-parser:protocol topo-fixed_core.xml
#-parser:view

-nstruct 1000

-in:file:fasta input/apo1-input2.fasta
-in:file:s input/apo1-try5_04.pdb
-in:file:native input/apo1-try5_04.pdb
-out:file:silent output/fixed_core.out
-out:file:silent_struct_type protein
#-out:path:silent out_pdbs

#-out:levels protocols.environment:debug
#-out:levels protocols.environment.EnvClaimBroker:debug
#-out:levels protocols.environment.EnvMover:debug
#-out:levels protocols.environment.movers.FragmentCM:debug

#-out:levels core.environment:debug
#-out:levels core.pose:debug
#-out:levels core.fragment:debug
#-out:levels protocols.jd2:debug
#-out:levels protocols.abinitio.abscript.RigidChunkCM:debug
#-out:levels core.kinematics.MoveMap:debug

#@denovo_flags
# --->copied here directly:


-abrelax true
#jumping
#-templates::topology_rank_cutoff 0.8
#-psipred_ss2: input/apo1-cterm.ppss2
-jumps:ramp_chainbreaks
-jumps:overlap_chainbreak


#magic energy fixes
-rsd_wt_helix 0.5
-rsd_wt_loop 0.5
-rg_reweight 0.5

# for loop closing
-overwrite_filter_scorefxn score3
-detect_disulf false

#loop-closing filter in SlidingWindow
-fast_loops:overwrite_filter_scorefxn score3

#log-output
#-unmute memory_usage
#-out:levels core.chemical:error
#-out:levels core.io.pdb:error
#-out:levels protocols.jobdist:error

-evaluation:rmsd input/apo1-try5_04.pdb _notail notail.rigid