error–rosetta fragment‐based refinement protocol for refinement against EM density

[Anonymous]

I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.

It always complaints:

core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.434133 seconds to load from binary

core.pack.pack_rotamers: built 185 rotamers at 21 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 27768 bytes

protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=A_asymm_refine.xml

protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: ‘%%denswt%%’=’25’;  ‘%%map%%’=’half1_34A.mrc’;  ‘%%reso%%’=’3.4’;  ‘%%rms%%’=’1.5’;  ‘%%testmap%%’=’half2_34A.mrc’;  

protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:

<ROSETTASCRIPTS>

 <SCOREFXNS>

    <cen weights=”score4_smooth_cart”>

    <Reweight scoretype=elec_dens_fast weight=20/>

    </cen>

    <dens_soft weights=”soft_rep”>

    <Reweight scoretype=cart_bonded weight=0.5/>

    <Reweight scoretype=pro_close weight=0.0/>

    <Reweight scoretype=fa_sol weight=0.0/> # remove this line if not a membrane protein

    <Reweight scoretype=elec_dens_fast weight=”25″/>

    </dens_soft>

    <dens weights=“talaris2014_cart”>

    <Reweight scoretype=elec_dens_fast weight=”25″/>

    <Reweight scoretype=fa_sol weight=0.0/> # remove this line if not a membrane protein

    <Set scale_sc_dens_byres=”R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88″/>

    </dens>

 </SCOREFXNS>

 <MOVERS>

    <SetupForDensityScoring name=setupdens/>

    <LoadDensityMap name=loaddens mapfile=”half1_34A.mrc”/>

    <SwitchResidueTypeSetMover name=tocen set=centroid/>

    <MinMover name=cenmin scorefxn=cen type=lbfgs_armijo_nonmonotone max_iter=200 tolerance=0.00001 bb=1 chi=1 jump=ALL/>

    <CartesianSampler name=cen5_50 automode_scorecut=-0.5 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

    <CartesianSampler name=cen5_60 automode_scorecut=-0.3 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

    <CartesianSampler name=cen5_70 automode_scorecut=-0.1 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

    <CartesianSampler name=cen5_80 automode_scorecut=0.0 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

   <ReportFSC name=report testmap=”half2_34A.mrc” res_low=10.0 res_high=3.4/>

   <BfactorFitting name=fit_bs max_iter=50 wt_adp=0.0005 init=1 exact=1/>

   <FastRelax name=relaxcart scorefxn=dens repeats=1 cartesian=1/>

 </MOVERS>

 <PROTOCOLS>

   <Add mover_name=setupdens/>

   <Add mover_name=loaddens/>

   <Add mover_name=tocen/>

   <Add mover_name=cenmin/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_50/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_60/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_70/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_80/>

   <Add mover_name=relaxcart/>

   <Add mover_name=relaxcart/>

   <Add mover_name=fit_bs/>

   <Add mover_name=report/>

 </PROTOCOLS>

 <OUTPUT scorefxn=dens/>

</ROSETTASCRIPTS>

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job ‘3j5p_transmem_A_sym_0001’

Error: Tag::read – parse error, printing backtrace.

 

Tag::read – parse error – file:istream line:1 column:1 – <ROSETTASCRIPTS>

Tag::read – parse error – file:istream line:1 column:1 – ^

Error: 

Error: Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 3j5p_transmem_A_sym_0001

protocols.jd2.JobDistributor: no more batches to process… 

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds

Error: ERROR: Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error: 

 

My flags is the following:

-in:file:s 3j5p_transmem_A.pdb

-database /Applications/rosetta_2016/main/database

-out:suffix _sym

-ignore_unrecognized_res

-edensity:mapreso 3.4

-edensity:cryoem_scatterers

-parser:script_vars denswt=25 rms=1.5 reso=3.4 map=half1_34A.mrc testmap=half2_34A.mrc

-crystal_refine

-default_max_cycles 200

-overwrite

-parser:protocol A_asymm_refine.xml

Thanks,

[Author]

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