# 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 0.5
# clash_penalty 30 nats/clash
# ss_bond_bonus 3
# known_ss_bond_bonus 0.1
# chain_break_penalty 30 nats/Angstrom
# wet_spot_weight 3
# dry_spot_weight 40
# command:# Prefix for input files set to 
# command:Created new target T0086 from ../T0086.seq
# command:# Will now start reporting scores to t86-6.5w-12d.rdb
# command:# created fragments for T0086 from 12asA-T0086-local.index
# command:# created fragments for T0086 from 1adjA-T0086-local.index
# command:# created fragments for T0086 from 1bxnA-T0086-local.index
# command:# created fragments for T0086 from 1c0aA-T0086-local.index
# command:# created fragments for T0086 from 1cg2A-T0086-local.index
# command:# created fragments for T0086 from 1ctt-T0086-local.index
# command:# created fragments for T0086 from 1ecmA-T0086-local.index
# command:# created fragments for T0086 from 1lylA-T0086-local.index
# command:# created fragments for T0086 from 1pymA-T0086-local.index
# command:# created fragments for T0086 from 1pysA-T0086-local.index
# command:# created fragments for T0086 from 1qf6A-T0086-local.index
# command:# created fragments for T0086 from 1qu9A-T0086-local.index
# command:# created fragments for T0086 from 1sesA-T0086-local.index
# command:# created fragments for T0086 from 5csmA-T0086-local.index
# command:# created fragments for T0086 from T0086-1auiA-local.index
# command:# created fragments for T0086 from T0086-1bouB-local.index
# command:# created fragments for T0086 from T0086-1burA-local.index
# command:# created fragments for T0086 from T0086-1bxnA-local.index
# command:# created fragments for T0086 from T0086-1c0aA-local.index
# command:# created fragments for T0086 from T0086-1cliA-local.index
# command:# created fragments for T0086 from T0086-1ecmA-local.index
# command:# created fragments for T0086 from T0086-1nal3-local.index
# command:# created fragments for T0086 from T0086-1pysA-local.index
# command:# created fragments for T0086 from T0086-1qf6A-local.index
# command:# created fragments for T0086 from T0086-1sesA-local.index
# command:# created fragments for T0086 from T0086-5csmA-local.index
# command:# naming current conformation t86-rand
# command:# command:# optimizing backbone with 50 conformations in pool
# doing 15 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# best score in initial pool at pool[11] 297.897 bits/residue, 163 clashes 23.1344 breaks
# best score after generation 1 291.516 bits/residue, 122 clashes 23.1344 breaks
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	12
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	2
##	ReduceBreak	10

# best score after generation 2 267.86 bits/residue, 68 clashes 15.7051 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	23
##	CrossOver	0
##	CrossAndInsert	22
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	3
##	ReduceBreak	12

# best score after generation 3 263.162 bits/residue, 46 clashes 15.7051 breaks
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	35
##	CrossOver	0
##	CrossAndInsert	33
##	TwoFragment	30
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	3
##	ReduceBreak	18

# best score after generation 4 261.031 bits/residue, 36 clashes 15.7051 breaks
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	45
##	CrossOver	0
##	CrossAndInsert	40
##	TwoFragment	39
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	3
##	ReduceBreak	21

# best score after generation 5 260.961 bits/residue, 41 clashes 15.7051 breaks
# Cumulative usage by method:
##	InsertFragment	32
##	ReduceClash	57
##	CrossOver	0
##	CrossAndInsert	56
##	TwoFragment	42
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	3
##	ReduceBreak	21

# best score after generation 6 258.334 bits/residue, 33 clashes 13.1311 breaks
# Cumulative usage by method:
##	InsertFragment	39
##	ReduceClash	66
##	CrossOver	0
##	CrossAndInsert	66
##	TwoFragment	44
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	21

# best score after generation 7 256.975 bits/residue, 26 clashes 13.1311 breaks
# Cumulative usage by method:
##	InsertFragment	52
##	ReduceClash	72
##	CrossOver	0
##	CrossAndInsert	73
##	TwoFragment	48
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	21

# best score after generation 8 255.824 bits/residue, 51 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	62
##	ReduceClash	78
##	CrossOver	0
##	CrossAndInsert	86
##	TwoFragment	49
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	21

# best score after generation 9 252.893 bits/residue, 54 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	71
##	ReduceClash	83
##	CrossOver	0
##	CrossAndInsert	101
##	TwoFragment	50
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	21

# best score after generation 10 252.604 bits/residue, 55 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	81
##	ReduceClash	88
##	CrossOver	0
##	CrossAndInsert	116
##	TwoFragment	50
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	21

# best score after generation 11 249.435 bits/residue, 58 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	91
##	ReduceClash	93
##	CrossOver	0
##	CrossAndInsert	127
##	TwoFragment	53
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	22

# best score after generation 12 249.42 bits/residue, 50 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	101
##	ReduceClash	98
##	CrossOver	0
##	CrossAndInsert	137
##	TwoFragment	58
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	22

# best score after generation 13 246.213 bits/residue, 55 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	112
##	ReduceClash	104
##	CrossOver	0
##	CrossAndInsert	150
##	TwoFragment	59
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	22

# best score after generation 14 243.317 bits/residue, 43 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	125
##	ReduceClash	106
##	CrossOver	0
##	CrossAndInsert	165
##	TwoFragment	59
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	22

# best score after generation 15 243.317 bits/residue, 43 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	134
##	ReduceClash	112
##	CrossOver	0
##	CrossAndInsert	172
##	TwoFragment	65
##	InsertSSBond	0
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	24

# command:# naming current conformation t86-opt
# command:# command:# Optimizing rotamers with 30 blocks of 100 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 30 nats/clash
# ss_bond bonus 3
# sidechain weight 0.5
# best score from archetype iter: 243.317 bits/residue, 43 clashes, rmsd= 0
# best score after iter 1 243.317 bits/residue, 43 clashes, rmsd= 0
# best score after iter 2 243.317 bits/residue, 43 clashes, rmsd= 0
# best score after iter 3 243.317 bits/residue, 43 clashes, rmsd= 0
# best score after iter 4 243.317 bits/residue, 43 clashes, rmsd= 0
# best score after iter 5 242.684 bits/residue, 39 clashes, rmsd= 0
# best score after iter 6 240.443 bits/residue, 50 clashes, rmsd= 0
# best score after iter 7 240.443 bits/residue, 50 clashes, rmsd= 0
# best score after iter 8 238.384 bits/residue, 43 clashes, rmsd= 0
# best score after iter 9 238.384 bits/residue, 43 clashes, rmsd= 0
# best score after iter 10 236.441 bits/residue, 38 clashes, rmsd= 0
# best score after iter 11 236.441 bits/residue, 38 clashes, rmsd= 0
# best score after iter 12 236.441 bits/residue, 38 clashes, rmsd= 0
# best score after iter 13 236.441 bits/residue, 38 clashes, rmsd= 0
# best score after iter 14 235.513 bits/residue, 35 clashes, rmsd= 0
# best score after iter 15 235.513 bits/residue, 35 clashes, rmsd= 0
# best score after iter 16 235.513 bits/residue, 35 clashes, rmsd= 0
# best score after iter 17 235.513 bits/residue, 35 clashes, rmsd= 0
# best score after iter 18 235.513 bits/residue, 35 clashes, rmsd= 0
# best score after iter 19 235.513 bits/residue, 35 clashes, rmsd= 0
# best score after iter 20 235.227 bits/residue, 34 clashes, rmsd= 0
# best score after iter 21 234.384 bits/residue, 35 clashes, rmsd= 0
# best score after iter 22 233.841 bits/residue, 38 clashes, rmsd= 0
# best score after iter 23 233.841 bits/residue, 38 clashes, rmsd= 0
# best score after iter 24 233.102 bits/residue, 33 clashes, rmsd= 0
# best score after iter 25 232.24 bits/residue, 33 clashes, rmsd= 0
# best score after iter 26 232.24 bits/residue, 33 clashes, rmsd= 0
# best score after iter 27 231.636 bits/residue, 33 clashes, rmsd= 0
# best score after iter 28 230.826 bits/residue, 29 clashes, rmsd= 0
# best score after iter 29 230.211 bits/residue, 29 clashes, rmsd= 0
# command:# naming current conformation t86-opt-rot
# command:# command:# optimizing backbone with 50 conformations in pool
# doing 15 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# best score in initial pool at pool[0] 230.211 bits/residue, 29 clashes 5.33677 breaks
# best score after generation 1 230.211 bits/residue, 29 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	3
##	CrossOver	0
##	CrossAndInsert	5
##	TwoFragment	15
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	3
##	ReduceBreak	8

# best score after generation 2 230.005 bits/residue, 34 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	27
##	ReduceClash	10
##	CrossOver	1
##	CrossAndInsert	12
##	TwoFragment	24
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	8

# best score after generation 3 230.005 bits/residue, 34 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	41
##	ReduceClash	17
##	CrossOver	5
##	CrossAndInsert	16
##	TwoFragment	27
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 4 230.005 bits/residue, 34 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	52
##	ReduceClash	24
##	CrossOver	7
##	CrossAndInsert	22
##	TwoFragment	31
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 5 229.587 bits/residue, 30 clashes 8.47767 breaks
# Cumulative usage by method:
##	InsertFragment	66
##	ReduceClash	26
##	CrossOver	13
##	CrossAndInsert	28
##	TwoFragment	33
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 6 229.587 bits/residue, 30 clashes 8.47767 breaks
# Cumulative usage by method:
##	InsertFragment	77
##	ReduceClash	30
##	CrossOver	23
##	CrossAndInsert	33
##	TwoFragment	33
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 7 229.195 bits/residue, 29 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	86
##	ReduceClash	33
##	CrossOver	38
##	CrossAndInsert	36
##	TwoFragment	33
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 8 229.195 bits/residue, 29 clashes 5.33677 breaks
# Cumulative usage by method:
##	InsertFragment	91
##	ReduceClash	35
##	CrossOver	57
##	CrossAndInsert	40
##	TwoFragment	33
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 9 228.325 bits/residue, 27 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	96
##	ReduceClash	37
##	CrossOver	77
##	CrossAndInsert	43
##	TwoFragment	33
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 10 228.227 bits/residue, 31 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	97
##	ReduceClash	37
##	CrossOver	103
##	CrossAndInsert	45
##	TwoFragment	34
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 11 227.702 bits/residue, 29 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	99
##	ReduceClash	37
##	CrossOver	130
##	CrossAndInsert	48
##	TwoFragment	34
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 12 227.197 bits/residue, 24 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	101
##	ReduceClash	37
##	CrossOver	157
##	CrossAndInsert	49
##	TwoFragment	34
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 13 227.014 bits/residue, 24 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	103
##	ReduceClash	37
##	CrossOver	188
##	CrossAndInsert	49
##	TwoFragment	34
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 14 226.407 bits/residue, 24 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	103
##	ReduceClash	37
##	CrossOver	220
##	CrossAndInsert	49
##	TwoFragment	34
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# best score after generation 15 226.407 bits/residue, 24 clashes 5.10629 breaks
# Cumulative usage by method:
##	InsertFragment	105
##	ReduceClash	37
##	CrossOver	252
##	CrossAndInsert	49
##	TwoFragment	35
##	InsertSSBond	1
##	OneRotamer	0
##	InsertAlignment	5
##	ReduceBreak	9

# command:# naming current conformation t86-opt-rot-opt
# command:# command:# Will now start reporting scores to t86-6.5w-12d-rot.rdb
# command:# Score parameters set to
# sidechain_weight 1.5
# clash_penalty 30 nats/clash
# ss_bond_bonus 3
# known_ss_bond_bonus 0.1
# chain_break_penalty 30 nats/Angstrom
# wet_spot_weight 1
# dry_spot_weight 2
# command:# Optimizing rotamers with 20 blocks of 100 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 30 nats/clash
# ss_bond bonus 3
# sidechain weight 1.5
# best score from archetype iter: 21.4356 bits/residue, 24 clashes, rmsd= 0
# best score after iter 1 21.4356 bits/residue, 24 clashes, rmsd= 0
# best score after iter 2 19.8657 bits/residue, 42 clashes, rmsd= 0
# best score after iter 3 14.861 bits/residue, 26 clashes, rmsd= 0
# best score after iter 4 14.861 bits/residue, 26 clashes, rmsd= 0
# best score after iter 5 14.8466 bits/residue, 28 clashes, rmsd= 0
# best score after iter 6 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 7 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 8 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 9 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 10 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 11 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 12 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 13 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 14 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 15 13.717 bits/residue, 24 clashes, rmsd= 0
# best score after iter 16 13.6387 bits/residue, 24 clashes, rmsd= 0
# best score after iter 17 13.6387 bits/residue, 24 clashes, rmsd= 0
# best score after iter 18 13.3715 bits/residue, 23 clashes, rmsd= 0
# best score after iter 19 13.3715 bits/residue, 23 clashes, rmsd= 0
# command:# naming current conformation t86-opt-rot-opt-rot
# command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_79563561.pdb -s /projects/compbio/tmp/to_scwrl_79563561.seq -o /projects/compbio/tmp/from_scwrl_79563561.pdb > /projects/compbio/tmp/scwrl.log
# conformation set from SCWRL output
# command:# naming current conformation t86-opt-rot-opt-scwrl
# command:# command:# ScoreConform
t86-rand -log2(score)= 22738.5 (138.649 bits/residue) 480 clashes 0 breaks
t86-opt -log2(score)= 3769.35 (22.9839 bits/residue) 43 clashes 5.33677 breaks
t86-opt-rot -log2(score)= 3743.93 (22.8288 bits/residue) 29 clashes 5.33677 breaks
t86-opt-rot-opt -log2(score)= 3515.44 (21.4356 bits/residue) 24 clashes 5.10629 breaks
t86-opt-rot-opt-rot -log2(score)= 2192.92 (13.3715 bits/residue) 23 clashes 5.10629 breaks
t86-opt-rot-opt-scwrl -log2(score)= 2841.41 (17.3257 bits/residue) 29 clashes 0 breaks
# command: