Branch: rosetta:main 「revision: №62162」
Test: ubuntu.gcc.integration.addsan
SubTest: rna_motif
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: rna_motif

LogFile log ******** (C) Copyright Rosetta Commons Member Institutions. *************** * Use of Rosetta for commercial purposes may require purchase of a license. * ******** See LICENSE.md or email license@uw.edu for more details. ********** core.init: Rosetta extras: [] core.init: command: /home/benchmark/rosetta/source/bin/rna_motif.default.linuxgccaddsan -in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/ubuntugccaddsan @flags -database /home/benchmark/rosetta/database -testing:INTEGRATION_TEST basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 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 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/rna/rna_atom_vdw.txt basic.io.database: Database file opened: scoring/rna/rnp_atom_vdw_min_distances_reformat_MIN.txt core.scoring.ScoringManager: Reading in: /home/benchmark/rosetta/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.import_pose.import_pose: File '1Q9A.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue U core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for H5' and H5'' for residue C core.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything. rna_motif: Created: 1Q9A.pdb.ligands.txt 1Q9A.pdb U_TURN: g-A:2659 a-A:2660 g-A:2661 PLATFORM: g-A:2655 u-A:2656 a-A:2657 g-A:2664 LOOP_E_SUBMOTIF: g-A:2663 g-A:2664 a-A:2665 u-A:2656 a-A:2657 c-A:2658 BULGED_G: g-A:2663 g-A:2664 a-A:2665 g-A:2655 u-A:2656 a-A:2657 c-A:2658 rna_motif: Created: 1Q9A.pdb.base_pairs.txt rna_motif: Created: 1Q9A.pdb.stacks.txt rna_motif: Created: 1Q9A.pdb.other_contacts.txt rna_motif: Created: 1Q9A.pdb.stems.txt rna_motif: Created: 1Q9A.pdb.motifs.txt rna_motif: Created: 1Q9A.pdb.fasta core.import_pose.import_pose: File '1ehz.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1 in file 1ehz.pdb. Best match rsd_type: RGU:LowerRNA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom OP3 (trying to store temperature in PDBInfo) rna_motif: Created: 1ehz.pdb.ligands.txt 1ehz.pdb U_TURN: u-A:33 X[OMG]-A:34 a-A:35 U_TURN: X[PSU]-A:55 c-A:56 g-A:57 UA_HANDLE: g-A:53 X[5MU]-A:54 X[1MA]-A:58 c-A:61 T_LOOP: g-A:53 X[5MU]-A:54 X[PSU]-A:55 c-A:56 g-A:57 X[1MA]-A:58 c-A:61 INTERCALATED_T_LOOP: g-A:53 X[5MU]-A:54 X[PSU]-A:55 c-A:56 g-A:57 X[1MA]-A:58 c-A:61 g-A:18 rna_motif: Created: 1ehz.pdb.base_pairs.txt rna_motif: Created: 1ehz.pdb.stacks.txt rna_motif: Created: 1ehz.pdb.other_contacts.txt rna_motif: Created: 1ehz.pdb.stems.txt rna_motif: Created: 1ehz.pdb.motifs.txt rna_motif: Created: 1ehz.pdb.fasta core.import_pose.import_pose: File '1ehz_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 74, 74 A core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1 in file 1ehz_RNA.pdb. Best match rsd_type: RGU:LowerRNA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 10 in file 1ehz_RNA.pdb. Best match rsd_type: RGU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 26 in file 1ehz_RNA.pdb. Best match rsd_type: RGU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 32 in file 1ehz_RNA.pdb. Best match rsd_type: RCY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 34 in file 1ehz_RNA.pdb. Best match rsd_type: RGU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 16 atoms at position 37 in file 1ehz_RNA.pdb. Best match rsd_type: RGU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 39 in file 1ehz_RNA.pdb. Best match rsd_type: RCY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 45 in file 1ehz_RNA.pdb. Best match rsd_type: RGU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 48 in file 1ehz_RNA.pdb. Best match rsd_type: RCY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 53 in file 1ehz_RNA.pdb. Best match rsd_type: URA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 56 in file 1ehz_RNA.pdb. Best match rsd_type: RAD core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom OP3 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 10 atom CM2 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 26 atom CM1 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 26 atom CM2 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 32 atom CM2 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 34 atom CM2 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C10 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C11 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C12 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C13 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C14 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C15 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C16 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C19 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C21 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C24 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom C3 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom N20 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom O17 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom O18 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom O22 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom O23 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 39 atom CM5 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 45 atom CM7 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 48 atom CM5 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 53 atom C5M (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 56 atom CM1 (trying to store temperature in PDBInfo) rna_motif: Created: 1ehz_RNA.pdb.ligands.txt 1ehz_RNA.pdb U_TURN: u-A:33 g-A:34 a-A:35 UA_HANDLE: g-A:52 u-A:53 a-A:56 c-A:59 rna_motif: Created: 1ehz_RNA.pdb.base_pairs.txt rna_motif: Created: 1ehz_RNA.pdb.stacks.txt rna_motif: Created: 1ehz_RNA.pdb.other_contacts.txt rna_motif: Created: 1ehz_RNA.pdb.stems.txt rna_motif: Created: 1ehz_RNA.pdb.motifs.txt rna_motif: Created: 1ehz_RNA.pdb.fasta core.import_pose.import_pose: File '1fmn_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1 in file 1fmn_RNA.pdb. Best match rsd_type: RGU:LowerRNA:5prime_end_OH core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom OP3 (trying to store temperature in PDBInfo) rna_motif: Created: 1fmn_RNA.pdb.ligands.txt 1fmn_RNA.pdb LOOP_E_SUBMOTIF: a-A:23 g-A:24 a-A:25 u-A:12 a-A:13 u-A:14 BULGED_G: a-A:23 g-A:24 a-A:25 g-A:10 u-A:12 a-A:13 u-A:14 Z_TURN: u-A:17 u-A:18 c-A:19 g-A:20 rna_motif: Created: 1fmn_RNA.pdb.base_pairs.txt rna_motif: Created: 1fmn_RNA.pdb.stacks.txt rna_motif: Created: 1fmn_RNA.pdb.other_contacts.txt rna_motif: Created: 1fmn_RNA.pdb.stems.txt rna_motif: Created: 1fmn_RNA.pdb.motifs.txt rna_motif: Created: 1fmn_RNA.pdb.fasta core.import_pose.import_pose: File '1gid_RNA.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: 1gid_RNA.pdb.ligands.txt 1gid_RNA.pdb U_TURN: g-A:150 a-A:151 a-A:152 UA_HANDLE: g-A:134 u-A:135 a-A:187 c-A:189 UA_HANDLE: a-A:196 c-A:197 c-A:124 g-A:126 UA_HANDLE: c-A:223 u-A:224 a-A:248 g-A:250 GNRA_TETRALOOP: g-A:150 a-A:151 a-A:152 a-A:153 A_MINOR: a-A:153 g-A:250 c-A:223 A_MINOR: a-A:183 g-A:110 c-A:211 PLATFORM: a-A:225 a-A:226 g-A:227 u-A:247 PLATFORM: a-A:171 a-A:172 a-A:173 u-A:167 TL_RECEPTOR: c-A:222 c-A:223 u-A:224 a-A:225 a-A:226 g-A:227 u-A:247 a-A:248 g-A:250 g-A:251 TETRALOOP_TL_RECEPTOR: g-A:150 a-A:151 a-A:152 a-A:153 c-A:222 c-A:223 u-A:224 a-A:225 a-A:226 g-A:227 u-A:247 a-A:248 g-A:250 g-A:251 rna_motif: Created: 1gid_RNA.pdb.base_pairs.txt rna_motif: Created: 1gid_RNA.pdb.stacks.txt rna_motif: Created: 1gid_RNA.pdb.other_contacts.txt rna_motif: Created: 1gid_RNA.pdb.stems.txt rna_motif: Created: 1gid_RNA.pdb.motifs.txt rna_motif: Created: 1gid_RNA.pdb.fasta core.import_pose.import_pose: File '1raw_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 37 in file 1raw_RNA.pdb. Best match rsd_type: RAD:UpperRNA:3prime_end_OH core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 37 atom O3P (trying to store temperature in PDBInfo) rna_motif: Created: 1raw_RNA.pdb.ligands.txt 1raw_RNA.pdb UA_HANDLE: g-A:6 g-A:7 g-A:11 c-A:31 Z_TURN: u-A:22 u-A:23 c-A:24 g-A:25 rna_motif: Created: 1raw_RNA.pdb.base_pairs.txt rna_motif: Created: 1raw_RNA.pdb.stacks.txt rna_motif: Created: 1raw_RNA.pdb.other_contacts.txt rna_motif: Created: 1raw_RNA.pdb.stems.txt rna_motif: Created: 1raw_RNA.pdb.motifs.txt rna_motif: Created: 1raw_RNA.pdb.fasta core.import_pose.import_pose: File '1xjr_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 47, 47 A core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 12 atoms at position 1 in file 1xjr_RNA.pdb. Best match rsd_type: RGU:LowerRNA:Virtual_Phosphate core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PA (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PB (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PG (trying to store temperature in PDBInfo) rna_motif: Created: 1xjr_RNA.pdb.ligands.txt 1xjr_RNA.pdb U_TURN: g-A:22 a-A:23 g-A:24 GNRA_TETRALOOP: g-A:22 a-A:23 g-A:24 a-A:26 PLATFORM: a-A:38 c-A:39 a-A:40 c-A:10 rna_motif: Created: 1xjr_RNA.pdb.base_pairs.txt rna_motif: Created: 1xjr_RNA.pdb.stacks.txt rna_motif: Created: 1xjr_RNA.pdb.other_contacts.txt rna_motif: Created: 1xjr_RNA.pdb.stems.txt rna_motif: Created: 1xjr_RNA.pdb.motifs.txt rna_motif: Created: 1xjr_RNA.pdb.fasta core.import_pose.import_pose: File '2gis_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 94, 94 A core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1 in file 2gis_RNA.pdb. Best match rsd_type: RGU:LowerRNA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom OP3 (trying to store temperature in PDBInfo) rna_motif: Created: 2gis_RNA.pdb.ligands.txt 2gis_RNA.pdb U_TURN: g-A:50 a-A:51 a-A:52 U_TURN: g-A:74 a-A:75 a-A:76 GNRA_TETRALOOP: g-A:50 a-A:51 a-A:52 a-A:53 GNRA_TETRALOOP: g-A:74 a-A:75 a-A:76 a-A:77 A_MINOR: a-A:61 c-A:30 g-A:22 TANDEM_GA_SHEARED: g-A:19 a-A:20 g-A:35 a-A:36 rna_motif: Created: 2gis_RNA.pdb.base_pairs.txt rna_motif: Created: 2gis_RNA.pdb.stacks.txt rna_motif: Created: 2gis_RNA.pdb.other_contacts.txt rna_motif: Created: 2gis_RNA.pdb.stems.txt rna_motif: Created: 2gis_RNA.pdb.motifs.txt rna_motif: Created: 2gis_RNA.pdb.fasta core.import_pose.import_pose: File '2lx1_RNA.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: 2lx1_RNA.pdb.ligands.txt 2lx1_RNA.pdb rna_motif: Created: 2lx1_RNA.pdb.base_pairs.txt rna_motif: Created: 2lx1_RNA.pdb.stacks.txt rna_motif: Created: 2lx1_RNA.pdb.other_contacts.txt rna_motif: Created: 2lx1_RNA.pdb.stems.txt rna_motif: Created: 2lx1_RNA.pdb.motifs.txt rna_motif: Created: 2lx1_RNA.pdb.fasta core.import_pose.import_pose: File '2oeu_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 12 atoms at position 1 in file 2oeu_RNA.pdb. Best match rsd_type: RGU:LowerRNA:Virtual_Phosphate core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 49 in file 2oeu_RNA.pdb. Best match rsd_type: RCY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 54 in file 2oeu_RNA.pdb. Best match rsd_type: URA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PA (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PB (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PG (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 49 atom CM2 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 54 atom BR (trying to store temperature in PDBInfo) rna_motif: Created: 2oeu_RNA.pdb.ligands.txt 2oeu_RNA.pdb U_TURN: u-A:16 g-A:17 a-A:18 UA_HANDLE: g-A:5 u-A:6 a-A:28 c-B:14 UA_HANDLE: a-B:12 u-B:13 a-A:31 u-A:9 rna_motif: Created: 2oeu_RNA.pdb.base_pairs.txt rna_motif: Created: 2oeu_RNA.pdb.stacks.txt rna_motif: Created: 2oeu_RNA.pdb.other_contacts.txt rna_motif: Created: 2oeu_RNA.pdb.stems.txt rna_motif: Created: 2oeu_RNA.pdb.motifs.txt rna_motif: Created: 2oeu_RNA.pdb.fasta core.import_pose.import_pose: File '3f2q_RNA_with_FMN.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 109, 112 X core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 12 atoms at position 1 in file 3f2q_RNA_with_FMN.pdb. Best match rsd_type: RGU:LowerRNA:Virtual_Phosphate core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 109 in file 3f2q_RNA_with_FMN.pdb. Best match rsd_type: RCY:UpperRNA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 20 atoms at position 124 in file 3f2q_RNA_with_FMN.pdb. Best match rsd_type: FMN core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O6 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C16 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C11 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C12 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C13 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C14 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C15 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: N2 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: C17 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue FMN 124 core.conformation.Conformation: [ WARNING ] missing heavyatom: O9 on residue FMN 124 core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O1G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O2G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3B (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom O3G (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PA (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PB (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom PG (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 109 atom O1C (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 109 atom O2C (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 109 atom PC (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C1' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C3' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C4' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C4A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C5' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C5A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C7M (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C8M (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom C9A (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom N10 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom N5 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O1P (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O2' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O2P (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O3' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O3P (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O4' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom O5' (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 124 atom P (trying to store temperature in PDBInfo) core.pack.pack_missing_sidechains: packing residue number 124 because of missing atom number 2 atom name C3 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 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/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.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 core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for FMN core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 124 FMN core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: Z, best_energy: 821.998 rna_motif: Created: 3f2q_RNA_with_FMN.pdb.ligands.txt 3f2q_RNA_with_FMN.pdb U_TURN: g-X:19 a-X:20 a-X:21 U_TURN: g-X:70 a-X:71 a-X:72 UA_HANDLE: g-X:17 u-X:18 a-X:22 c-X:25 UA_HANDLE: g-X:36 u-X:37 a-X:40 c-X:43 UA_HANDLE: g-X:68 u-X:69 a-X:73 c-X:76 UA_HANDLE: g-X:88 u-X:89 a-X:92 c-X:95 T_LOOP: g-X:17 u-X:18 g-X:19 a-X:20 a-X:21 a-X:22 c-X:25 T_LOOP: g-X:68 u-X:69 g-X:70 a-X:71 a-X:72 a-X:73 c-X:76 INTERCALATED_T_LOOP: g-X:17 u-X:18 g-X:19 a-X:20 a-X:21 a-X:22 c-X:25 a-X:90 INTERCALATED_T_LOOP: g-X:68 u-X:69 g-X:70 a-X:71 a-X:72 a-X:73 c-X:76 a-X:38 rna_motif: Created: 3f2q_RNA_with_FMN.pdb.base_pairs.txt rna_motif: Created: 3f2q_RNA_with_FMN.pdb.stacks.txt rna_motif: Created: 3f2q_RNA_with_FMN.pdb.other_contacts.txt rna_motif: Created: 3f2q_RNA_with_FMN.pdb.stems.txt rna_motif: Created: 3f2q_RNA_with_FMN.pdb.motifs.txt rna_motif: Created: 3f2q_RNA_with_FMN.pdb.fasta core.import_pose.import_pose: File '3l0u_RNA.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 73, 73 A core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1 in file 3l0u_RNA.pdb. Best match rsd_type: RGU:LowerRNA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom OP3 (trying to store temperature in PDBInfo) rna_motif: Created: 3l0u_RNA.pdb.ligands.txt 3l0u_RNA.pdb U_TURN: u-A:33 g-A:34 a-A:35 U_TURN: u-A:55 c-A:56 g-A:57 UA_HANDLE: g-A:53 u-A:54 a-A:58 c-A:61 T_LOOP: g-A:53 u-A:54 u-A:55 c-A:56 g-A:57 a-A:58 c-A:61 INTERCALATED_T_LOOP: g-A:53 u-A:54 u-A:55 c-A:56 g-A:57 a-A:58 c-A:61 g-A:18 rna_motif: Created: 3l0u_RNA.pdb.base_pairs.txt rna_motif: Created: 3l0u_RNA.pdb.stacks.txt rna_motif: Created: 3l0u_RNA.pdb.other_contacts.txt rna_motif: Created: 3l0u_RNA.pdb.stems.txt rna_motif: Created: 3l0u_RNA.pdb.motifs.txt rna_motif: Created: 3l0u_RNA.pdb.fasta core.import_pose.import_pose: File '3p49_native_RNA.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: 3p49_native_RNA.pdb.ligands.txt 3p49_native_RNA.pdb U_TURN: u-A:22 u-A:23 u-A:24 UA_HANDLE: g-A:42 u-A:43 a-A:46 c-A:48 UA_HANDLE: g-A:117 c-A:118 a-A:137 c-A:139 A_MINOR: a-A:44 g-A:157 c-A:83 A_MINOR: a-A:45 g-A:156 u-A:84 A_MINOR: a-A:119 a-A:8 u-A:66 A_MINOR: a-A:120 g-A:7 c-A:67 rna_motif: Created: 3p49_native_RNA.pdb.base_pairs.txt rna_motif: Created: 3p49_native_RNA.pdb.stacks.txt rna_motif: Created: 3p49_native_RNA.pdb.other_contacts.txt rna_motif: Created: 3p49_native_RNA.pdb.stems.txt rna_motif: Created: 3p49_native_RNA.pdb.motifs.txt rna_motif: Created: 3p49_native_RNA.pdb.fasta core.import_pose.import_pose: File '3P49_erraser.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 181, 746 A core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file 3P49_erraser.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 189 in file 3P49_erraser.pdb. Best match rsd_type: HIS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 210 in file 3P49_erraser.pdb. Best match rsd_type: HIS core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLY 180. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 180 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 276 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 180 with connection point 1 core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 180 atom OXT (trying to store temperature in PDBInfo) rna_motif: Created: 3P49_erraser.pdb.ligands.txt 3P49_erraser.pdb UA_HANDLE: g-A:41 u-A:42 a-A:45 c-A:47 UA_HANDLE: a-A:105 c-A:106 g-A:89 u-A:91 UA_HANDLE: g-A:116 c-A:117 a-A:136 c-A:138 A_MINOR: a-A:43 g-A:156 c-A:82 A_MINOR: a-A:44 g-A:155 u-A:83 A_MINOR: a-A:118 a-A:7 u-A:65 A_MINOR: a-A:135 u-A:65 a-A:7 PLATFORM: u-A:50 c-A:51 a-A:52 g-A:35 PLATFORM: u-A:141 c-A:142 a-A:143 g-A:110 GA_MINOR: a-A:43 c-A:47 g-A:41 u-A:42 a-A:43 rna_motif: Created: 3P49_erraser.pdb.base_pairs.txt rna_motif: Created: 3P49_erraser.pdb.stacks.txt rna_motif: Created: 3P49_erraser.pdb.other_contacts.txt rna_motif: Created: 3P49_erraser.pdb.stems.txt rna_motif: Created: 3P49_erraser.pdb.motifs.txt rna_motif: Created: 3P49_erraser.pdb.fasta core.import_pose.import_pose: File '4lck_tbox_RNABC.pdb' automatically determined to be of type PDB from contents. core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 177, 102 C core.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue URA 12 core.conformation.Conformation: [ WARNING ] missing heavyatom: N1 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: C2 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: N3 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: C4 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: C5 on residue URA 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: C6 on residue URA 42 core.pack.pack_missing_sidechains: packing residue number 12 because of missing atom number 13 atom name N1 core.pack.pack_missing_sidechains: packing residue number 42 because of missing atom number 13 atom name N1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 12 URA core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 42 URA core.pack.pack_rotamers: built 2 rotamers at 2 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: uu, best_energy: 2013.42 rna_motif: Created: 4lck_tbox_RNABC.pdb.ligands.txt 4lck_tbox_RNABC.pdb U_TURN: u-B:54 c-B:55 g-B:56 U_TURN: g-B:72 a-B:73 a-B:74 U_TURN: g-C:43 c-C:44 g-C:45 U_TURN: g-C:59 a-C:60 a-C:61 UA_HANDLE: g-B:52 u-B:53 a-B:57 c-B:60 UA_HANDLE: g-C:57 u-C:58 a-C:62 g-C:45 T_LOOP: g-B:52 u-B:53 u-B:54 c-B:55 g-B:56 a-B:57 c-B:60 T_LOOP: g-C:57 u-C:58 g-C:59 a-C:60 a-C:61 a-C:62 g-C:45 INTERCALATED_T_LOOP: g-B:52 u-B:53 u-B:54 c-B:55 g-B:56 a-B:57 c-B:60 g-B:17 INTERCALATED_T_LOOP: g-C:57 u-C:58 g-C:59 a-C:60 a-C:61 a-C:62 g-C:45 a-C:46 PLATFORM: g-C:20 u-C:21 a-C:22 g-C:84 LOOP_E_SUBMOTIF: a-C:83 g-C:84 a-C:85 u-C:21 a-C:22 u-C:23 BULGED_G: a-C:83 g-C:84 a-C:85 g-C:20 u-C:21 a-C:22 u-C:23 TANDEM_GA_SHEARED: g-C:10 a-C:11 g-C:95 a-C:96 rna_motif: Created: 4lck_tbox_RNABC.pdb.base_pairs.txt rna_motif: Created: 4lck_tbox_RNABC.pdb.stacks.txt rna_motif: Created: 4lck_tbox_RNABC.pdb.other_contacts.txt rna_motif: Created: 4lck_tbox_RNABC.pdb.stems.txt rna_motif: Created: 4lck_tbox_RNABC.pdb.motifs.txt rna_motif: Created: 4lck_tbox_RNABC.pdb.fasta core.import_pose.import_pose: File 'chunk002_1lnt_RNA.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: chunk002_1lnt_RNA.pdb.ligands.txt chunk002_1lnt_RNA.pdb LOOP_E_SUBMOTIF: u-A:1 c-A:2 a-A:3 c-A:10 a-A:11 g-A:12 rna_motif: Created: chunk002_1lnt_RNA.pdb.base_pairs.txt rna_motif: Created: chunk002_1lnt_RNA.pdb.stacks.txt rna_motif: Created: chunk002_1lnt_RNA.pdb.other_contacts.txt rna_motif: Created: chunk002_1lnt_RNA.pdb.stems.txt rna_motif: Created: chunk002_1lnt_RNA.pdb.motifs.txt rna_motif: Created: chunk002_1lnt_RNA.pdb.fasta core.import_pose.import_pose: File '11-nt-ac_model1.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: 11-nt-ac_model1.pdb.ligands.txt 11-nt-ac_model1.pdb U_TURN: g-A:2 a-A:3 a-A:4 UA_HANDLE: c-A:8 u-A:9 a-A:18 g-A:20 GNRA_TETRALOOP: g-A:2 a-A:3 a-A:4 a-A:5 A_MINOR: a-A:5 g-A:20 c-A:8 PLATFORM: a-A:10 c-A:11 g-A:12 u-A:17 TL_RECEPTOR: c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 a-A:10 c-A:11 g-A:12 u-A:17 a-A:18 g-A:20 g-A:21 TETRALOOP_TL_RECEPTOR: g-A:2 a-A:3 a-A:4 a-A:5 c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 a-A:10 c-A:11 g-A:12 u-A:17 a-A:18 g-A:20 g-A:21 rna_motif: Created: 11-nt-ac_model1.pdb.base_pairs.txt rna_motif: Created: 11-nt-ac_model1.pdb.stacks.txt rna_motif: Created: 11-nt-ac_model1.pdb.other_contacts.txt rna_motif: Created: 11-nt-ac_model1.pdb.stems.txt rna_motif: Created: 11-nt-ac_model1.pdb.motifs.txt rna_motif: Created: 11-nt-ac_model1.pdb.fasta core.import_pose.import_pose: File '11-nt_model1.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: 11-nt_model1.pdb.ligands.txt 11-nt_model1.pdb U_TURN: g-A:2 a-A:3 a-A:4 UA_HANDLE: c-A:8 u-A:9 a-A:18 g-A:20 GNRA_TETRALOOP: g-A:2 a-A:3 a-A:4 a-A:5 A_MINOR: a-A:5 g-A:20 c-A:8 PLATFORM: a-A:10 a-A:11 g-A:12 u-A:17 TL_RECEPTOR: c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 a-A:10 a-A:11 g-A:12 u-A:17 a-A:18 g-A:20 g-A:21 TETRALOOP_TL_RECEPTOR: g-A:2 a-A:3 a-A:4 a-A:5 c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 a-A:10 a-A:11 g-A:12 u-A:17 a-A:18 g-A:20 g-A:21 rna_motif: Created: 11-nt_model1.pdb.base_pairs.txt rna_motif: Created: 11-nt_model1.pdb.stacks.txt rna_motif: Created: 11-nt_model1.pdb.other_contacts.txt rna_motif: Created: 11-nt_model1.pdb.stems.txt rna_motif: Created: 11-nt_model1.pdb.motifs.txt rna_motif: Created: 11-nt_model1.pdb.fasta core.import_pose.import_pose: File 'R1_model1.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: R1_model1.pdb.ligands.txt R1_model1.pdb U_TURN: g-A:2 g-A:3 a-A:4 GNRA_TETRALOOP: g-A:2 g-A:3 a-A:4 a-A:5 A_MINOR: a-A:5 g-A:21 c-A:8 PLATFORM: g-A:10 u-A:11 g-A:12 a-A:17 TL_RECEPTOR: c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 g-A:10 u-A:11 g-A:12 a-A:17 u-A:20 g-A:21 g-A:22 TETRALOOP_TL_RECEPTOR: g-A:2 g-A:3 a-A:4 a-A:5 c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 g-A:10 u-A:11 g-A:12 a-A:17 u-A:20 g-A:21 g-A:22 rna_motif: Created: R1_model1.pdb.base_pairs.txt rna_motif: Created: R1_model1.pdb.stacks.txt rna_motif: Created: R1_model1.pdb.other_contacts.txt rna_motif: Created: R1_model1.pdb.stems.txt rna_motif: Created: R1_model1.pdb.motifs.txt rna_motif: Created: R1_model1.pdb.fasta core.import_pose.import_pose: File 'c7.10_model1.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: c7.10_model1.pdb.ligands.txt c7.10_model1.pdb U_TURN: g-A:2 a-A:3 a-A:4 UA_HANDLE: c-A:8 u-A:9 a-A:18 g-A:20 GNRA_TETRALOOP: g-A:2 a-A:3 a-A:4 a-A:5 A_MINOR: a-A:5 g-A:20 c-A:8 PLATFORM: g-A:10 u-A:11 g-A:12 u-A:17 TL_RECEPTOR: c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 g-A:10 u-A:11 g-A:12 u-A:17 a-A:18 g-A:20 g-A:21 TETRALOOP_TL_RECEPTOR: g-A:2 a-A:3 a-A:4 a-A:5 c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 g-A:10 u-A:11 g-A:12 u-A:17 a-A:18 g-A:20 g-A:21 rna_motif: Created: c7.10_model1.pdb.base_pairs.txt rna_motif: Created: c7.10_model1.pdb.stacks.txt rna_motif: Created: c7.10_model1.pdb.other_contacts.txt rna_motif: Created: c7.10_model1.pdb.stems.txt rna_motif: Created: c7.10_model1.pdb.motifs.txt rna_motif: Created: c7.10_model1.pdb.fasta core.import_pose.import_pose: File 'c7.2_model1.pdb' automatically determined to be of type PDB from contents. rna_motif: Created: c7.2_model1.pdb.ligands.txt c7.2_model1.pdb U_TURN: g-A:2 a-A:3 a-A:4 UA_HANDLE: c-A:8 u-A:9 a-A:19 g-A:21 GNRA_TETRALOOP: g-A:2 a-A:3 a-A:4 a-A:5 A_MINOR: a-A:5 g-A:21 c-A:8 PLATFORM: g-A:10 a-A:12 c-A:13 g-A:18 TL_RECEPTOR: c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 g-A:10 a-A:12 c-A:13 g-A:18 a-A:19 g-A:21 g-A:22 TETRALOOP_TL_RECEPTOR: g-A:2 a-A:3 a-A:4 a-A:5 c[RCY:Virtual_Phosphate]-A:7 c-A:8 u-A:9 g-A:10 a-A:12 c-A:13 g-A:18 a-A:19 g-A:21 g-A:22 rna_motif: Created: c7.2_model1.pdb.base_pairs.txt rna_motif: Created: c7.2_model1.pdb.stacks.txt rna_motif: Created: c7.2_model1.pdb.other_contacts.txt rna_motif: Created: c7.2_model1.pdb.stems.txt rna_motif: Created: c7.2_model1.pdb.motifs.txt rna_motif: Created: c7.2_model1.pdb.fasta rna_motif: Created: color_motifs.pml