# 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 1
# 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 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:# Reading conformation from PDB file try5/t111-opt.pdb
# command:# naming current conformation t111-try5
# command:# ScoreConform
t111-rand 28.7929 bits/residue, 435 clashes 
t111-try5 at pool[1] 20.3106 bits/residue, 33 clashes 
# 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: 20.3106 bits/residue, 33 clashes, rmsd= 0
# best score after iter 1 20.3106 bits/residue, 33 clashes, rmsd= 0
# best score after iter 2 20.3106 bits/residue, 33 clashes, rmsd= 0
# best score after iter 3 19.8521 bits/residue, 47 clashes, rmsd= 0
# best score after iter 4 19.5484 bits/residue, 50 clashes, rmsd= 0
# best score after iter 5 19.3085 bits/residue, 36 clashes, rmsd= 0
# best score after iter 6 19.3014 bits/residue, 42 clashes, rmsd= 0
# best score after iter 7 19.2321 bits/residue, 44 clashes, rmsd= 0
# best score after iter 8 19.172 bits/residue, 43 clashes, rmsd= 0
# best score after iter 9 19.1564 bits/residue, 43 clashes, rmsd= 0
# command:# naming current conformation t111-rot
# command:# command:# Will do 10 iterations of optimization

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	6
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	25
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	16
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	33
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	26
##	ReduceClash	30
##	CrossOver	0
##	CrossAndInsert	15
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	33
##	ReduceBreak	0

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	36
##	ReduceClash	41
##	CrossOver	2
##	CrossAndInsert	21
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	33
##	ReduceBreak	0

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	49
##	ReduceClash	51
##	CrossOver	2
##	CrossAndInsert	27
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	33
##	ReduceBreak	0

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	65
##	ReduceClash	56
##	CrossOver	4
##	CrossAndInsert	32
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	33
##	ReduceBreak	0

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	80
##	ReduceClash	61
##	CrossOver	8
##	CrossAndInsert	37
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	33
##	ReduceBreak	0

# generation 8: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	87
##	ReduceClash	70
##	CrossOver	14
##	CrossAndInsert	44
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	33
##	ReduceBreak	0

# generation 9: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	97
##	ReduceClash	76
##	CrossOver	22
##	CrossAndInsert	49
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	33
##	ReduceBreak	0

# generation 10: best score 18.9008 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	110
##	ReduceClash	77
##	CrossOver	35
##	CrossAndInsert	52
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	33
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	6
##	CrossOver	0
##	CrossAndInsert	9
##	TwoFragment	1
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	24
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	20
##	CrossOver	0
##	CrossAndInsert	13
##	TwoFragment	5
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	24
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	28
##	CrossOver	0
##	CrossAndInsert	23
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	13
##	InsertAlignment	24
##	ReduceBreak	0

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	24
##	ReduceClash	40
##	CrossOver	0
##	CrossAndInsert	31
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	24
##	ReduceBreak	0

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	32
##	ReduceClash	47
##	CrossOver	1
##	CrossAndInsert	41
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	17
##	InsertAlignment	24
##	ReduceBreak	0

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	38
##	ReduceClash	54
##	CrossOver	3
##	CrossAndInsert	52
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	20
##	InsertAlignment	24
##	ReduceBreak	0

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	45
##	ReduceClash	59
##	CrossOver	5
##	CrossAndInsert	64
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	24
##	InsertAlignment	24
##	ReduceBreak	0

# generation 8: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	51
##	ReduceClash	65
##	CrossOver	11
##	CrossAndInsert	72
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	24
##	ReduceBreak	0

# generation 9: best score 18.9018 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	58
##	ReduceClash	68
##	CrossOver	16
##	CrossAndInsert	84
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	27
##	InsertAlignment	24
##	ReduceBreak	0

# generation 10: best score 18.9018 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	65
##	ReduceClash	71
##	CrossOver	24
##	CrossAndInsert	95
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	27
##	InsertAlignment	24
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	1
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	4
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	21
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	22
##	CrossOver	0
##	CrossAndInsert	14
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	27
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	34
##	CrossOver	0
##	CrossAndInsert	24
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	27
##	ReduceBreak	0

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	42
##	CrossOver	0
##	CrossAndInsert	34
##	TwoFragment	26
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	27
##	ReduceBreak	0

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	52
##	CrossOver	0
##	CrossAndInsert	46
##	TwoFragment	29
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	27
##	ReduceBreak	0

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	18
##	ReduceClash	59
##	CrossOver	2
##	CrossAndInsert	59
##	TwoFragment	32
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	27
##	ReduceBreak	0

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	69
##	CrossOver	4
##	CrossAndInsert	73
##	TwoFragment	32
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	27
##	ReduceBreak	0

# generation 8: best score 18.8883 bits/residue, 44 clashes 
# Cumulative usage by method:
##	InsertFragment	28
##	ReduceClash	74
##	CrossOver	9
##	CrossAndInsert	84
##	TwoFragment	33
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	27
##	ReduceBreak	0

# generation 9: best score 18.8883 bits/residue, 44 clashes 
# Cumulative usage by method:
##	InsertFragment	32
##	ReduceClash	82
##	CrossOver	14
##	CrossAndInsert	95
##	TwoFragment	35
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	12
##	InsertAlignment	27
##	ReduceBreak	0

# generation 10: best score 18.8883 bits/residue, 44 clashes 
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	89
##	CrossOver	20
##	CrossAndInsert	109
##	TwoFragment	36
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	13
##	InsertAlignment	27
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	16
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	14
##	CrossOver	0
##	CrossAndInsert	6
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	34
##	ReduceBreak	1

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	16
##	CrossOver	1
##	CrossAndInsert	11
##	TwoFragment	23
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	34
##	ReduceBreak	1

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	36
##	ReduceClash	22
##	CrossOver	1
##	CrossAndInsert	16
##	TwoFragment	30
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	15
##	InsertAlignment	34
##	ReduceBreak	1

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	42
##	ReduceClash	28
##	CrossOver	3
##	CrossAndInsert	21
##	TwoFragment	31
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	34
##	ReduceBreak	1

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	53
##	ReduceClash	31
##	CrossOver	5
##	CrossAndInsert	25
##	TwoFragment	32
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	34
##	InsertAlignment	34
##	ReduceBreak	1

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	64
##	ReduceClash	36
##	CrossOver	7
##	CrossAndInsert	29
##	TwoFragment	35
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	39
##	InsertAlignment	34
##	ReduceBreak	1

# generation 8: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	76
##	ReduceClash	41
##	CrossOver	9
##	CrossAndInsert	37
##	TwoFragment	36
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	41
##	InsertAlignment	34
##	ReduceBreak	1

# generation 9: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	86
##	ReduceClash	44
##	CrossOver	16
##	CrossAndInsert	44
##	TwoFragment	37
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	43
##	InsertAlignment	34
##	ReduceBreak	1

# generation 10: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	94
##	ReduceClash	45
##	CrossOver	26
##	CrossAndInsert	51
##	TwoFragment	38
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	46
##	InsertAlignment	34
##	ReduceBreak	1

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	9
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	26
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	23
##	CrossOver	0
##	CrossAndInsert	4
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	37
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	39
##	CrossOver	1
##	CrossAndInsert	9
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	37
##	ReduceBreak	0

# generation 4: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	28
##	ReduceClash	51
##	CrossOver	2
##	CrossAndInsert	15
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	37
##	ReduceBreak	0

# generation 5: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	61
##	CrossOver	4
##	CrossAndInsert	20
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	37
##	ReduceBreak	0

# generation 6: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	42
##	ReduceClash	74
##	CrossOver	7
##	CrossAndInsert	24
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	10
##	InsertAlignment	37
##	ReduceBreak	0

# generation 7: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	48
##	ReduceClash	84
##	CrossOver	15
##	CrossAndInsert	28
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	37
##	ReduceBreak	0

# generation 8: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	52
##	ReduceClash	89
##	CrossOver	28
##	CrossAndInsert	32
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	37
##	ReduceBreak	0

# generation 9: best score 18.8666 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	60
##	ReduceClash	94
##	CrossOver	41
##	CrossAndInsert	35
##	TwoFragment	25
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	37
##	ReduceBreak	0

# generation 10: best score 18.8666 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	66
##	ReduceClash	99
##	CrossOver	59
##	CrossAndInsert	36
##	TwoFragment	25
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	11
##	InsertAlignment	37
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	3
##	CrossOver	1
##	CrossAndInsert	12
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	20
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	11
##	CrossOver	2
##	CrossAndInsert	21
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	22
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	15
##	CrossOver	4
##	CrossAndInsert	29
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	22
##	ReduceBreak	0

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	22
##	ReduceClash	18
##	CrossOver	9
##	CrossAndInsert	37
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	20
##	InsertAlignment	22
##	ReduceBreak	0

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	27
##	ReduceClash	22
##	CrossOver	14
##	CrossAndInsert	48
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	24
##	InsertAlignment	22
##	ReduceBreak	0

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	32
##	ReduceClash	24
##	CrossOver	24
##	CrossAndInsert	59
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	22
##	ReduceBreak	0

# generation 7: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	34
##	ReduceClash	26
##	CrossOver	39
##	CrossAndInsert	69
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	22
##	ReduceBreak	0

# generation 8: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	38
##	ReduceClash	26
##	CrossOver	62
##	CrossAndInsert	72
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	22
##	ReduceBreak	0

# generation 9: best score 18.9019 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	39
##	ReduceClash	26
##	CrossOver	89
##	CrossAndInsert	74
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	22
##	ReduceBreak	0

# generation 10: best score 18.9018 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	39
##	ReduceClash	26
##	CrossOver	118
##	CrossAndInsert	75
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	25
##	InsertAlignment	22
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	4
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	17
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	9
##	CrossOver	0
##	CrossAndInsert	19
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	17
##	InsertAlignment	19
##	ReduceBreak	0

# generation 3: best score 18.8852 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	11
##	CrossOver	1
##	CrossAndInsert	24
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	33
##	InsertAlignment	19
##	ReduceBreak	0

# generation 4: best score 18.8852 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	11
##	CrossOver	1
##	CrossAndInsert	34
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	48
##	InsertAlignment	19
##	ReduceBreak	0

# generation 5: best score 18.8852 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	13
##	CrossOver	3
##	CrossAndInsert	41
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	62
##	InsertAlignment	19
##	ReduceBreak	0

# generation 6: best score 18.8852 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	17
##	CrossOver	6
##	CrossAndInsert	48
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	72
##	InsertAlignment	19
##	ReduceBreak	0

# generation 7: best score 18.8852 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	36
##	ReduceClash	18
##	CrossOver	10
##	CrossAndInsert	52
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	87
##	InsertAlignment	19
##	ReduceBreak	0

# generation 8: best score 18.885 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	19
##	CrossOver	16
##	CrossAndInsert	59
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	96
##	InsertAlignment	19
##	ReduceBreak	0

# generation 9: best score 18.8849 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	45
##	ReduceClash	19
##	CrossOver	27
##	CrossAndInsert	65
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	107
##	InsertAlignment	19
##	ReduceBreak	0

# generation 10: best score 18.8849 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	51
##	ReduceClash	19
##	CrossOver	45
##	CrossAndInsert	69
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	109
##	InsertAlignment	19
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	4
##	ReduceClash	9
##	CrossOver	0
##	CrossAndInsert	4
##	TwoFragment	2
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	27
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	22
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	8
##	InsertAlignment	35
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	34
##	CrossOver	0
##	CrossAndInsert	13
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	16
##	InsertAlignment	35
##	ReduceBreak	0

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	24
##	ReduceClash	43
##	CrossOver	0
##	CrossAndInsert	18
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	22
##	InsertAlignment	35
##	ReduceBreak	0

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	28
##	ReduceClash	52
##	CrossOver	2
##	CrossAndInsert	27
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	24
##	InsertAlignment	35
##	ReduceBreak	0

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	37
##	ReduceClash	60
##	CrossOver	3
##	CrossAndInsert	34
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	27
##	InsertAlignment	35
##	ReduceBreak	0

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	72
##	CrossOver	3
##	CrossAndInsert	43
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	29
##	InsertAlignment	35
##	ReduceBreak	0

# generation 8: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	51
##	ReduceClash	82
##	CrossOver	4
##	CrossAndInsert	53
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	29
##	InsertAlignment	35
##	ReduceBreak	0

# generation 9: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	59
##	ReduceClash	90
##	CrossOver	6
##	CrossAndInsert	62
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	32
##	InsertAlignment	35
##	ReduceBreak	0

# generation 10: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	68
##	ReduceClash	95
##	CrossOver	9
##	CrossAndInsert	73
##	TwoFragment	15
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	34
##	InsertAlignment	35
##	ReduceBreak	0

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	4
##	ReduceClash	9
##	CrossOver	1
##	CrossAndInsert	5
##	TwoFragment	3
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	22
##	ReduceBreak	1

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	19
##	CrossOver	1
##	CrossAndInsert	12
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	30
##	ReduceBreak	1

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	30
##	CrossOver	1
##	CrossAndInsert	15
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	13
##	InsertAlignment	30
##	ReduceBreak	1

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	48
##	CrossOver	2
##	CrossAndInsert	19
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	30
##	ReduceBreak	1

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	36
##	ReduceClash	57
##	CrossOver	3
##	CrossAndInsert	23
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	15
##	InsertAlignment	30
##	ReduceBreak	1

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	45
##	ReduceClash	68
##	CrossOver	3
##	CrossAndInsert	28
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	20
##	InsertAlignment	30
##	ReduceBreak	1

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	55
##	ReduceClash	75
##	CrossOver	5
##	CrossAndInsert	36
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	22
##	InsertAlignment	30
##	ReduceBreak	1

# generation 8: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	63
##	ReduceClash	85
##	CrossOver	6
##	CrossAndInsert	39
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	27
##	InsertAlignment	30
##	ReduceBreak	1

# generation 9: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	70
##	ReduceClash	93
##	CrossOver	10
##	CrossAndInsert	46
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	31
##	InsertAlignment	30
##	ReduceBreak	1

# generation 10: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	83
##	ReduceClash	97
##	CrossOver	18
##	CrossAndInsert	49
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	33
##	InsertAlignment	30
##	ReduceBreak	1

# best score in initial pool 18.902 bits/residue, 43 clashes 
# 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 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	4
##	CrossOver	0
##	CrossAndInsert	7
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	17
##	ReduceBreak	0

# generation 2: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	12
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	3
##	InsertAlignment	28
##	ReduceBreak	0

# generation 3: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	31
##	ReduceClash	18
##	CrossOver	1
##	CrossAndInsert	18
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 4: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	27
##	CrossOver	3
##	CrossAndInsert	24
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 5: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	55
##	ReduceClash	36
##	CrossOver	4
##	CrossAndInsert	30
##	TwoFragment	23
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 6: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	68
##	ReduceClash	40
##	CrossOver	8
##	CrossAndInsert	38
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 7: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	86
##	ReduceClash	43
##	CrossOver	12
##	CrossAndInsert	43
##	TwoFragment	24
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 8: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	99
##	ReduceClash	48
##	CrossOver	17
##	CrossAndInsert	49
##	TwoFragment	25
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 9: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	109
##	ReduceClash	54
##	CrossOver	27
##	CrossAndInsert	53
##	TwoFragment	25
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	4
##	InsertAlignment	28
##	ReduceBreak	0

# generation 10: best score 18.902 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	120
##	ReduceClash	55
##	CrossOver	39
##	CrossAndInsert	58
##	TwoFragment	25
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	5
##	InsertAlignment	28
##	ReduceBreak	0

# best score in super_pool at pool[4] 18.8666 bits/residue, 43 clashes 
# 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 18.8666 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	1
##	ReduceClash	10
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	9
##	InsertAlignment	0
##	ReduceBreak	0

# generation 2: best score 18.8666 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	16
##	CrossOver	1
##	CrossAndInsert	16
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	20
##	InsertAlignment	0
##	ReduceBreak	0

# generation 3: best score 18.8666 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	22
##	CrossOver	3
##	CrossAndInsert	24
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	28
##	InsertAlignment	0
##	ReduceBreak	0

# generation 4: best score 18.8588 bits/residue, 45 clashes 
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	23
##	CrossOver	5
##	CrossAndInsert	37
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	35
##	InsertAlignment	0
##	ReduceBreak	0

# generation 5: best score 18.8432 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	28
##	CrossOver	9
##	CrossAndInsert	47
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	40
##	InsertAlignment	0
##	ReduceBreak	0

# generation 6: best score 18.8432 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	31
##	CrossOver	20
##	CrossAndInsert	56
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	44
##	InsertAlignment	0
##	ReduceBreak	0

# generation 7: best score 18.8432 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	26
##	ReduceClash	32
##	CrossOver	32
##	CrossAndInsert	65
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	46
##	InsertAlignment	0
##	ReduceBreak	0

# generation 8: best score 18.8432 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	33
##	CrossOver	49
##	CrossAndInsert	72
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	46
##	InsertAlignment	0
##	ReduceBreak	0

# generation 9: best score 18.8432 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	33
##	CrossOver	72
##	CrossAndInsert	78
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	46
##	InsertAlignment	0
##	ReduceBreak	0

# generation 10: best score 18.843 bits/residue, 43 clashes 
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	33
##	CrossOver	101
##	CrossAndInsert	79
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	46
##	InsertAlignment	0
##	ReduceBreak	0

# command:# naming current conformation t111-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: 18.843 bits/residue, 43 clashes, rmsd= 0
# best score after iter 1 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 2 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 3 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 4 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 5 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 6 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 7 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 8 18.7021 bits/residue, 33 clashes, rmsd= 0
# best score after iter 9 18.7021 bits/residue, 33 clashes, rmsd= 0
# command:# naming current conformation t111-opt-rot
# command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1688832442.pdb -s /projects/compbio/tmp/to_scwrl_1688832442.seq -o /projects/compbio/tmp/from_scwrl_1688832442.pdb > /projects/compbio/tmp/scwrl.log
# conformation set from SCWRL output
# command:# naming current conformation t111-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: 18.914 bits/residue, 44 clashes, rmsd= 0
# best score after iter 1 18.8113 bits/residue, 37 clashes, rmsd= 0
# best score after iter 2 18.5874 bits/residue, 26 clashes, rmsd= 0
# best score after iter 3 18.5874 bits/residue, 26 clashes, rmsd= 0
# best score after iter 4 18.5874 bits/residue, 26 clashes, rmsd= 0
# best score after iter 5 18.586 bits/residue, 31 clashes, rmsd= 0
# best score after iter 6 18.586 bits/residue, 31 clashes, rmsd= 0
# best score after iter 7 18.586 bits/residue, 31 clashes, rmsd= 0
# best score after iter 8 18.5752 bits/residue, 34 clashes, rmsd= 0
# best score after iter 9 18.5752 bits/residue, 34 clashes, rmsd= 0
# command:# naming current conformation t111-opt-scwrl-rot
# command:# command:# ScoreConform
t111-rand 28.7929 bits/residue, 435 clashes 
t111-try5 at pool[1] 20.3106 bits/residue, 33 clashes 
t111-rot at pool[2] 19.1564 bits/residue, 43 clashes 
t111-opt at pool[3] 18.843 bits/residue, 43 clashes 
t111-opt-rot at pool[4] 18.7021 bits/residue, 33 clashes 
t111-opt-scwrl at pool[5] 18.914 bits/residue, 44 clashes 
t111-opt-scwrl-rot at pool[6] 18.5752 bits/residue, 34 clashes 
# command: