23.7037 bits/residue, 19 clashes 8.76591 breaks
# Cumulative usage by method:
##	InsertFragment	72
##	ReduceClash	36
##	CrossOver	16
##	CrossAndInsert	36
##	TwoFragment	15
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	45
##	InsertAlignment	51
##	ReduceBreak	19

# generation 10: best score 23.7037 bits/residue, 19 clashes 8.76591 breaks
# Cumulative usage by method:
##	InsertFragment	77
##	ReduceClash	37
##	CrossOver	26
##	CrossAndInsert	41
##	TwoFragment	16
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	47
##	InsertAlignment	53
##	ReduceBreak	23

# best score in initial pool at pool[5] 26.0406 bits/residue, 57 clashes 8.69288 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 26.0068 bits/residue, 57 clashes 10.097 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	13
##	CrossOver	1
##	CrossAndInsert	0
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	13
##	ReduceBreak	3

# generation 2: best score 25.3515 bits/residue, 39 clashes 12.411 breaks
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	24
##	CrossOver	2
##	CrossAndInsert	3
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	20
##	ReduceBreak	5

# generation 3: best score 24.8292 bits/residue, 32 clashes 7.44714 breaks
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	32
##	CrossOver	4
##	CrossAndInsert	7
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	25
##	ReduceBreak	5

# generation 4: best score 24.8291 bits/residue, 32 clashes 7.44714 breaks
# Cumulative usage by method:
##	InsertFragment	29
##	ReduceClash	38
##	CrossOver	6
##	CrossAndInsert	7
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	34
##	ReduceBreak	6

# generation 5: best score 24.6299 bits/residue, 23 clashes 13.9451 breaks
# Cumulative usage by method:
##	InsertFragment	37
##	ReduceClash	45
##	CrossOver	12
##	CrossAndInsert	9
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	41
##	ReduceBreak	6

# generation 6: best score 24.4433 bits/residue, 30 clashes 5.05394 breaks
# Cumulative usage by method:
##	InsertFragment	46
##	ReduceClash	47
##	CrossOver	20
##	CrossAndInsert	10
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	49
##	ReduceBreak	6

# generation 7: best score 24.4396 bits/residue, 30 clashes 5.05394 breaks
# Cumulative usage by method:
##	InsertFragment	51
##	ReduceClash	50
##	CrossOver	33
##	CrossAndInsert	10
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	57
##	ReduceBreak	6

# generation 8: best score 24.1758 bits/residue, 17 clashes 6.7832 breaks
# Cumulative usage by method:
##	InsertFragment	58
##	ReduceClash	53
##	CrossOver	50
##	CrossAndInsert	11
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	59
##	ReduceBreak	6

# generation 9: best score 23.884 bits/residue, 17 clashes 4.92716 breaks
# Cumulative usage by method:
##	InsertFragment	62
##	ReduceClash	56
##	CrossOver	71
##	CrossAndInsert	13
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	60
##	ReduceBreak	6

# generation 10: best score 23.7673 bits/residue, 21 clashes 4.92716 breaks
# Cumulative usage by method:
##	InsertFragment	66
##	ReduceClash	58
##	CrossOver	91
##	CrossAndInsert	15
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	62
##	ReduceBreak	6

# best score in initial pool at pool[44] 27.7979 bits/residue, 108 clashes 6.57178 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 25.7422 bits/residue, 51 clashes 10.3192 breaks
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	7
##	CrossOver	1
##	CrossAndInsert	7
##	TwoFragment	1
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	12
##	ReduceBreak	2

# generation 2: best score 25.5176 bits/residue, 48 clashes 8.74017 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	15
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	1
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	29
##	ReduceBreak	2

# generation 3: best score 25.1374 bits/residue, 45 clashes 8.74017 breaks
# Cumulative usage by method:
##	InsertFragment	26
##	ReduceClash	22
##	CrossOver	2
##	CrossAndInsert	13
##	TwoFragment	3
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	39
##	ReduceBreak	3

# generation 4: best score 24.6218 bits/residue, 26 clashes 6.19008 breaks
# Cumulative usage by method:
##	InsertFragment	35
##	ReduceClash	30
##	CrossOver	4
##	CrossAndInsert	16
##	TwoFragment	3
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	50
##	ReduceBreak	4

# generation 5: best score 24.6218 bits/residue, 26 clashes 6.19008 breaks
# Cumulative usage by method:
##	InsertFragment	44
##	ReduceClash	43
##	CrossOver	5
##	CrossAndInsert	16
##	TwoFragment	3
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	59
##	ReduceBreak	4

# generation 6: best score 24.6217 bits/residue, 26 clashes 6.19008 breaks
# Cumulative usage by method:
##	InsertFragment	54
##	ReduceClash	45
##	CrossOver	8
##	CrossAndInsert	17
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	68
##	ReduceBreak	6

# generation 7: best score 24.2691 bits/residue, 18 clashes 15.8184 breaks
# Cumulative usage by method:
##	InsertFragment	63
##	ReduceClash	52
##	CrossOver	14
##	CrossAndInsert	19
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	74
##	ReduceBreak	6

# generation 8: best score 24.0431 bits/residue, 14 clashes 15.2099 breaks
# Cumulative usage by method:
##	InsertFragment	78
##	ReduceClash	55
##	CrossOver	18
##	CrossAndInsert	22
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	79
##	ReduceBreak	6

# generation 9: best score 24.0431 bits/residue, 14 clashes 15.2099 breaks
# Cumulative usage by method:
##	InsertFragment	86
##	ReduceClash	59
##	CrossOver	27
##	CrossAndInsert	24
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	85
##	ReduceBreak	6

# generation 10: best score 23.9925 bits/residue, 22 clashes 3.78879 breaks
# Cumulative usage by method:
##	InsertFragment	94
##	ReduceClash	63
##	CrossOver	35
##	CrossAndInsert	28
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	91
##	ReduceBreak	6

# best score in initial pool at pool[16] 25.3171 bits/residue, 32 clashes 11.4686 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 25.0479 bits/residue, 29 clashes 11.4686 breaks
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	12
##	ReduceBreak	1

# generation 2: best score 25.0479 bits/residue, 29 clashes 11.4686 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	13
##	CrossOver	0
##	CrossAndInsert	15
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	21
##	ReduceBreak	1

# generation 3: best score 24.6941 bits/residue, 20 clashes 11.2529 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	19
##	CrossOver	0
##	CrossAndInsert	21
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	15
##	InsertAlignment	28
##	ReduceBreak	1

# generation 4: best score 24.6076 bits/residue, 9 clashes 11.4686 breaks
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	19
##	CrossOver	1
##	CrossAndInsert	25
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	27
##	InsertAlignment	37
##	ReduceBreak	2

# generation 5: best score 24.4831 bits/residue, 9 clashes 11.4686 breaks
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	19
##	CrossOver	1
##	CrossAndInsert	28
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	39
##	InsertAlignment	46
##	ReduceBreak	3

# generation 6: best score 24.3064 bits/residue, 18 clashes 6.27695 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	21
##	CrossOver	1
##	CrossAndInsert	29
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	61
##	InsertAlignment	47
##	ReduceBreak	3

# generation 7: best score 24.3064 bits/residue, 18 clashes 6.27695 breaks
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	23
##	CrossOver	1
##	CrossAndInsert	31
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	83
##	InsertAlignment	49
##	ReduceBreak	3

# generation 8: best score 24.1093 bits/residue, 16 clashes 6.27695 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	27
##	CrossOver	2
##	CrossAndInsert	35
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	101
##	InsertAlignment	49
##	ReduceBreak	3

# generation 9: best score 23.7005 bits/residue, 16 clashes 6.27695 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	29
##	CrossOver	2
##	CrossAndInsert	38
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	123
##	InsertAlignment	52
##	ReduceBreak	3

# generation 10: best score 23.6336 bits/residue, 10 clashes 6.27695 breaks
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	31
##	CrossOver	4
##	CrossAndInsert	41
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	144
##	InsertAlignment	52
##	ReduceBreak	3

# best score in initial pool at pool[34] 27.1074 bits/residue, 17 clashes 32.3099 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 25.9682 bits/residue, 73 clashes 7.49525 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	8
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	7
##	ReduceBreak	6

# generation 2: best score 24.9233 bits/residue, 28 clashes 14.4644 breaks
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	16
##	CrossOver	1
##	CrossAndInsert	6
##	TwoFragment	11
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	14
##	ReduceBreak	10

# generation 3: best score 24.7023 bits/residue, 49 clashes 7.99112 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	28
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	14
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	18
##	ReduceBreak	10

# generation 4: best score 24.5495 bits/residue, 28 clashes 11.482 breaks
# Cumulative usage by method:
##	InsertFragment	29
##	ReduceClash	37
##	CrossOver	2
##	CrossAndInsert	18
##	TwoFragment	17
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	21
##	ReduceBreak	10

# generation 5: best score 24.1775 bits/residue, 29 clashes 5.43376 breaks
# Cumulative usage by method:
##	InsertFragment	41
##	ReduceClash	42
##	CrossOver	5
##	CrossAndInsert	21
##	TwoFragment	21
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	23
##	ReduceBreak	11

# generation 6: best score 23.9721 bits/residue, 15 clashes 12.6779 breaks
# Cumulative usage by method:
##	InsertFragment	51
##	ReduceClash	50
##	CrossOver	8
##	CrossAndInsert	24
##	TwoFragment	22
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	24
##	ReduceBreak	12

# generation 7: best score 23.9607 bits/residue, 24 clashes 11.4568 breaks
# Cumulative usage by method:
##	InsertFragment	63
##	ReduceClash	54
##	CrossOver	11
##	CrossAndInsert	29
##	TwoFragment	24
##	InsertSSBond	3
##	OneRotamer	0
##	ClashingRotamer	13
##	InsertAlignment	25
##	ReduceBreak	14

# generation 8: best score 23.9607 bits/residue, 24 clashes 11.4568 breaks
# Cumulative usage by method:
##	InsertFragment	72
##	ReduceClash	63
##	CrossOver	18
##	CrossAndInsert	31
##	TwoFragment	25
##	InsertSSBond	4
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	25
##	ReduceBreak	14

# generation 9: best score 23.9106 bits/residue, 28 clashes 4.87827 breaks
# Cumulative usage by method:
##	InsertFragment	83
##	ReduceClash	66
##	CrossOver	25
##	CrossAndInsert	32
##	TwoFragment	27
##	InsertSSBond	4
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	28
##	ReduceBreak	15

# generation 10: best score 23.3322 bits/residue, 19 clashes 6.26721 breaks
# Cumulative usage by method:
##	InsertFragment	90
##	ReduceClash	70
##	CrossOver	36
##	CrossAndInsert	36
##	TwoFragment	28
##	InsertSSBond	4
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	31
##	ReduceBreak	15

# best score in initial pool at pool[39] 27.1817 bits/residue, 86 clashes 12.0358 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 25.4331 bits/residue, 29 clashes 14.0132 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	5
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	14
##	ReduceBreak	2

# generation 2: best score 24.8659 bits/residue, 34 clashes 12.5044 breaks
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	21
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	9
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	22
##	ReduceBreak	4

# generation 3: best score 24.419 bits/residue, 41 clashes 7.64589 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	26
##	CrossOver	2
##	CrossAndInsert	13
##	TwoFragment	11
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	29
##	ReduceBreak	5

# generation 4: best score 24.1134 bits/residue, 35 clashes 7.64589 breaks
# Cumulative usage by method:
##	InsertFragment	34
##	ReduceClash	32
##	CrossOver	4
##	CrossAndInsert	16
##	TwoFragment	14
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	17
##	InsertAlignment	31
##	ReduceBreak	5

# generation 5: best score 24.1133 bits/residue, 35 clashes 7.64589 breaks
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	38
##	CrossOver	7
##	CrossAndInsert	18
##	TwoFragment	17
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	19
##	InsertAlignment	36
##	ReduceBreak	5

# generation 6: best score 24.0853 bits/residue, 23 clashes 9.09566 breaks
# Cumulative usage by method:
##	InsertFragment	52
##	ReduceClash	43
##	CrossOver	10
##	CrossAndInsert	22
##	TwoFragment	18
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	40
##	ReduceBreak	6

# generation 7: best score 23.7631 bits/residue, 18 clashes 9.09566 breaks
# Cumulative usage by method:
##	InsertFragment	59
##	ReduceClash	52
##	CrossOver	15
##	CrossAndInsert	25
##	TwoFragment	19
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	45
##	ReduceBreak	6

# generation 8: best score 23.6432 bits/residue, 9 clashes 9.09566 breaks
# Cumulative usage by method:
##	InsertFragment	67
##	ReduceClash	56
##	CrossOver	26
##	CrossAndInsert	29
##	TwoFragment	21
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	46
##	ReduceBreak	6

# generation 9: best score 23.6255 bits/residue, 9 clashes 9.09566 breaks
# Cumulative usage by method:
##	InsertFragment	77
##	ReduceClash	66
##	CrossOver	30
##	CrossAndInsert	32
##	TwoFragment	22
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	22
##	InsertAlignment	47
##	ReduceBreak	6

# generation 10: best score 23.5508 bits/residue, 14 clashes 9.09566 breaks
# Cumulative usage by method:
##	InsertFragment	84
##	ReduceClash	70
##	CrossOver	42
##	CrossAndInsert	37
##	TwoFragment	23
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	22
##	InsertAlignment	47
##	ReduceBreak	7

# best score in initial pool at pool[17] 25.8054 bits/residue, 35 clashes 12.796 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 25.6011 bits/residue, 34 clashes 12.796 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	5
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	9
##	ReduceBreak	4

# generation 2: best score 25.0355 bits/residue, 30 clashes 11.7998 breaks
# Cumulative usage by method:
##	InsertFragment	18
##	ReduceClash	14
##	CrossOver	0
##	CrossAndInsert	6
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	13
##	ReduceBreak	5

# generation 3: best score 25.0287 bits/residue, 30 clashes 11.7998 breaks
# Cumulative usage by method:
##	InsertFragment	24
##	ReduceClash	22
##	CrossOver	1
##	CrossAndInsert	12
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	16
##	ReduceBreak	6

# generation 4: best score 24.8816 bits/residue, 31 clashes 8.64653 breaks
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	28
##	CrossOver	1
##	CrossAndInsert	19
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	22
##	InsertAlignment	21
##	ReduceBreak	6

# generation 5: best score 24.5423 bits/residue, 14 clashes 11.8219 breaks
# Cumulative usage by method:
##	InsertFragment	39
##	ReduceClash	36
##	CrossOver	4
##	CrossAndInsert	23
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	23
##	InsertAlignment	27
##	ReduceBreak	6

# generation 6: best score 24.5423 bits/residue, 14 clashes 11.8219 breaks
# Cumulative usage by method:
##	InsertFragment	50
##	ReduceClash	40
##	CrossOver	9
##	CrossAndInsert	28
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	24
##	InsertAlignment	30
##	ReduceBreak	7

# generation 7: best score 24.4998 bits/residue, 23 clashes 11.7998 breaks
# Cumulative usage by method:
##	InsertFragment	61
##	ReduceClash	43
##	CrossOver	11
##	CrossAndInsert	32
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	26
##	InsertAlignment	37
##	ReduceBreak	7

# generation 8: best score 24.4331 bits/residue, 23 clashes 8.16495 breaks
# Cumulative usage by method:
##	InsertFragment	68
##	ReduceClash	51
##	CrossOver	15
##	CrossAndInsert	35
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	27
##	InsertAlignment	44
##	ReduceBreak	7

# generation 9: best score 24.2621 bits/residue, 25 clashes 8.16495 breaks
# Cumulative usage by method:
##	InsertFragment	76
##	ReduceClash	54
##	CrossOver	24
##	CrossAndInsert	38
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	28
##	InsertAlignment	50
##	ReduceBreak	7

# generation 10: best score 24.1283 bits/residue, 17 clashes 8.16495 breaks
# Cumulative usage by method:
##	InsertFragment	85
##	ReduceClash	57
##	CrossOver	34
##	CrossAndInsert	43
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	30
##	InsertAlignment	51
##	ReduceBreak	7

# best score in initial pool at pool[43] 25.8611 bits/residue, 28 clashes 15.0835 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 25.843 bits/residue, 45 clashes 12.8044 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	9
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	10
##	ReduceBreak	6

# generation 2: best score 25.1102 bits/residue, 29 clashes 9.66574 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	14
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	16
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	18
##	ReduceBreak	9

# generation 3: best score 24.8766 bits/residue, 17 clashes 9.66574 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	21
##	CrossOver	0
##	CrossAndInsert	12
##	TwoFragment	23
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	23
##	ReduceBreak	14

# generation 4: best score 24.8766 bits/residue, 17 clashes 9.66574 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	30
##	CrossOver	0
##	CrossAndInsert	16
##	TwoFragment	25
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	29
##	ReduceBreak	17

# generation 5: best score 24.6252 bits/residue, 13 clashes 9.1246 breaks
# Cumulative usage by method:
##	InsertFragment	22
##	ReduceClash	36
##	CrossOver	2
##	CrossAndInsert	21
##	TwoFragment	27
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	6
##	InsertAlignment	36
##	ReduceBreak	19

# generation 6: best score 24.1319 bits/residue, 24 clashes 4.51031 breaks
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	42
##	CrossOver	2
##	CrossAndInsert	24
##	TwoFragment	28
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	41
##	ReduceBreak	20

# generation 7: best score 24.1319 bits/residue, 24 clashes 4.51031 breaks
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	51
##	CrossOver	4
##	CrossAndInsert	25
##	TwoFragment	33
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	43
##	ReduceBreak	21

# generation 8: best score 24.1319 bits/residue, 24 clashes 4.51031 breaks
# Cumulative usage by method:
##	InsertFragment	49
##	ReduceClash	58
##	CrossOver	6
##	CrossAndInsert	30
##	TwoFragment	36
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	48
##	ReduceBreak	22

# generation 9: best score 24.069 bits/residue, 22 clashes 4.51031 breaks
# Cumulative usage by method:
##	InsertFragment	59
##	ReduceClash	65
##	CrossOver	9
##	CrossAndInsert	33
##	TwoFragment	37
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	52
##	ReduceBreak	22

# generation 10: best score 24.069 bits/residue, 22 clashes 4.51031 breaks
# Cumulative usage by method:
##	InsertFragment	63
##	ReduceClash	73
##	CrossOver	10
##	CrossAndInsert	38
##	TwoFragment	38
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	13
##	InsertAlignment	61
##	ReduceBreak	23

# best score in initial pool at pool[30] 27.4999 bits/residue, 63 clashes 24.9826 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 25.665 bits/residue, 62 clashes 9.36188 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	6
##	CrossOver	0
##	CrossAndInsert	7
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	12
##	ReduceBreak	3

# generation 2: best score 25.4148 bits/residue, 29 clashes 7.91765 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	11
##	TwoFragment	11
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	26
##	ReduceBreak	4

# generation 3: best score 25.4118 bits/residue, 16 clashes 11.1985 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	16
##	CrossOver	0
##	CrossAndInsert	17
##	TwoFragment	14
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	33
##	ReduceBreak	5

# generation 4: best score 24.5979 bits/residue, 20 clashes 11.5234 breaks
# Cumulative usage by method:
##	InsertFragment	26
##	ReduceClash	22
##	CrossOver	0
##	CrossAndInsert	20
##	TwoFragment	15
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	43
##	ReduceBreak	5

# generation 5: best score 24.4112 bits/residue, 27 clashes 9.60542 breaks
# Cumulative usage by method:
##	InsertFragment	32
##	ReduceClash	27
##	CrossOver	0
##	CrossAndInsert	26
##	TwoFragment	17
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	54
##	ReduceBreak	5

# generation 6: best score 24.2682 bits/residue, 27 clashes 8.18599 breaks
# Cumulative usage by method:
##	InsertFragment	39
##	ReduceClash	31
##	CrossOver	0
##	CrossAndInsert	32
##	TwoFragment	17
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	65
##	ReduceBreak	6

# generation 7: best score 24.2682 bits/residue, 27 clashes 8.18599 breaks
# Cumulative usage by method:
##	InsertFragment	48
##	ReduceClash	38
##	CrossOver	0
##	CrossAndInsert	38
##	TwoFragment	19
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	68
##	ReduceBreak	6

# generation 8: best score 24.2682 bits/residue, 27 clashes 8.18637 breaks
# Cumulative usage by method:
##	InsertFragment	59
##	ReduceClash	44
##	CrossOver	1
##	CrossAndInsert	41
##	TwoFragment	20
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	74
##	ReduceBreak	6

# generation 9: best score 24.1912 bits/residue, 33 clashes 4.63133 breaks
# Cumulative usage by method:
##	InsertFragment	71
##	ReduceClash	47
##	CrossOver	3
##	CrossAndInsert	46
##	TwoFragment	21
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	17
##	InsertAlignment	80
##	ReduceBreak	6

# generation 10: best score 23.9467 bits/residue, 29 clashes 4.63133 breaks
# Cumulative usage by method:
##	InsertFragment	84
##	ReduceClash	51
##	CrossOver	4
##	CrossAndInsert	53
##	TwoFragment	24
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	18
##	InsertAlignment	81
##	ReduceBreak	6

# best score in super_pool 23.2798 bits/residue, 6 clashes 7.49616 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 23.2798 bits/residue, 6 clashes 7.49616 breaks
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	5
##	CrossOver	0
##	CrossAndInsert	10
##	TwoFragment	5
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	4
##	ReduceBreak	1

# generation 2: best score 23.1883 bits/residue, 10 clashes 9.3316 breaks
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	13
##	CrossOver	1
##	CrossAndInsert	17
##	TwoFragment	7
##	InsertSSBond	1
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	4
##	ReduceBreak	1

# generation 3: best score 23.1883 bits/residue, 10 clashes 9.3316 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	17
##	CrossOver	5
##	CrossAndInsert	28
##	TwoFragment	7
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	20
##	InsertAlignment	4
##	ReduceBreak	1

# generation 4: best score 23.1883 bits/residue, 10 clashes 9.3316 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	20
##	CrossOver	9
##	CrossAndInsert	36
##	TwoFragment	8
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	28
##	InsertAlignment	5
##	ReduceBreak	1

# generation 5: best score 23.0984 bits/residue, 9 clashes 6.26721 breaks
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	22
##	CrossOver	19
##	CrossAndInsert	43
##	TwoFragment	8
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	35
##	InsertAlignment	5
##	ReduceBreak	1

# generation 6: best score 23.0984 bits/residue, 9 clashes 6.26721 breaks
# Cumulative usage by method:
##	InsertFragment	24
##	ReduceClash	26
##	CrossOver	30
##	CrossAndInsert	47
##	TwoFragment	9
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	41
##	InsertAlignment	6
##	ReduceBreak	1

# generation 7: best score 23.086 bits/residue, 10 clashes 5.01509 breaks
# Cumulative usage by method:
##	InsertFragment	27
##	ReduceClash	29
##	CrossOver	43
##	CrossAndInsert	56
##	TwoFragment	10
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	42
##	InsertAlignment	6
##	ReduceBreak	1

# generation 8: best score 22.9953 bits/residue, 9 clashes 6.26721 breaks
# Cumulative usage by method:
##	InsertFragment	29
##	ReduceClash	29
##	CrossOver	65
##	CrossAndInsert	60
##	TwoFragment	10
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	44
##	InsertAlignment	6
##	ReduceBreak	1

# generation 9: best score 22.8682 bits/residue, 12 clashes 6.26721 breaks
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	29
##	CrossOver	86
##	CrossAndInsert	64
##	TwoFragment	10
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	48
##	InsertAlignment	6
##	ReduceBreak	1

# generation 10: best score 22.5968 bits/residue, 15 clashes 3.58433 breaks
# Cumulative usage by method:
##	InsertFragment	34
##	ReduceClash	29
##	CrossOver	109
##	CrossAndInsert	67
##	TwoFragment	10
##	InsertSSBond	2
##	OneRotamer	0
##	ClashingRotamer	48
##	InsertAlignment	6
##	ReduceBreak	1

# command:# naming current conformation t125-opt
# command:# command:# Optimizing rotamers with 10 blocks of 50 conformations
# P(change) = 0.9 * 0.9^ iter
# P(new) = 0.5 * 0.95^ iter
# P(neighbor) = 0.5 * 0.95^ iter
# P(archetype) = 0.9 * 0.9^ iter
# P(best_residue) = 0.9 * 0.9^ iter
# clash penalty 4 nats/clash
# ss_bond bonus 50
# sidechain weight 1
# best score from archetype iter: 22.5289 bits/residue, 27 clashes, rmsd= 0
# best score after iter 1 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 2 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 3 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 4 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 5 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 6 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 7 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 8 22.5246 bits/residue, 27 clashes, rmsd= 0
# best score after iter 9 22.1796 bits/residue, 32 clashes, rmsd= 0
# command:# naming current conformation t125-opt-rot
# command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1174385075.pdb -s /projects/compbio/tmp/to_scwrl_1174385075.seq -o /projects/compbio/tmp/from_scwrl_1174385075.pdb > /projects/compbio/tmp/scwrl.log
# conformation set from SCWRL output
# command:# naming current conformation t125-opt-scwrl
# command:# command:# Optimizing rotamers with 10 blocks of 50 conformations
# P(change) = 0.9 * 0.9^ iter
# P(new) = 0.5 * 0.95^ iter
# P(neighbor) = 0.5 * 0.95^ iter
# P(archetype) = 0.9 * 0.9^ iter
# P(best_residue) = 0.9 * 0.9^ iter
# clash penalty 4 nats/clash
# ss_bond bonus 50
# sidechain weight 1
# best score from archetype iter: 22.3782 bits/residue, 21 clashes, rmsd= 0
# best score after iter 1 22.3782 bits/residue, 21 clashes, rmsd= 0
# best score after iter 2 22.3319 bits/residue, 20 clashes, rmsd= 0
# best score after iter 3 22.2964 bits/residue, 21 clashes, rmsd= 0
# best score after iter 4 22.2964 bits/residue, 21 clashes, rmsd= 0
# best score after iter 5 22.2964 bits/residue, 21 clashes, rmsd= 0
# best score after iter 6 22.2964 bits/residue, 21 clashes, rmsd= 0
# best score after iter 7 22.2964 bits/residue, 21 clashes, rmsd= 0
# best score after iter 8 22.2964 bits/residue, 21 clashes, rmsd= 0
# best score after iter 9 22.2964 bits/residue, 21 clashes, rmsd= 0
# command:# naming current conformation t125-opt-scwrl-rot
# command:# command:# ScoreConform
t125-rand 589.533 bits/residue, 191 clashes 
t125-2lisA at pool[1] 74.2495 bits/residue, 160 clashes 26.1115 breaks
t125-3lynA at pool[2] 77.2752 bits/residue, 239 clashes 28.3199 breaks
t125-opt at pool[3] 22.5968 bits/residue, 15 clashes 3.58433 breaks
t125-opt-rot at pool[4] 22.1796 bits/residue, 32 clashes 3.58433 breaks
t125-opt-scwrl at pool[5] 22.3782 bits/residue, 21 clashes 3.58433 breaks
t125-opt-scwrl-rot at pool[6] 22.2964 bits/residue, 21 clashes 3.58433 breaks
# command: