core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: command: rosetta_scripts.linuxgccrelease @ ../../flags/4TSYout_relax.flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=230419043 seed_offset=0 real_seed=230419043 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=230419043 RG_type=mt19937 core.init: Resolved executable path: /home/miguel/Programs/rosetta_src_2021.16.61629_bundle/main/source/build/src/release/linux/5.15/64/x86/gcc/10/default/rosetta_scripts.default.linuxgccrelease core.init: Looking for database based on location of executable: /home/miguel/Programs/rosetta_src_2021.16.61629_bundle/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed ../../input_models/4TSYout.pdb nstruct indices 1 - 100 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB ../../input_models/4TSYout.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.405353 seconds. core.import_pose.import_pose: File '../../input_models/4TSYout.pdb' automatically determined to be of type PDB 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/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/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 basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/miguel/Programs/rosetta_src_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/miguel/Programs/rosetta_src_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.10407 seconds to load from binary core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 4472 rotamers at 1408 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.io.pdb.file_data: [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 236 HIS HIS core.io.pdb.file_data: [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 518 HIS HIS core.io.pdb.file_data: [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 940 HIS HIS core.io.pdb.file_data: [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 2 position: 1222 HIS HIS protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=../../xml/4TSYout_relax.xml protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: 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/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt 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 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. core.scoring.etable: Using alternate parameters: LK_DGFREE in MembEtable construction. core.scoring.etable: Using alternate parameters: MEMB_LK_DGFREE in MembEtable construction. core.scoring.etable: Using alternate parameters: LK_DGREFCE in MembEtable construction. core.scoring.etable: Using alternate parameters: MEMB_LK_DGREFCE in MembEtable construction. core.scoring.etable: Starting membrane specific energy table calculation core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating membrane specific energy tables. basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_Menv_smooth_log.txt protocols.jd2.parser.ScoreFunctionLoader: defined score function "mpframework_smooth_fa_2012" with weights "mpframework_smooth_fa_2012" protocols.membrane.AddMembraneMover: [ WARNING ] Spanfile not given, topology will be created from PDB! protocols.membrane.AddMembraneMover: [ WARNING ] Make sure your PDB is transformed into membrane coordinates!!! protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "addMembraneMover" of type AddMembraneMover protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "init" of type MembranePositionFromTopologyMover protocols.relax.RelaxScriptManager: Reading relax scripts list from database. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt protocols.relax.RelaxScriptManager: ================== Reading script file: /home/miguel/Programs/rosetta_src_2021.16.61629_bundle/main/database/sampling/relax_scripts/MonomerRelax2019.txt ================== protocols.relax.RelaxScriptManager: repeat %%nrepeats%% protocols.relax.RelaxScriptManager: coord_cst_weight 1.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.040 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.051 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.5 protocols.relax.RelaxScriptManager: scale:fa_rep 0.265 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.280 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.559 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.581 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 1 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: min 0.00001 protocols.relax.RelaxScriptManager: accept_to_best protocols.relax.RelaxScriptManager: endrepeat protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "fastRelax" of type FastRelax protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings protocols.rosetta_scripts.ParsedProtocol: Added mover "addMembraneMover" protocols.rosetta_scripts.ParsedProtocol: Added mover "init" protocols.rosetta_scripts.ParsedProtocol: Added mover "fastRelax" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ../../input_models/4TSYout.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddMembraneMover - addMembraneMover======================= protocols.membrane.AddMembraneMover: ===================================================================== protocols.membrane.AddMembraneMover: || WELCOME TO THE WORLD OF MEMBRANE PROTEINS... || protocols.membrane.AddMembraneMover: ===================================================================== protocols.membrane.AddMembraneMover: No membrane residue was found protocols.membrane.AddMembraneMover: Adding a new membrane residue to the pose protocols.membrane.AddMembraneMover: Adding a membrane residue representing the position of the membrane after residue 1408 core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MEM' from the PDB components dictionary for residue type 'pdb_MEM' protocols.membrane.AddMembraneMover: Edge Jump Jump # 1409--0001 008 0001--0176 0001--0177 001 0177--0352 0001--0353 002 0353--0528 0001--0529 003 0529--0704 0001--0705 004 0705--0880 0001--0881 005 0881--1056 0001--1057 006 1057--1232 0001--1233 007 1233--1408 protocols.DsspMover: LLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELL core.conformation.membrane.SpanningTopology: Filling membrane spanning topology from structure with thickness 15 core.conformation.membrane.SpanningTopology: create topology from structure core.conformation.membrane.SpanningTopology: TMspan start at 3 core.conformation.membrane.SpanningTopology: TMspan end at 22 core.conformation.membrane.SpanningTopology: prev_end: 0, end: 22 core.conformation.membrane.SpanningTopology: Adding TMspan from 3 to 22 core.conformation.membrane.SpanningTopology: TMspan start at 179 core.conformation.membrane.SpanningTopology: TMspan end at 198 core.conformation.membrane.SpanningTopology: prev_end: 22, end: 198 core.conformation.membrane.SpanningTopology: Adding TMspan from 179 to 198 core.conformation.membrane.SpanningTopology: TMspan start at 355 core.conformation.membrane.SpanningTopology: TMspan end at 375 core.conformation.membrane.SpanningTopology: prev_end: 198, end: 375 core.conformation.membrane.SpanningTopology: Adding TMspan from 355 to 375 core.conformation.membrane.SpanningTopology: TMspan start at 531 core.conformation.membrane.SpanningTopology: TMspan end at 551 core.conformation.membrane.SpanningTopology: prev_end: 375, end: 551 core.conformation.membrane.SpanningTopology: Adding TMspan from 531 to 551 core.conformation.membrane.SpanningTopology: TMspan start at 707 core.conformation.membrane.SpanningTopology: TMspan end at 726 core.conformation.membrane.SpanningTopology: prev_end: 551, end: 726 core.conformation.membrane.SpanningTopology: Adding TMspan from 707 to 726 core.conformation.membrane.SpanningTopology: TMspan start at 883 core.conformation.membrane.SpanningTopology: TMspan end at 902 core.conformation.membrane.SpanningTopology: prev_end: 726, end: 902 core.conformation.membrane.SpanningTopology: Adding TMspan from 883 to 902 core.conformation.membrane.SpanningTopology: TMspan start at 1059 core.conformation.membrane.SpanningTopology: TMspan end at 1079 core.conformation.membrane.SpanningTopology: prev_end: 902, end: 1079 core.conformation.membrane.SpanningTopology: Adding TMspan from 1059 to 1079 core.conformation.membrane.SpanningTopology: TMspan start at 1235 core.conformation.membrane.SpanningTopology: TMspan end at 1255 core.conformation.membrane.SpanningTopology: prev_end: 1079, end: 1255 core.conformation.membrane.SpanningTopology: Adding TMspan from 1235 to 1255 core.conformation.membrane.SpanningTopology: Total # of TM spans: 8 core.conformation.membrane.SpanningTopology: Number of residues in spanfile: 1573 core.conformation.membrane.SpanningTopology: Span 1: start: 3, end: 22 orientation: 1 core.conformation.membrane.SpanningTopology: Span 2: start: 179, end: 198 orientation: 1 core.conformation.membrane.SpanningTopology: Span 3: start: 355, end: 375 orientation: 1 core.conformation.membrane.SpanningTopology: Span 4: start: 531, end: 551 orientation: 1 core.conformation.membrane.SpanningTopology: Span 5: start: 707, end: 726 orientation: 1 core.conformation.membrane.SpanningTopology: Span 6: start: 883, end: 902 orientation: 1 core.conformation.membrane.SpanningTopology: Span 7: start: 1059, end: 1079 orientation: 1 core.conformation.membrane.SpanningTopology: Span 8: start: 1235, end: 1255 orientation: 1 core.conformation.membrane.SpanningTopology: Total # of TM spans: 8 core.conformation.membrane.SpanningTopology: Number of residues in spanfile: 1573 core.conformation.membrane.SpanningTopology: Span 1: start: 3, end: 22 orientation: 1 core.conformation.membrane.SpanningTopology: Span 2: start: 179, end: 198 orientation: 1 core.conformation.membrane.SpanningTopology: Span 3: start: 355, end: 375 orientation: 1 core.conformation.membrane.SpanningTopology: Span 4: start: 531, end: 551 orientation: 1 core.conformation.membrane.SpanningTopology: Span 5: start: 707, end: 726 orientation: 1 core.conformation.membrane.SpanningTopology: Span 6: start: 883, end: 902 orientation: 1 core.conformation.membrane.SpanningTopology: Span 7: start: 1059, end: 1079 orientation: 1 core.conformation.membrane.SpanningTopology: Span 8: start: 1235, end: 1255 orientation: 1 core.conformation.membrane.SpanningTopology: WATCH OUT: Writing spanfile out.span! core.conformation.membrane.SpanningTopology: wrote out.span basic.io.database: Database file opened: membrane/implicit_lipid_parameters.txt protocols.membrane.SetMembranePositionMover: Calling SetMembranePositionMover protocols.membrane.SetMembranePositionMover: Starting foldtree: Is membrane fixed? 1 protocols.membrane.SetMembranePositionMover: Edge Jump Jump # 1409--0001 008 0001--0176 0001--0177 001 0177--0352 0001--0353 002 0353--0528 0001--0529 003 0529--0704 0001--0705 004 0705--0880 0001--0881 005 0881--1056 0001--1057 006 1057--1232 0001--1233 007 1233--1408 protocols.membrane.SetMembranePositionMover: Final foldtree: Is membrane fixed? 1 protocols.membrane.SetMembranePositionMover: Edge Jump Jump # 1409--0001 008 0001--0176 0001--0177 001 0177--0352 0001--0353 002 0353--0528 0001--0529 003 0529--0704 0001--0705 004 0705--0880 0001--0881 005 0881--1056 0001--1057 006 1057--1232 0001--1233 007 1233--1408 protocols.membrane.AddMembraneMover: Final foldtree: Is membrane fixed? 1 protocols.membrane.AddMembraneMover: Edge Jump Jump # 1409--0001 008 0001--0176 0001--0177 001 0177--0352 0001--0353 002 0353--0528 0001--0529 003 0529--0704 0001--0705 004 0705--0880 0001--0881 005 0881--1056 0001--1057 006 1057--1232 0001--1233 007 1233--1408 core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes. protocols.DsspMover: LLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHHHHHHHHLLLEEEEEEEEELLLLEEEEEEEEEELELLLLLLLEELLLEEEEEEEELLLLLLLLLEEEEEEEEELLLLEEEEEEEELLLLLLLLLEEEEEEELLLLLLLHHHHHHHHHLLLLEELLLEEEEEEEELLEEEEEEELLLLEEEEEEEEEELL protocols.membrane.MPLipidAccessibility: nbeta: 0 nmem: 184 beta: 0 protocols.membrane.MPLipidAccessibility: -15.351 15.351 10.234 6 10 core.membrane.hull: concave shell core.membrane.hull: convex hull core.membrane.hull: concave hull core.membrane.hull: adding shell core.membrane.hull: convex hull core.membrane.hull: concave hull core.membrane.hull: adding shell core.membrane.hull: convex hull core.membrane.hull: concave hull core.membrane.hull: adding shell core.membrane.hull: convex hull core.membrane.hull: concave hull core.membrane.hull: adding shell protocols.membrane.MPLipidAccessibility: tm alpha? 1 (helical proteins with <= 7 TMs will show up as 'not helical') protocols.membrane.AqueousPoreFinder: Initializing a custom aqueous pore boundary protocols.membrane.AqueousPoreFinder: Writing skeleton ellipse layers to an output file