# 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 try2/t111-2oneA.2.10.pdb
# command:# naming current conformation t111-2oneA
# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1509860569.pdb -s /projects/compbio/tmp/to_scwrl_1509860569.seq -o /projects/compbio/tmp/from_scwrl_1509860569.pdb > /projects/compbio/tmp/scwrl.log
# conformation set from SCWRL output
# command:# naming current conformation t111-2oneA-scwrl
# command:# command:# ScoreConform
t111-rand 28.7929 bits/residue, 435 clashes 
t111-2oneA at pool[1] 21.7207 bits/residue, 53 clashes 
t111-2oneA-scwrl at pool[2] 20.9659 bits/residue, 52 clashes 
# command:# naming current conformation t111-opt
# command:# Will do 10 iterations of optimization

# best score in initial pool 20.9664 bits/residue, 52 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 20.9664 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	5
##	ReduceClash	6
##	CrossOver	0
##	CrossAndInsert	4
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	2
##	InsertAlignment	25
##	ReduceBreak	0

# generation 2: best score 20.9664 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	12
##	CrossOver	0
##	CrossAndInsert	9
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	7
##	InsertAlignment	43
##	ReduceBreak	0

# generation 3: best score 20.9664 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	17
##	ReduceClash	19
##	CrossOver	0
##	CrossAndInsert	13
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	14
##	InsertAlignment	47
##	ReduceBreak	0

# generation 4: best score 20.95 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	25
##	ReduceClash	25
##	CrossOver	2
##	CrossAndInsert	17
##	TwoFragment	13
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	18
##	InsertAlignment	50
##	ReduceBreak	0

# generation 5: best score 20.95 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	33
##	ReduceClash	31
##	CrossOver	5
##	CrossAndInsert	23
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	51
##	ReduceBreak	0

# generation 6: best score 20.95 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	45
##	ReduceClash	36
##	CrossOver	8
##	CrossAndInsert	30
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	53
##	ReduceBreak	0

# generation 7: best score 20.9276 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	56
##	ReduceClash	40
##	CrossOver	15
##	CrossAndInsert	38
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	53
##	ReduceBreak	0

# generation 8: best score 20.8655 bits/residue, 47 clashes 
# Cumulative usage by method:
##	InsertFragment	67
##	ReduceClash	44
##	CrossOver	25
##	CrossAndInsert	42
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	53
##	ReduceBreak	0

# generation 9: best score 20.8655 bits/residue, 47 clashes 
# Cumulative usage by method:
##	InsertFragment	76
##	ReduceClash	48
##	CrossOver	35
##	CrossAndInsert	47
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	53
##	ReduceBreak	0

# generation 10: best score 20.8655 bits/residue, 47 clashes 
# Cumulative usage by method:
##	InsertFragment	83
##	ReduceClash	49
##	CrossOver	50
##	CrossAndInsert	54
##	TwoFragment	20
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	21
##	InsertAlignment	53
##	ReduceBreak	0

# best score in initial pool 20.9664 bits/residue, 52 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 20.9664 bits/residue, 52 clashes 
# Cumulative usage by method:
##	InsertFragment	3
##	ReduceClash	7
##	CrossOver	0
##	CrossAndInsert	8
##	TwoFragment	2
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	27
##	ReduceBreak	0