# 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 try3/t128-opt-rot.pdb
# command:# naming current conformation t128-try3
# command:# created fragments for T0128 from T0128-1c3qX-karplus.index
# command:# created conformation for T0128 by applying fragments
# command:# naming current conformation t128-try3-his
# command:# created fragments for T0128 from T0128-1avmA-karplus.index
# command:# created conformation for T0128 by applying fragments
# command:# naming current conformation t128-init
# command:# 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-try3 at pool[1] -5.13461 bits/residue, 56 clashes 
t128-try3-his at pool[2] -3.93933 bits/residue, 40 clashes 0 breaks
t128-init at pool[3] 6.74257 bits/residue, 68 clashes 0 breaks
t128-init-scwrl at pool[4] 6.82878 bits/residue, 71 clashes 0 breaks
# command:# naming current conformation t128-opt
# command:# Will do 6 iterations of optimization

# best score in initial pool at pool[32] 4.50589 bits/residue, 59 clashes 0 breaks
# 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 3.44269 bits/residue, 49 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	6
##	ReduceClash	5
##	CrossOver	0
##	CrossAndInsert	5
##	TwoFragment	12
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	17
##	ReduceBreak	0

# generation 2: best score 3.20393 bits/residue, 52 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	10
##	ReduceClash	10
##	CrossOver	0
##	CrossAndInsert	10
##	TwoFragment	16
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	42
##	ReduceBreak	0

# generation 3: best score 3.04093 bits/residue, 46 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	11
##	ReduceClash	14
##	CrossOver	0
##	CrossAndInsert	12
##	TwoFragment	17
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	73
##	ReduceBreak	0

# generation 4: best score 2.8452 bits/residue, 51 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	15
##	CrossOver	0
##	CrossAndInsert	15
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	102
##	ReduceBreak	0

# generation 5: best score 2.83519 bits/residue, 51 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	16
##	CrossOver	0
##	CrossAndInsert	18
##	TwoFragment	18
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	0
##	InsertAlignment	134
##	ReduceBreak	0

# best score in initial pool at pool[26] 5.72481 bits/residue, 68 clashes 0 breaks
# 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 5.10313 bits/residue, 37 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	7
##	ReduceClash	4
##	CrossOver	2
##	CrossAndInsert	6
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	14
##	ReduceBreak	0

# generation 2: best score 4.87269 bits/residue, 32 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	7
##	CrossOver	2
##	CrossAndInsert	10
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	35
##	ReduceBreak	0

# generation 3: best score 4.73495 bits/residue, 70 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	18
##	ReduceClash	9
##	CrossOver	3
##	CrossAndInsert	14
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	58
##	ReduceBreak	0

# generation 4: best score 4.22698 bits/residue, 18 clashes 
# Cumulative usage by method:
##	InsertFragment	20
##	ReduceClash	10
##	CrossOver	5
##	CrossAndInsert	16
##	TwoFragment	10
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	82
##	ReduceBreak	0

# generation 5: best score 3.83083 bits/residue, 19 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	22
##	ReduceClash	14
##	CrossOver	6
##	CrossAndInsert	18
##	TwoFragment	11
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	105
##	ReduceBreak	0

# best score in initial pool 5.93687 bits/residue, 71 clashes 0 breaks
# 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 5.65954 bits/residue, 69 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	8
##	ReduceClash	8
##	CrossOver	1
##	CrossAndInsert	4
##	TwoFragment	5
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	18
##	ReduceBreak	0

# generation 2: best score 5.24228 bits/residue, 57 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	10
##	CrossOver	1
##	CrossAndInsert	8
##	TwoFragment	6
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	49
##	ReduceBreak	0

# generation 3: best score 4.94116 bits/residue, 10 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	12
##	ReduceClash	13
##	CrossOver	1
##	CrossAndInsert	10
##	TwoFragment	7
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	78
##	ReduceBreak	0

# generation 4: best score 4.08292 bits/residue, 9 clashes 
# Cumulative usage by method:
##	InsertFragment	15
##	ReduceClash	13
##	CrossOver	2
##	CrossAndInsert	13
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	109
##	ReduceBreak	0

# generation 5: best score 4.07845 bits/residue, 9 clashes 0 breaks
# Cumulative usage by method:
##	InsertFragment	19
##	ReduceClash	14
##	CrossOver	2
##	CrossAndInsert	16
##	TwoFragment	8
##	InsertSSBond	0
##	OneRotamer	0
##	ClashingRotamer	1
##	InsertAlignment	143
##	ReduceBreak	0

# best score in initial pool at pool[30] 5.46684 bits/residue, 19 clashes 0 breaks
# 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