Basic usage: /home/domi/RosettaUb/rosetta.binary.ubuntu.release-340/main/source/bin/rna_denovo.linuxgccrelease -fasta [ -native ] Type -help for full slate of options. core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.ubuntu.release-340 r340 2023.06+release.27ba97a7573 27ba97a7573364daceed93c6163b5ac79b4860c9 https://www.rosettacommons.org 2023-02-11T03:43:05.087004 core.init: command: /home/domi/RosettaUb/rosetta.binary.ubuntu.release-340/main/source/bin/rna_denovo.linuxgccrelease @flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1644475301 seed_offset=0 real_seed=1644475301 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1644475301 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /home/domi/RosettaUb/rosetta.binary.ubuntu.release-340/main/database core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.621034 seconds. core.pose.rna.RNA_SecStruct: Reading RNA secstruct file: secstruct.txt core.pose.rna.RNA_SecStruct: [ WARNING ] Expanding secstruct by one, as it looks like a virtual residue was appended to the sequence core.import_pose.import_pose: File 'unbound_protein.pdb' automatically determined to be of type PDB core.import_pose.import_pose: File 'RNA_helix.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue G core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue G core.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything. protocols.rna.denovo.movers.RNA_DeNovoProtocolMover: Sequence: SMSKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDSGLPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGRSKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGRggcacagaagauauggcuucgugccX protocols.rna.denovo.movers.RNA_DeNovoProtocolMover: Secstruct: ................................................................................................................................................................................................................................................(((((.((((......))))))))). protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed unbound_protein.pdb nstruct indices 1 - 5 protocols.jd2.PDBJobInputter: pushed RNA_helix.pdb nstruct indices 1 - 5 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... basic.io.database: Database file opened: scoring/rna/rna_atom_vdw.txt basic.io.database: Database file opened: scoring/rna/rnp_atom_vdw_min_distances_reformat_MIN_actual_centroid.txt core.scoring.ScoringManager: Reading in: /home/domi/RosettaUb/rosetta.binary.ubuntu.release-340/main/database/scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Finished reading basepair x - y potential file: scoring/rna/rna_base_pair_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading non - base - base x - y potential file: scoring/rna/rna_base_backbone_xy.dat core.scoring.rna.RNA_LowResolutionPotential: Reading RNA backbone backbone potential file: scoring/rna/rna_backbone_backbone.dat core.scoring.rna.RNP_LowResPotential: Reading RNP basepair x - y potential file: scoring/rna/rnp_base_pair_actual_centroid.txt core.scoring.rna.RNP_LowResPotential: Finished reading RNP basepair x - y potential file: scoring/rna/rnp_base_pair_actual_centroid.txt core.scoring.rna.RNP_LowResPotential: Reading RNP AA RNA backbone potential file: scoring/rna/rnp_backbone_potential_actual_centroid.txt core.scoring.rna.RNP_LowResPotential: Finished reading RNP AA RNA backbone potential file: scoring/rna/rnp_backbone_potential_actual_centroid.txt core.scoring.rna.RNP_LowResPairDistPotential: Reading RNP pair distance potential file: scoring/rna/rnp_pair_dist_potential_renorm_actual_centroid.txt core.scoring.rna.RNP_LowResPairDistPotential: Finished reading RNP pair distance potential file: scoring/rna/rnp_pair_dist_potential_renorm_actual_centroid.txt core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/carbon_hbond/ch_o_bond_potential.dat core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHXHHHHXXXXXXHHHHHHHHHX core.import_pose.import_pose: File 'unbound_protein.pdb' automatically determined to be of type PDB core.import_pose.import_pose: File 'RNA_helix.pdb' automatically determined to be of type PDB protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Reading in vall_torsions file: /home/domi/RosettaUb/rosetta.binary.ubuntu.release-340/main/database/sampling/rna/RNA18_HUB_2.154_2.5.torsions protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Lines read from vall_torsions file: 28032 protocols.rna.denovo.RNA_FragmentMonteCarlo: Using user-defined 1000 cycles in de novo modeling. protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting up fold tree through build full model info protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 262 with attachments BOND_TO_NEXT:263 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 244 with attachments BOND_TO_PREVIOUS:243 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 261 with attachments BOND_TO_NEXT:262 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 245 with attachments BOND_TO_PREVIOUS:244 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 260 with attachments BOND_TO_NEXT:261 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 259 with attachments BOND_TO_NEXT:260 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 246 with attachments BOND_TO_PREVIOUS:245 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 258 with attachments BOND_TO_NEXT:259 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 247 with attachments BOND_TO_PREVIOUS:246 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 257 with attachments BOND_TO_NEXT:258 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 256 with attachments BOND_TO_NEXT:257 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 255 with attachments BOND_TO_NEXT:256 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 248 with attachments BOND_TO_PREVIOUS:247 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 249 with attachments BOND_TO_PREVIOUS:248 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 250 with attachments BOND_TO_PREVIOUS:249 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 251 with attachments BOND_TO_PREVIOUS:250 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 252 with attachments BOND_TO_PREVIOUS:251 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 253 with attachments BOND_TO_PREVIOUS:252 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 254 with attachments BOND_TO_NEXT:255 core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 N3 <--> H1 . [ 16-31] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 O2 <--> H21. [ 15-33] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 H41 <--> O6 . [ 29-20] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 O6 <--> H41. [ 20-29] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 O6 <--> H41. [ 20-29] protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 75 cycles. protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence c and sec. struct X ... found 7283 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence u and sec. struct X ... found 5506 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence a and sec. struct X ... found 6317 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence g and sec. struct X ... found 8902 potential fragments protocols.geometry.RB_geometry: random_reorientation_matrix phi: 196.648 psi: 11.2563 theta: 133.243 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 9.265 trans_mag: 4.6325 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aca and sec. struct XXX ... found 289 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aga and sec. struct XXX ... found 421 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cuu and sec. struct XXX ... found 284 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cag and sec. struct XXX ... found 411 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uuc and sec. struct XXX ... found 290 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cgu and sec. struct XXX ... found 372 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ugg and sec. struct XXX ... found 517 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ggc and sec. struct XXX ... found 691 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aua and sec. struct XXX ... found 261 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gug and sec. struct XXX ... found 535 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gaa and sec. struct XXX ... found 616 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gcu and sec. struct XXX ... found 438 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gcc and sec. struct XXX ... found 624 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gca and sec. struct XXX ... found 396 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gau and sec. struct XXX ... found 358 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ugc and sec. struct XXX ... found 438 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aag and sec. struct XXX ... found 578 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aug and sec. struct XXX ... found 353 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uau and sec. struct XXX ... found 221 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ucg and sec. struct XXX ... found 394 potential fragments protocols.moves.TrialCounter: frag 3 trials= 43; accepts= 0.1628; energy_drop/trial= -78.57889 protocols.moves.TrialCounter: rigid_body trials= 48; accepts= 0.0417; energy_drop/trial= -4.53311 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 8.53 trans_mag: 4.265 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cac and sec. struct XXX ... found 360 potential fragments protocols.moves.TrialCounter: frag 3 trials= 46; accepts= 0.1087; energy_drop/trial= -57.32845 protocols.moves.TrialCounter: rigid_body trials= 38; accepts= 0.0526; energy_drop/trial= -1.58219 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.795 trans_mag: 3.8975 protocols.moves.TrialCounter: frag 3 trials= 45; accepts= 0.1333; energy_drop/trial= -26.68827 protocols.moves.TrialCounter: rigid_body trials= 45; accepts= 0.0444; energy_drop/trial= -0.74516 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.06 trans_mag: 3.53 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence aa and sec. struct XX ... found 1844 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cu and sec. struct XX ... found 1385 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ca and sec. struct XX ... found 1315 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uu and sec. struct XX ... found 1301 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ug and sec. struct XX ... found 1723 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gc and sec. struct XX ... found 2323 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gg and sec. struct XX ... found 2865 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ag and sec. struct XX ... found 1929 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ga and sec. struct XX ... found 2003 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ac and sec. struct XX ... found 1426 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence ua and sec. struct XX ... found 1149 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence gu and sec. struct XX ... found 1704 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence au and sec. struct XX ... found 1114 potential fragments protocols.moves.TrialCounter: frag 2 trials= 42; accepts= 0.0714; energy_drop/trial= -1.92165 protocols.moves.TrialCounter: rigid_body trials= 48; accepts= 0.1250; energy_drop/trial= -4.59478 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 6.325 trans_mag: 3.1625 protocols.moves.TrialCounter: frag 2 trials= 44; accepts= 0.0455; energy_drop/trial= -3.97294 protocols.moves.TrialCounter: rigid_body trials= 45; accepts= 0.0222; energy_drop/trial= -0.17679 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 5.59 trans_mag: 2.795 protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence uc and sec. struct XX ... found 1330 potential fragments protocols.rna.denovo.fragments.FullAtomRNA_Fragments: Picked Fragment Library for sequence cg and sec. struct XX ... found 2375 potential fragments protocols.moves.TrialCounter: frag 2 trials= 47; accepts= 0.0213; energy_drop/trial= -0.40072 protocols.moves.TrialCounter: rigid_body trials= 42 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.855 trans_mag: 2.4275 protocols.moves.TrialCounter: frag 1 trials= 52; accepts= 0.1154; energy_drop/trial= -15.01507 protocols.moves.TrialCounter: rigid_body trials= 38; accepts= 0.0789; energy_drop/trial= -0.76399 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.12 trans_mag: 2.06 protocols.moves.TrialCounter: frag 1 trials= 49; accepts= 0.0408; energy_drop/trial= -0.35533 protocols.moves.TrialCounter: rigid_body trials= 41 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 3.385 trans_mag: 1.6925 protocols.moves.TrialCounter: frag 1 trials= 48; accepts= 0.0208; energy_drop/trial= 0.04877 protocols.moves.TrialCounter: rigid_body trials= 42; accepts= 0.0238; energy_drop/trial= -0.17740 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 2.65 trans_mag: 1.325 protocols.moves.TrialCounter: frag 1 trials= 51; accepts= 0.0784; energy_drop/trial= -2.69427 protocols.moves.TrialCounter: rigid_body trials= 42; accepts= 0.0714; energy_drop/trial= -0.53869 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of in 12 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 2.000 0.000 0.000 rna_vdw 2.000 55.973 111.947 rnp_vdw 50.000 0.311 15.528 rna_base_backbone 2.000 -3.216 -6.432 rna_backbone_backbone 2.000 0.000 0.000 rna_repulsive 5.000 12.937 64.686 rna_base_pair 2.000 -79.265 -158.530 rna_base_axis 0.400 -46.420 -18.568 rna_base_stagger 2.000 -25.186 -50.373 rna_base_stack 2.000 -5.088 -10.177 rna_base_stack_axis 0.400 -30.596 -12.238 rnp_base_pair 2.000 -35.870 -71.740 rnp_stack 5.000 0.000 0.000 rnp_pair_dist 0.200 -252.020 -50.404 rnp_aa_to_rna_backbone 1.000 -16.664 -16.664 rna_rg 0.500 21.645 10.823 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 1823.158 1823.158 linear_chainbreak 8.000 6.736 53.889 --------------------------------------------------- Total weighted score: 1684.904 protocols.rna.denovo.RNA_FragmentMonteCarlo: core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. protocols.jd2.JobDistributor: S_000001 reported success in 13 seconds protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHXHHHHXXXXXXHHHHHHHHHX core.import_pose.import_pose: File 'unbound_protein.pdb' automatically determined to be of type PDB core.import_pose.import_pose: File 'RNA_helix.pdb' automatically determined to be of type PDB protocols.rna.denovo.RNA_FragmentMonteCarlo: Using user-defined 1000 cycles in de novo modeling. protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting up fold tree through build full model info protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 244 with attachments BOND_TO_PREVIOUS:243 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 245 with attachments BOND_TO_PREVIOUS:244 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 246 with attachments BOND_TO_PREVIOUS:245 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 247 with attachments BOND_TO_PREVIOUS:246 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 262 with attachments BOND_TO_NEXT:263 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 248 with attachments BOND_TO_PREVIOUS:247 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 249 with attachments BOND_TO_PREVIOUS:248 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 250 with attachments BOND_TO_PREVIOUS:249 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 251 with attachments BOND_TO_PREVIOUS:250 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 261 with attachments BOND_TO_NEXT:262 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 252 with attachments BOND_TO_PREVIOUS:251 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 253 with attachments BOND_TO_PREVIOUS:252 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 260 with attachments BOND_TO_NEXT:261 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 259 with attachments BOND_TO_NEXT:260 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 254 with attachments BOND_TO_PREVIOUS:253 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 258 with attachments BOND_TO_NEXT:259 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 255 with attachments BOND_TO_PREVIOUS:254 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 257 with attachments BOND_TO_NEXT:258 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 256 with attachments BOND_TO_PREVIOUS:255 core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 N3 <--> H1 . [ 16-31] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 O2 <--> H21. [ 15-33] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 H41 <--> O6 . [ 29-20] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 O6 <--> H41. [ 20-29] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H1 <--> N3 . [ 31-17] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H21 <--> O2 . [ 33-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 O6 <--> H41. [ 20-30] protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 75 cycles. protocols.geometry.RB_geometry: random_reorientation_matrix phi: 320.55 psi: 175.769 theta: 35.7563 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 9.265 trans_mag: 4.6325 protocols.moves.TrialCounter: frag 3 trials= 51; accepts= 0.2157; energy_drop/trial= -204.92350 protocols.moves.TrialCounter: rigid_body trials= 40; accepts= 0.2750; energy_drop/trial= -146.08608 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 8.53 trans_mag: 4.265 protocols.moves.TrialCounter: frag 3 trials= 57; accepts= 0.1228; energy_drop/trial= -19.49371 protocols.moves.TrialCounter: rigid_body trials= 34 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.795 trans_mag: 3.8975 protocols.moves.TrialCounter: frag 3 trials= 55; accepts= 0.0909; energy_drop/trial= -6.46453 protocols.moves.TrialCounter: rigid_body trials= 32 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.06 trans_mag: 3.53 protocols.moves.TrialCounter: frag 2 trials= 56; accepts= 0.0536; energy_drop/trial= -5.50734 protocols.moves.TrialCounter: rigid_body trials= 34 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 6.325 trans_mag: 3.1625 protocols.moves.TrialCounter: frag 2 trials= 54; accepts= 0.1296; energy_drop/trial= -7.44147 protocols.moves.TrialCounter: rigid_body trials= 44; accepts= 0.0227; energy_drop/trial= -0.07839 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 5.59 trans_mag: 2.795 protocols.moves.TrialCounter: frag 2 trials= 50; accepts= 0.0600; energy_drop/trial= -0.09028 protocols.moves.TrialCounter: rigid_body trials= 38; accepts= 0.0526; energy_drop/trial= -0.47744 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.855 trans_mag: 2.4275 protocols.moves.TrialCounter: frag 1 trials= 52; accepts= 0.0385; energy_drop/trial= -5.43087 protocols.moves.TrialCounter: rigid_body trials= 42 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.12 trans_mag: 2.06 protocols.moves.TrialCounter: frag 1 trials= 40; accepts= 0.0750; energy_drop/trial= -0.49367 protocols.moves.TrialCounter: rigid_body trials= 47; accepts= 0.0213; energy_drop/trial= -2.16977 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 3.385 trans_mag: 1.6925 protocols.moves.TrialCounter: frag 1 trials= 43; accepts= 0.0233; energy_drop/trial= -0.26916 protocols.moves.TrialCounter: rigid_body trials= 46 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 2.65 trans_mag: 1.325 protocols.moves.TrialCounter: frag 1 trials= 45; accepts= 0.0222; energy_drop/trial= -0.00874 protocols.moves.TrialCounter: rigid_body trials= 43 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of in 17 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 2.000 0.000 0.000 rna_vdw 2.000 331.758 663.517 rnp_vdw 50.000 0.027 1.328 rna_base_backbone 2.000 -12.664 -25.329 rna_backbone_backbone 2.000 -2.819 -5.638 rna_repulsive 5.000 32.404 162.020 rna_base_pair 2.000 -55.554 -111.108 rna_base_axis 0.400 -28.020 -11.208 rna_base_stagger 2.000 -18.544 -37.087 rna_base_stack 2.000 -3.150 -6.301 rna_base_stack_axis 0.400 -14.960 -5.984 rnp_base_pair 2.000 -36.510 -73.020 rnp_stack 5.000 0.000 0.000 rnp_pair_dist 0.200 -542.620 -108.524 rnp_aa_to_rna_backbone 1.000 -49.138 -49.138 rna_rg 0.500 9.307 4.653 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 2469.310 2469.310 linear_chainbreak 8.000 13.508 108.063 --------------------------------------------------- Total weighted score: 2975.554 protocols.rna.denovo.RNA_FragmentMonteCarlo: core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. protocols.jd2.JobDistributor: S_000002 reported success in 18 seconds protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHXHHHHXXXXXXHHHHHHHHHX core.import_pose.import_pose: File 'unbound_protein.pdb' automatically determined to be of type PDB core.import_pose.import_pose: File 'RNA_helix.pdb' automatically determined to be of type PDB protocols.rna.denovo.RNA_FragmentMonteCarlo: Using user-defined 1000 cycles in de novo modeling. protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting up fold tree through build full model info protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 262 with attachments BOND_TO_NEXT:263 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 261 with attachments BOND_TO_NEXT:262 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 244 with attachments BOND_TO_PREVIOUS:243 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 260 with attachments BOND_TO_NEXT:261 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 245 with attachments BOND_TO_PREVIOUS:244 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 259 with attachments BOND_TO_NEXT:260 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 246 with attachments BOND_TO_PREVIOUS:245 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 258 with attachments BOND_TO_NEXT:259 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 257 with attachments BOND_TO_NEXT:258 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 247 with attachments BOND_TO_PREVIOUS:246 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 248 with attachments BOND_TO_PREVIOUS:247 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 249 with attachments BOND_TO_PREVIOUS:248 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 250 with attachments BOND_TO_PREVIOUS:249 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 251 with attachments BOND_TO_PREVIOUS:250 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 252 with attachments BOND_TO_PREVIOUS:251 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 253 with attachments BOND_TO_PREVIOUS:252 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 254 with attachments BOND_TO_PREVIOUS:253 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 256 with attachments BOND_TO_NEXT:257 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 255 with attachments BOND_TO_PREVIOUS:254 core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 N3 <--> H1 . [ 16-31] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 O2 <--> H21. [ 15-33] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 H41 <--> O6 . [ 29-20] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 O6 <--> H41. [ 20-29] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 O6 <--> H41. [ 20-29] protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 75 cycles. protocols.geometry.RB_geometry: random_reorientation_matrix phi: 177.084 psi: 351.378 theta: 99.5056 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 9.265 trans_mag: 4.6325 protocols.moves.TrialCounter: frag 3 trials= 51; accepts= 0.3529; energy_drop/trial= -187.27852 protocols.moves.TrialCounter: rigid_body trials= 37; accepts= 0.9189; energy_drop/trial= 0.11410 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 8.53 trans_mag: 4.265 protocols.moves.TrialCounter: frag 3 trials= 56; accepts= 0.2143; energy_drop/trial= -28.51468 protocols.moves.TrialCounter: rigid_body trials= 35; accepts= 0.8286; energy_drop/trial= -0.01435 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.795 trans_mag: 3.8975 protocols.moves.TrialCounter: frag 3 trials= 48; accepts= 0.1042; energy_drop/trial= -6.63158 protocols.moves.TrialCounter: rigid_body trials= 43; accepts= 0.9302; energy_drop/trial= -0.09940 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.06 trans_mag: 3.53 protocols.moves.TrialCounter: frag 2 trials= 51; accepts= 0.0196; energy_drop/trial= -0.21062 protocols.moves.TrialCounter: rigid_body trials= 42; accepts= 0.8810; energy_drop/trial= -0.02529 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 6.325 trans_mag: 3.1625 protocols.moves.TrialCounter: frag 2 trials= 54; accepts= 0.0556; energy_drop/trial= -0.59241 protocols.moves.TrialCounter: rigid_body trials= 35; accepts= 0.8857; energy_drop/trial= 0.00015 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 5.59 trans_mag: 2.795 protocols.moves.TrialCounter: frag 2 trials= 46; accepts= 0.0217; energy_drop/trial= 0.01166 protocols.moves.TrialCounter: rigid_body trials= 44; accepts= 0.5455; energy_drop/trial= -0.63548 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.855 trans_mag: 2.4275 protocols.moves.TrialCounter: frag 1 trials= 57; accepts= 0.0351; energy_drop/trial= -0.04300 protocols.moves.TrialCounter: rigid_body trials= 31; accepts= 0.0323; energy_drop/trial= 0.15174 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.12 trans_mag: 2.06 protocols.moves.TrialCounter: frag 1 trials= 57 NO ACCEPTS. protocols.moves.TrialCounter: rigid_body trials= 34; accepts= 0.1765; energy_drop/trial= -0.61587 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 3.385 trans_mag: 1.6925 protocols.moves.TrialCounter: frag 1 trials= 54; accepts= 0.0185; energy_drop/trial= -0.16186 protocols.moves.TrialCounter: rigid_body trials= 39; accepts= 0.0256; energy_drop/trial= -0.18051 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 2.65 trans_mag: 1.325 protocols.moves.TrialCounter: frag 1 trials= 56; accepts= 0.0536; energy_drop/trial= -0.77344 protocols.moves.TrialCounter: rigid_body trials= 39; accepts= 0.0256; energy_drop/trial= 0.08290 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of in 15 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 2.000 0.000 0.000 rna_vdw 2.000 50.826 101.652 rnp_vdw 50.000 0.032 1.604 rna_base_backbone 2.000 -7.122 -14.243 rna_backbone_backbone 2.000 0.000 0.000 rna_repulsive 5.000 0.083 0.414 rna_base_pair 2.000 -82.596 -165.192 rna_base_axis 0.400 -46.728 -18.691 rna_base_stagger 2.000 -21.754 -43.507 rna_base_stack 2.000 -6.980 -13.960 rna_base_stack_axis 0.400 -42.504 -17.002 rnp_base_pair 2.000 -10.910 -21.820 rnp_stack 5.000 0.000 0.000 rnp_pair_dist 0.200 -125.930 -25.186 rnp_aa_to_rna_backbone 1.000 -6.484 -6.484 rna_rg 0.500 19.347 9.673 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 194.219 194.219 linear_chainbreak 8.000 0.239 1.916 --------------------------------------------------- Total weighted score: -16.608 protocols.rna.denovo.RNA_FragmentMonteCarlo: core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. protocols.jd2.JobDistributor: S_000003 reported success in 16 seconds protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHXHHHHXXXXXXHHHHHHHHHX core.import_pose.import_pose: File 'unbound_protein.pdb' automatically determined to be of type PDB core.import_pose.import_pose: File 'RNA_helix.pdb' automatically determined to be of type PDB protocols.rna.denovo.RNA_FragmentMonteCarlo: Using user-defined 1000 cycles in de novo modeling. protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting up fold tree through build full model info protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 262 with attachments BOND_TO_NEXT:263 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 244 with attachments BOND_TO_PREVIOUS:243 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 245 with attachments BOND_TO_PREVIOUS:244 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 261 with attachments BOND_TO_NEXT:262 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 246 with attachments BOND_TO_PREVIOUS:245 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 260 with attachments BOND_TO_NEXT:261 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 259 with attachments BOND_TO_NEXT:260 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 258 with attachments BOND_TO_NEXT:259 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 257 with attachments BOND_TO_NEXT:258 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 256 with attachments BOND_TO_NEXT:257 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 255 with attachments BOND_TO_NEXT:256 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 247 with attachments BOND_TO_PREVIOUS:246 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 248 with attachments BOND_TO_PREVIOUS:247 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 254 with attachments BOND_TO_NEXT:255 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 253 with attachments BOND_TO_NEXT:254 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 252 with attachments BOND_TO_NEXT:253 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 249 with attachments BOND_TO_PREVIOUS:248 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 251 with attachments BOND_TO_NEXT:252 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 250 with attachments BOND_TO_NEXT:251 core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 N3 <--> H1 . [ 16-31] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 O2 <--> H21. [ 15-33] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 H41 <--> O6 . [ 29-20] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 O6 <--> H41. [ 20-29] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 N1 <--> H3 . [ 15-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 H61 <--> O4 . [ 33-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H1 <--> N3 . [ 32-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H21 <--> O2 . [ 34-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 O6 <--> H41. [ 21-29] protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 75 cycles. protocols.geometry.RB_geometry: random_reorientation_matrix phi: 190.079 psi: 315.637 theta: 74.7259 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 9.265 trans_mag: 4.6325 protocols.moves.TrialCounter: frag 3 trials= 55; accepts= 0.2364; energy_drop/trial= -218.02512 protocols.moves.TrialCounter: rigid_body trials= 36; accepts= 0.9167; energy_drop/trial= 0.03597 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 8.53 trans_mag: 4.265 protocols.moves.TrialCounter: frag 3 trials= 49; accepts= 0.0612; energy_drop/trial= -11.24030 protocols.moves.TrialCounter: rigid_body trials= 39; accepts= 0.2821; energy_drop/trial= -0.36717 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.795 trans_mag: 3.8975 protocols.moves.TrialCounter: frag 3 trials= 50; accepts= 0.1000; energy_drop/trial= -17.55804 protocols.moves.TrialCounter: rigid_body trials= 36; accepts= 0.1111; energy_drop/trial= -9.82888 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.06 trans_mag: 3.53 protocols.moves.TrialCounter: frag 2 trials= 49; accepts= 0.0408; energy_drop/trial= -5.53002 protocols.moves.TrialCounter: rigid_body trials= 44; accepts= 0.1136; energy_drop/trial= 0.03673 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 6.325 trans_mag: 3.1625 protocols.moves.TrialCounter: frag 2 trials= 46 NO ACCEPTS. protocols.moves.TrialCounter: rigid_body trials= 43; accepts= 0.2093; energy_drop/trial= -1.07064 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 5.59 trans_mag: 2.795 protocols.moves.TrialCounter: frag 2 trials= 55 NO ACCEPTS. protocols.moves.TrialCounter: rigid_body trials= 41; accepts= 0.0488; energy_drop/trial= -0.55245 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.855 trans_mag: 2.4275 protocols.moves.TrialCounter: frag 1 trials= 50; accepts= 0.0400; energy_drop/trial= -1.07836 protocols.moves.TrialCounter: rigid_body trials= 37 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.12 trans_mag: 2.06 protocols.moves.TrialCounter: frag 1 trials= 47; accepts= 0.0851; energy_drop/trial= -13.63884 protocols.moves.TrialCounter: rigid_body trials= 46 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 3.385 trans_mag: 1.6925 protocols.moves.TrialCounter: frag 1 trials= 45; accepts= 0.0222; energy_drop/trial= -1.36781 protocols.moves.TrialCounter: rigid_body trials= 40 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 2.65 trans_mag: 1.325 protocols.moves.TrialCounter: frag 1 trials= 45; accepts= 0.0444; energy_drop/trial= -2.59547 protocols.moves.TrialCounter: rigid_body trials= 41; accepts= 0.0244; energy_drop/trial= 0.05124 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of in 14 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 2.000 0.000 0.000 rna_vdw 2.000 65.563 131.126 rnp_vdw 50.000 0.000 0.000 rna_base_backbone 2.000 -1.352 -2.705 rna_backbone_backbone 2.000 0.000 0.000 rna_repulsive 5.000 0.334 1.671 rna_base_pair 2.000 -60.795 -121.590 rna_base_axis 0.400 -26.761 -10.704 rna_base_stagger 2.000 -19.891 -39.781 rna_base_stack 2.000 -1.945 -3.890 rna_base_stack_axis 0.400 -8.768 -3.507 rnp_base_pair 2.000 -14.020 -28.040 rnp_stack 5.000 0.000 0.000 rnp_pair_dist 0.200 -168.800 -33.760 rnp_aa_to_rna_backbone 1.000 -12.676 -12.676 rna_rg 0.500 18.659 9.330 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 2669.837 2669.837 linear_chainbreak 8.000 1.392 11.137 --------------------------------------------------- Total weighted score: 2566.448 protocols.rna.denovo.RNA_FragmentMonteCarlo: core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. protocols.jd2.JobDistributor: S_000004 reported success in 15 seconds protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting desired secondary structure to: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHXHHHHXXXXXXHHHHHHHHHX core.import_pose.import_pose: File 'unbound_protein.pdb' automatically determined to be of type PDB core.import_pose.import_pose: File 'RNA_helix.pdb' automatically determined to be of type PDB protocols.rna.denovo.RNA_FragmentMonteCarlo: Using user-defined 1000 cycles in de novo modeling. protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer: Setting up fold tree through build full model info protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 244 with attachments BOND_TO_PREVIOUS:243 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 262 with attachments BOND_TO_NEXT:263 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 261 with attachments BOND_TO_NEXT:262 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 245 with attachments BOND_TO_PREVIOUS:244 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 260 with attachments BOND_TO_NEXT:261 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 246 with attachments BOND_TO_PREVIOUS:245 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 247 with attachments BOND_TO_PREVIOUS:246 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 259 with attachments BOND_TO_NEXT:260 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 258 with attachments BOND_TO_NEXT:259 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 248 with attachments BOND_TO_PREVIOUS:247 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 249 with attachments BOND_TO_PREVIOUS:248 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 257 with attachments BOND_TO_NEXT:258 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 256 with attachments BOND_TO_NEXT:257 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 255 with attachments BOND_TO_NEXT:256 protocols.stepwise.monte_carlo.StepWiseMoveSelector: made it protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 250 with attachments BOND_TO_PREVIOUS:249 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 251 with attachments BOND_TO_PREVIOUS:250 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 254 with attachments BOND_TO_NEXT:255 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 253 with attachments BOND_TO_NEXT:254 protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 252 with attachments BOND_TO_NEXT:253 core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a244 <--> u262 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 N3 <--> H1 . [ 16-31] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 O2 <--> H21. [ 15-33] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: c245 <--> g261 H41 <--> O6 . [ 29-20] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g247 <--> c260 O6 <--> H41. [ 20-29] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a248 <--> u259 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 N1 <--> H3 . [ 13-28] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: a249 <--> u258 H61 <--> O4 . [ 31-18] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H1 <--> N3 . [ 31-16] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 H21 <--> O2 . [ 33-15] core.pose.rna.RNA_Util: BASEPAIR: Adding rna_force_atom_pair constraint: g250 <--> c257 O6 <--> H41. [ 20-29] protocols.rna.denovo.movers.RNA_DeNovoMasterMover: Heating up... 75 cycles. protocols.geometry.RB_geometry: random_reorientation_matrix phi: 327.547 psi: 25.0043 theta: 85.2796 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning main loop... protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 1 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 9.265 trans_mag: 4.6325 protocols.moves.TrialCounter: frag 3 trials= 50; accepts= 0.1000; energy_drop/trial= -52.75248 protocols.moves.TrialCounter: rigid_body trials= 42; accepts= 0.0952; energy_drop/trial= -1.86962 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 2 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 8.53 trans_mag: 4.265 protocols.moves.TrialCounter: frag 3 trials= 58; accepts= 0.0862; energy_drop/trial= -59.89691 protocols.moves.TrialCounter: rigid_body trials= 34; accepts= 0.0588; energy_drop/trial= -1.51646 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 3 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.795 trans_mag: 3.8975 protocols.moves.TrialCounter: frag 3 trials= 59; accepts= 0.0169; energy_drop/trial= -0.15497 protocols.moves.TrialCounter: rigid_body trials= 37; accepts= 0.0270; energy_drop/trial= -0.03469 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 4 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 2 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 7.06 trans_mag: 3.53 protocols.moves.TrialCounter: frag 2 trials= 42; accepts= 0.1190; energy_drop/trial= -52.29933 protocols.moves.TrialCounter: rigid_body trials= 44; accepts= 0.1136; energy_drop/trial= -5.15271 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 5 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 6.325 trans_mag: 3.1625 protocols.moves.TrialCounter: frag 2 trials= 55; accepts= 0.0182; energy_drop/trial= -0.52811 protocols.moves.TrialCounter: rigid_body trials= 37 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 6 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 5.59 trans_mag: 2.795 protocols.moves.TrialCounter: frag 2 trials= 47; accepts= 0.0426; energy_drop/trial= -1.85582 protocols.moves.TrialCounter: rigid_body trials= 37 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 7 of 10 protocols.rna.denovo.RNA_FragmentMonteCarlo: Fragment size: 1 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.855 trans_mag: 2.4275 protocols.moves.TrialCounter: frag 1 trials= 54; accepts= 0.1111; energy_drop/trial= -14.86015 protocols.moves.TrialCounter: rigid_body trials= 36 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 8 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 4.12 trans_mag: 2.06 protocols.moves.TrialCounter: frag 1 trials= 57 NO ACCEPTS. protocols.moves.TrialCounter: rigid_body trials= 32 NO ACCEPTS. protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 9 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 3.385 trans_mag: 1.6925 protocols.moves.TrialCounter: frag 1 trials= 48; accepts= 0.0625; energy_drop/trial= -6.39176 protocols.moves.TrialCounter: rigid_body trials= 36; accepts= 0.0556; energy_drop/trial= -0.51830 protocols.rna.denovo.RNA_FragmentMonteCarlo: Beginning round 10 of 10 protocols.rna.denovo.movers.RNA_DeNovoMasterMover: rot_mag: 2.65 trans_mag: 1.325 protocols.moves.TrialCounter: frag 1 trials= 46; accepts= 0.0217; energy_drop/trial= -0.07225 protocols.moves.TrialCounter: rigid_body trials= 41; accepts= 0.0244; energy_drop/trial= -0.23823 protocols.rna.denovo.RNA_FragmentMonteCarlo: Finished fragment assembly of in 14 seconds. protocols.rna.denovo.RNA_FragmentMonteCarlo: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ rna_data_backbone 2.000 0.000 0.000 rna_vdw 2.000 321.209 642.418 rnp_vdw 50.000 0.073 3.658 rna_base_backbone 2.000 -12.287 -24.574 rna_backbone_backbone 2.000 -1.563 -3.126 rna_repulsive 5.000 49.922 249.612 rna_base_pair 2.000 -38.018 -76.035 rna_base_axis 0.400 -19.134 -7.654 rna_base_stagger 2.000 -14.045 -28.091 rna_base_stack 2.000 -5.510 -11.020 rna_base_stack_axis 0.400 -26.591 -10.637 rnp_base_pair 2.000 -16.880 -33.760 rnp_stack 5.000 0.000 0.000 rnp_pair_dist 0.200 -248.280 -49.656 rnp_aa_to_rna_backbone 1.000 -21.233 -21.233 rna_rg 0.500 15.366 7.683 atom_pair_constraint 1.000 0.000 0.000 base_pair_constraint 1.000 3763.565 3763.565 linear_chainbreak 8.000 17.701 141.605 --------------------------------------------------- Total weighted score: 4542.756 protocols.rna.denovo.RNA_FragmentMonteCarlo: core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. protocols.jd2.JobDistributor: S_000005 reported success in 15 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 5 jobs considered, 5 jobs attempted in 77 seconds