# 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 5
# clash_penalty 4 nats/clash
# ss_bond_bonus 50
# known_ss_bond_bonus 1
# chain_break_penalty 5 nats/Angstrom
# wet_spot_weight 1
# dry_spot_weight 5
# command:# Prefix for input files set to 
# command:Created new target T0128 from ../T0128.seq
# command:# Will now start reporting scores to t128-6.5-12+rot.rdb
# command:# naming current conformation t128-rand
# command:# Reading conformation from PDB file try5/t128-opt.2.5.pdb
# command:# naming current conformation t128-try5
# command:# created fragments for T0128 from T0128-1avmA-karplus.index
# command:# created fragments for T0128 from T0128-1c3qX-karplus.index
# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_711767493.pdb -s /projects/compbio/tmp/to_scwrl_711767493.seq -o /projects/compbio/tmp/from_scwrl_711767493.pdb > /projects/compbio/tmp/scwrl.log
# conformation set from SCWRL output
# command:# naming current conformation t128-init-scwrl
# command:# command:# ScoreConform
t128-rand 24.1937 bits/residue, 277 clashes 
t128-try5 at pool[1] 2.22828 bits/residue, 16 clashes 
t128-init-scwrl at pool[2] 3.48499 bits/residue, 39 clashes 
# command:# naming current conformation t128-opt
# command:# Will do 6 iterations of optimization

# best score in initial pool 3.45123 bits/residue, 39 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 3.07196 bits/residue, 29 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	4
##	ReduceClash	4
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	15
##	ReduceBreak	0

# generation 2: best score 2.71069 bits/residue, 22 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	9
##	CrossOver	0
##	CrossAndInsert	12
##	TwoFragment	19
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	33
##	ReduceBreak	0

# generation 3: best score 2.4597 bits/residue, 18 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	10
##	CrossOver	0
##	CrossAndInsert	19
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	52
##	ReduceBreak	0

# generation 4: best score 2.45932 bits/residue, 18 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	22
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	79
##	ReduceBreak	0

# generation 5: best score 2.3993 bits/residue, 16 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	21
##	ReduceClash	12
##	CrossOver	1
##	CrossAndInsert	24
##	TwoFragment	21
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	109
##	ReduceBreak	0

# best score in initial pool 3.45123 bits/residue, 39 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 3.45123 bits/residue, 39 clashes 
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	11
##	CrossOver	0
##	CrossAndInsert	9
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	12
##	ReduceBreak	0

# generation 2: best score 3.30324 bits/residue, 30 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	15
##	CrossOver	0
##	CrossAndInsert	17
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	30
##	ReduceBreak	0

# generation 3: best score 2.63176 bits/residue, 23 clashes 
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	18
##	CrossOver	0
##	CrossAndInsert	22
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	53
##	ReduceBreak	0

# generation 4: best score 2.44952 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	26
##	CrossOver	0
##	CrossAndInsert	27
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	71
##	ReduceBreak	0

# generation 5: best score 2.44952 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	27
##	CrossOver	0
##	CrossAndInsert	32
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	91
##	ReduceBreak	0

# best score in initial pool 3.45123 bits/residue, 39 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 3.45123 bits/residue, 39 clashes 
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	12
##	CrossOver	0
##	CrossAndInsert	3
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	18
##	ReduceBreak	0

# generation 2: best score 3.15259 bits/residue, 29 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	9
##	ReduceClash	21
##	CrossOver	1
##	CrossAndInsert	6
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	36
##	ReduceBreak	0

# generation 3: best score 2.67484 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	29
##	CrossOver	2
##	CrossAndInsert	12
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	49
##	ReduceBreak	0

# generation 4: best score 2.61701 bits/residue, 31 clashes 
# Cumulative usage by method:
##	InsertFragment	16
##	ReduceClash	30
##	CrossOver	2
##	CrossAndInsert	19
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	66
##	ReduceBreak	0

# generation 5: best score 2.44501 bits/residue, 29 clashes 
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	35
##	CrossOver	3
##	CrossAndInsert	23
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	82
##	ReduceBreak	0

# best score in initial pool 3.45123 bits/residue, 39 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 3.45123 bits/residue, 39 clashes 
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	6
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	14
##	ReduceBreak	0

# generation 2: best score 3.19137 bits/residue, 30 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	9
##	CrossOver	0
##	CrossAndInsert	16
##	TwoFragment	9
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	35
##	ReduceBreak	0

# generation 3: best score 2.48378 bits/residue, 18 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	18
##	ReduceClash	12
##	CrossOver	2
##	CrossAndInsert	18
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	55
##	ReduceBreak	0

# generation 4: best score 2.48378 bits/residue, 18 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	23
##	ReduceClash	17
##	CrossOver	4
##	CrossAndInsert	21
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	77
##	ReduceBreak	0

# generation 5: best score 2.32934 bits/residue, 16 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	28
##	ReduceClash	18
##	CrossOver	7
##	CrossAndInsert	26
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	95
##	ReduceBreak	0

# best score in initial pool 3.45123 bits/residue, 39 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 3.4306 bits/residue, 41 clashes 
# Cumulative usage by method:
##	InsertFragment	14
##	ReduceClash	3
##	CrossOver	0
##	CrossAndInsert	6
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	10
##	ReduceBreak	0

# generation 2: best score 2.43311 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	26
##	ReduceClash	5
##	CrossOver	0
##	CrossAndInsert	14
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	23
##	ReduceBreak	0

# generation 3: best score 2.43311 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	37
##	ReduceClash	8
##	CrossOver	0
##	CrossAndInsert	19
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	35
##	ReduceBreak	0

# generation 4: best score 2.41777 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	43
##	ReduceClash	12
##	CrossOver	1
##	CrossAndInsert	24
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	47
##	ReduceBreak	0

# generation 5: best score 2.40874 bits/residue, 21 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	55
##	ReduceClash	14
##	CrossOver	1
##	CrossAndInsert	28
##	TwoFragment	14
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	60
##	ReduceBreak	0

# best score in initial pool 3.45123 bits/residue, 39 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 3.23176 bits/residue, 21 clashes 
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	4
##	CrossOver	1
##	CrossAndInsert	9
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	10
##	ReduceBreak	0

# generation 2: best score 2.40808 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	5
##	CrossOver	1
##	CrossAndInsert	16
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	24
##	ReduceBreak	0

# generation 3: best score 2.40808 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	30
##	ReduceClash	9
##	CrossOver	3
##	CrossAndInsert	22
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	32
##	ReduceBreak	0

# generation 4: best score 2.40808 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	35
##	ReduceClash	14
##	CrossOver	7
##	CrossAndInsert	27
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	41
##	ReduceBreak	0

# generation 5: best score 2.23848 bits/residue, 31 clashes 
# Cumulative usage by method:
##	InsertFragment	42
##	ReduceClash	20
##	CrossOver	9
##	CrossAndInsert	32
##	TwoFragment	22
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	49
##	ReduceBreak	0

# best score in super_pool at pool[5] 2.23848 bits/residue, 31 clashes 
# optimizing backbone with 50 conformations in pool
# doing 5 generations, with 200 new conformations in each generation.
# keep at most 20 conformations from old pool
# generation 1: best score 1.90362 bits/residue, 25 clashes 
# Cumulative usage by method:
##	InsertFragment	4
##	ReduceClash	7
##	CrossOver	2
##	CrossAndInsert	11
##	TwoFragment	4
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	10
##	ReduceBreak	0

# generation 2: best score 1.8041 bits/residue, 31 clashes 
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	13
##	CrossOver	6
##	CrossAndInsert	16
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	20
##	ReduceBreak	0

# generation 3: best score 1.8041 bits/residue, 31 clashes 
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	17
##	CrossOver	15
##	CrossAndInsert	18
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	34
##	ReduceBreak	0

# generation 4: best score 1.80149 bits/residue, 19 clashes 
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	19
##	CrossOver	30
##	CrossAndInsert	23
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	39
##	ReduceBreak	0

# generation 5: best score 1.75919 bits/residue, 19 clashes 
# Cumulative usage by method:
##	InsertFragment	13
##	ReduceClash	22
##	CrossOver	49
##	CrossAndInsert	27
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	41
##	ReduceBreak	0

# command:# naming current conformation t128-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 5
# best score from archetype iter: 1.75919 bits/residue, 19 clashes, rmsd= 0
# best score after iter 1 1.75919 bits/residue, 19 clashes, rmsd= 0
# best score after iter 2 -2.19585 bits/residue, 24 clashes, rmsd= 0
# best score after iter 3 -4.01681 bits/residue, 22 clashes, rmsd= 0
# best score after iter 4 -5.40284 bits/residue, 23 clashes, rmsd= 0
# best score after iter 5 -5.69719 bits/residue, 21 clashes, rmsd= 0
# best score after iter 6 -5.74391 bits/residue, 21 clashes, rmsd= 0
# best score after iter 7 -5.86076 bits/residue, 20 clashes, rmsd= 0
# best score after iter 8 -5.96499 bits/residue, 19 clashes, rmsd= 0
# best score after iter 9 -6.10111 bits/residue, 19 clashes, rmsd= 0
# command:# naming current conformation 128-opt-rot
# command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1634458317.pdb -s /projects/compbio/tmp/to_scwrl_1634458317.seq -o /projects/compbio/tmp/from_scwrl_1634458317.pdb > /projects/compbio/tmp/scwrl.log
# conformation set from SCWRL output
# command:# naming current conformation t128-opt-scwrl
# command:# command:# ScoreConform
t128-rand 24.1937 bits/residue, 277 clashes 
t128-try5 at pool[1] 2.22828 bits/residue, 16 clashes 
t128-opt at pool[2] 3.48499 bits/residue, 39 clashes 
t128-opt at pool[3] 1.75919 bits/residue, 19 clashes 
128-opt-rot at pool[4] -6.10111 bits/residue, 19 clashes 
t128-opt-scwrl at pool[5] -5.71617 bits/residue, 32 clashes 
# command: