Branch: rosetta:commits 「revision: №20594」
Test: m1.clang.python39.PyRosetta.unit
SubTest: C001_Carbohydrates_Demo01
SubTest files: 「file-system-view」
Daemon: yoji-1    
State: C001_Carbohydrates_Demo01

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.42.post.dev+15.HEAD.ef59a96932c326d6e64c65f6bc6fc7cf9828a0fd 2024-11-07T18:09:09] retrieved from: git@github.com:RosettaCommons/rosetta.git PDB file name: alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp Total residues: 3 Sequence: ZZZ Fold tree: FOLD_TREE EDGE 1 3 -1 PDB file name: alpha-D-Glcp-(1->6)-alpha-D-Glcp Total residues: 2 Sequence: ZZ Fold tree: FOLD_TREE EDGE 1 2 -1 PDB file name: beta-D-Galp-(1->4)-alpha-D-Glcp Total residues: 2 Sequence: ZZ Fold tree: FOLD_TREE EDGE 1 2 -1 alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-alpha-D-Glcp alpha-D-Glcp-(1->6)-alpha-D-Glcp beta-D-Galp-(1->4)-alpha-D-Glcp 1 ->4)-alpha-D-Glcp:reducing_end 2 ->4)-beta-D-Galp:non-reducing_end 1 ->4)-alpha-D-Glcp:reducing_end 2 ->4)-alpha-D-Glcp 3 ->4)-alpha-D-Glcp:non-reducing_end Residue 1: ->4)-alpha-D-Glcp:reducing_end:non-reducing_end (Glc, Z): Base: ->4)-alpha-D-Glcp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: glucose IUPAC Name: alpha-D-glucopyranose Abbreviation: alpha-D-Glcp Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: alpha Modifications: none Polymeric Information: Reducing?: yes Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : axial O2 : equatorial O3 : equatorial O4 : equatorial C6 : equatorial Atom Coordinates: C1 : 0, 0, 0 C2 : 1.55, 0, 0 C3 : 2.04812, 1.44664, 0 C4 : 1.50806, 2.11919, -1.26369 O4 : 1.94666, 3.46908, -1.30661 C5 : -0.0200415, 2.06186, -1.21358 O5 : -0.475077, 0.686176, -1.1593 VO5: -0.492509, 0.676579, -1.17187 (virtual) VC1: 0.031762, 0.00822503, 0.00564973 (virtual) O1 : -0.494034, 0.697555, 1.2082 O2 : 2.02401, -0.669275, 1.15922 O3 : 3.4779, 1.4716, 1.64563e-16 C6 : -0.614146, 2.71298, -2.43962 O6 : -0.225074, 4.07556, -2.53127 H1 : -0.370662, -1.03564, 0.00767336 H2 : 1.90812, -0.520035, -0.900727 H3 : 1.67301, 1.95456, 0.900727 H4 : 1.88381, 1.57916, -2.14527 HO4: 1.61609, 3.94572, -0.516717 H5 : -0.369153, 2.59396, -0.316372 HO1: -0.167832, 1.62167, 1.20877 HO2: 3.00401, -0.669275, 1.15922 HO3: 3.78886, 2.40096, 5.03844e-17 1H6 : -1.71106, 2.65811, -2.3783 2H6 : -0.261365, 2.17983, -3.33478 HO6: -0.621924, 4.47587, -3.33293 Mirrored relative to coordinates in ResidueType: FALSE Residue 1: ->4)-alpha-D-Galp:reducing_end:non-reducing_end (Gal, Z): Base: ->4)-alpha-D-Galp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: galactose IUPAC Name: alpha-D-galactopyranose Abbreviation: alpha-D-Galp Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: alpha Modifications: none Polymeric Information: Reducing?: yes Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : axial O2 : equatorial O3 : equatorial O4 : axial C6 : equatorial Atom Coordinates: C1 : 0, 0, 0 C2 : 1.55, 0, 0 C3 : 2.04812, 1.44664, 0 C4 : 1.50806, 2.11919, -1.26369 O4 : 1.98701, 1.42994, -2.4091 C5 : -0.0200415, 2.06186, -1.21358 O5 : -0.475077, 0.686176, -1.1593 VO5: -0.492509, 0.676579, -1.17187 (virtual) VC1: 0.031762, 0.00822503, 0.00564973 (virtual) O1 : -0.494034, 0.697555, 1.2082 O2 : 2.02401, -0.669275, 1.15922 O3 : 3.4779, 1.4716, 1.64563e-16 C6 : -0.614146, 2.71298, -2.43962 O6 : -0.225074, 4.07556, -2.53127 H1 : -0.370662, -1.03564, 0.00767336 H2 : 1.90812, -0.520035, -0.900727 H3 : 1.67301, 1.95456, 0.900727 H4 : 1.85245, 3.16359, -1.28863 HO4: 2.96665, 1.45445, -2.41977 H5 : -0.369153, 2.59396, -0.316372 HO1: -0.167832, 1.62167, 1.20877 HO2: 3.00401, -0.669275, 1.15922 HO3: 3.78886, 2.40096, 5.03844e-17 1H6 : -1.71106, 2.65811, -2.3783 2H6 : -0.261365, 2.17983, -3.33478 HO6: -0.621924, 4.47587, -3.33293 Mirrored relative to coordinates in ResidueType: FALSE Residue 1: ->3)-alpha-D-Manp:reducing_end:non-reducing_end (Man, Z): Base: ->3)-alpha-D-Manp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE ALPHA_SUGAR Variant types: UPPER_TERMINUS_VARIANT LOWER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 O3 Backbone atoms: C1 C2 C3 O3 C4 C5 O5 VO5 VC1 H1 H2 H3 HO3 H4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O4 C6 O6 HO1 HO2 HO4 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: mannose IUPAC Name: alpha-D-mannopyranose Abbreviation: alpha-D-Manp Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: alpha Modifications: none Polymeric Information: Reducing?: yes Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : axial O2 : axial O3 : equatorial O4 : equatorial C6 : equatorial Atom Coordinates: C1 : 0, 0, 0 C2 : 1.55, 0, 0 C3 : 2.04812, 1.44664, 0 O3 : 3.4779, 1.4716, 1.64563e-16 C4 : 1.50806, 2.11919, -1.26369 C5 : -0.0200415, 2.06186, -1.21358 O5 : -0.475077, 0.686176, -1.1593 VO5: -0.492509, 0.676579, -1.17187 (virtual) VC1: 0.031762, 0.00822503, 0.00564973 (virtual) O1 : -0.494034, 0.697555, 1.2082 O2 : 2.02401, -0.669275, -1.15922 O4 : 1.94666, 3.46908, -1.30661 C6 : -0.614146, 2.71298, -2.43962 O6 : -0.225074, 4.07556, -2.53127 H1 : -0.370662, -1.03564, 0.00767336 H2 : 1.90812, -0.520035, 0.900727 H3 : 1.67301, 1.95456, 0.900727 HO3: 3.78886, 2.40096, 5.03844e-17 H4 : 1.88381, 1.57916, -2.14527 H5 : -0.369153, 2.59396, -0.316372 HO1: -0.167832, 1.62167, 1.20877 HO2: 3.00401, -0.669275, -1.15922 HO4: 1.61609, 3.94572, -0.516717 1H6 : -1.71106, 2.65811, -2.3783 2H6 : -0.261365, 2.17983, -3.33478 HO6: -0.621924, 4.47587, -3.33293 Mirrored relative to coordinates in ResidueType: FALSE 59.99999999999999 -59.99999999999999 60.00000000000001 -59.999999999999986 59.99999999999999 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 PDB file name: ../test/data/carbohydrates/Lex.pdb Total residues: 3 Sequence: ZZZ Fold tree: FOLD_TREE EDGE 1 2 -1 EDGE 1 3 -2 O3 C1 beta-D-Galp-(1->4)-beta-D-GlcpNAc alpha-L-Fucp- Residue 1: ->4)-beta-D-Glcp:reducing_end:->3)-branch:2-AcNH (Glc, Z): Base: ->4)-beta-D-Glcp Properties: POLYMER CARBOHYDRATE LOWER_TERMINUS BRANCH_POINT POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR C2_MODIFIED ACETYLAMINO_SUGAR Variant types: LOWER_TERMINUS_VARIANT C3_BRANCH_POINT C2_ACETYLAMINO_SUGAR Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO4 HO3 HO2 N2 CN2 CAN2 OCN2 HO1 1H6 2H6 HO6 HN2 1HC2 2HC2 3HC2 Branch-point atoms: O3 Carbohydrate Properties for this Residue: Basic Name: glucosamine IUPAC Name: ->4)-beta-2-(N-acetylamino)-2-deoxy-D-glucopyranose Abbreviation: ->4)-beta-D-GlcpNAc Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: beta Modifications: acetylamino sugar Polymeric Information: Reducing?: yes Main chain connection: (_->4) Branch connections: (_->3) Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O1 : equatorial N2 : equatorial O3 : equatorial O4 : equatorial C6 : equatorial Atom Coordinates: C1 : 35.71, 122.693, 36.907 C2 : 36.264, 121.664, 35.887 C3 : 35.396, 120.362, 35.896 C4 : 35.215, 119.833, 37.36 O4 : 34.235, 118.792, 37.37 C5 : 34.756, 121.002, 38.316 O5 : 35.66, 122.104, 38.21 VO5: 35.66, 122.104, 38.21 (virtual) VC1: 35.7109, 122.617, 36.8656 (virtual) O1 : 36.369, 123.964, 36.94 O2 : 36.2371, 122.227, 34.5836 (virtual) O3 : 36.026, 119.359, 35.094 C6 : 34.689, 120.7, 39.82 O6 : 35.928, 120.224, 40.287 HO4: 34.615, 117.665, 38.155 (virtual) HO3: 35.546, 119.238, 33.75 (virtual) HO2: 36.5871, 121.577, 33.9392 (virtual) N2 : 36.245, 122.328, 34.583 CN2: 37.363, 122.3, 33.878 CAN2: 37.043, 123.112, 32.473 OCN2: 38.517, 122.472, 34.271 H1 : 34.6514, 122.845, 36.6496 H2 : 37.299, 121.411, 36.1601 H3 : 34.408, 120.587, 35.4681 H4 : 36.1743, 119.429, 37.7162 H5 : 33.7421, 121.32, 38.0316 HO1: 36.301, 124.391, 36.0604 1H6 : 33.9192, 119.935, 39.9976 2H6 : 34.4315, 121.623, 40.3596 HO6: 35.8659, 120.037, 41.247 HN2: 35.4316, 122.782, 34.2477 1HC2: 36.3241, 123.919, 32.671 2HC2: 36.5729, 122.428, 31.7525 3HC2: 37.9836, 123.478, 32.0377 Mirrored relative to coordinates in ResidueType: FALSE Residue 2: ->4)-beta-D-Galp:non-reducing_end (Gal, Z): Base: ->4)-beta-D-Galp Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE D_SUGAR PYRANOSE BETA_SUGAR Variant types: UPPER_TERMINUS_VARIANT Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO2 HO3 1H6 2H6 HO6 Carbohydrate Properties for this Residue: Basic Name: galactose IUPAC Name: beta-D-galactopyranosyl Abbreviation: beta-D-Galp- Classification: aldohexose Stereochemistry: D Ring Form: pyranose Anomeric Form: beta Modifications: none Polymeric Information: Reducing?: no Main chain connection: N/A Branch connections: none Ring Conformer: 4C1 (chair): C-P parameters (q, phi, theta): 0.55, 180, 0; nu angles (degrees): 60, -60, 60, -60, 60, -60 O2 : equatorial O3 : equatorial O4 : axial C6 : equatorial Atom Coordinates: C1 : 34.615, 117.665, 38.155 C2 : 33.365, 116.921, 38.692 C3 : 33.836, 115.668, 39.463 C4 : 34.765, 114.785, 38.592 O4 : 33.936, 114.234, 37.591 C5 : 35.931, 115.629, 38.011 O5 : 35.406, 116.786, 37.348 VO5: 35.406, 116.786, 37.348 (virtual) VC1: 34.6528, 117.616, 38.2521 (virtual) O1 : 34.235, 118.792, 37.37 (virtual) O2 : 32.626, 117.74, 39.575 O3 : 32.706, 114.881, 39.893 C6 : 36.818, 114.855, 37.032 O6 : 37.611, 113.891, 37.692 HO1: 35.215, 119.833, 37.36 (virtual) H1 : 35.2209, 118.009, 39.0061 H2 : 32.7301, 116.628, 37.8427 H3 : 34.3885, 115.986, 40.3595 H4 : 35.1785, 113.978, 39.2143 HO4: 33.2273, 113.702, 38.0094 H5 : 36.5692, 115.975, 38.8375 HO2: 31.8431, 117.248, 39.8996 HO3: 33.0232, 114.092, 40.3795 1H6 : 37.4842, 115.562, 36.5164 2H6 : 36.1787, 114.34, 36.2998 HO6: 38.1635, 113.417, 37.0358 Mirrored relative to coordinates in ResidueType: FALSE Residue 3: ->4)-alpha-L-Fucp:non-reducing_end (Fuc, Z): Base: ->4)-alpha-L-Fucp Properties: POLYMER CARBOHYDRATE UPPER_TERMINUS POLAR CYCLIC HEXOSE ALDOSE L_SUGAR PYRANOSE ALPHA_SUGAR C6_MODIFIED DEOXY_SUGAR Variant types: UPPER_TERMINUS_VARIANT C6_DEOXY_SUGAR Main-chain atoms: C1 C2 C3 C4 O4 Backbone atoms: C1 C2 C3 C4 O4 C5 O5 VO5 VC1 H1 H2 H3 H4 HO4 H5 Ring atoms: C1 C2 C3 C4 C5 O5 Side-chain atoms: O1 O2 O3 C6 O6 HO1 HO6 HO2 HO3 1H6 2H6 3H6 Carbohydrate Properties for this Residue: Basic Name: fucose IUPAC Name: alpha-L-fucopyranosyl Abbreviation: alpha-L-Fucp- Classification: aldohexose Stereochemistry: L Ring Form: pyranose Anomeric Form: alpha Modifications: deoxy sugar Polymeric Information: Reducing?: no Main chain connection: N/A Branch connections: none Ring Conformer: 1C4 (chair): C-P parameters (q, phi, theta): 0.55, 180, 180; nu angles (degrees): -60, 60, -60, 60, -60, 60 O2 : equatorial O3 : equatorial O4 : axial C6 : equatorial Atom Coordinates: C1 : 35.546, 119.238, 33.75 C2 : 36.615, 118.464, 32.939 C3 : 36.681, 116.991, 33.421 C4 : 35.284, 116.331, 33.366 O4 : 34.915, 116.247, 31.999 C5 : 34.24, 117.183, 34.142 O5 : 34.28, 118.546, 33.673 VO5: 34.28, 118.546, 33.673 (virtual) VC1: 35.5799, 119.134, 33.8691 (virtual) O1 : 36.026, 119.359, 35.094 (virtual) O2 : 37.839, 119.137, 33.073 O3 : 37.527, 116.202, 32.617 C6 : 32.809, 116.64, 34.044 O6 : 32.372, 116.598, 32.6936 (virtual) HO1: 35.396, 120.362, 35.896 (virtual) HO6: 31.4572, 116.249, 32.6565 (virtual) H1 : 35.3955, 120.244, 33.3315 H2 : 36.3437, 118.489, 31.8733 H3 : 37.0471, 116.97, 34.4581 H4 : 35.3419, 115.332, 33.8218 HO4: 34.8869, 117.147, 31.6118 H5 : 34.5158, 117.205, 35.2067 HO2: 38.5305, 118.662, 32.5661 HO3: 37.538, 115.283, 32.9572 1H6 : 32.7831, 115.622, 34.4596 2H6 : 32.137, 117.296, 34.6166 3H6 : 32.5045, 116.622, 32.9871 Mirrored relative to coordinates in ResidueType: FALSE PDB file name: ../test/data/carbohydrates/N-linked_14-mer_glycan.pdb Total residues: 19 Sequence: ANASAZZZZZZZZZZZZZZ Fold tree: FOLD_TREE EDGE 1 5 -1 EDGE 2 6 -2 ND2 C1 EDGE 6 14 -1 EDGE 8 15 -2 O6 C1 EDGE 15 17 -1 EDGE 15 18 -2 O6 C1 EDGE 18 19 -1 ANASA alpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-beta-D-GlcpNAc- alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)-alpha-D-Manp- alpha-D-Manp-(1->2)-alpha-D-Manp- PDB file name: ../test/data/carbohydrates/O_glycan.pdb Total residues: 4 Sequence: ASAZ Fold tree: FOLD_TREE EDGE 1 3 -1 EDGE 2 4 -2 OG C1 ASA alpha-D-Glcp- core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.42.post.dev+15.HEAD.ef59a96932 ef59a96932c326d6e64c65f6bc6fc7cf9828a0fd git@github.com:RosettaCommons/rosetta.git 2024-11-07T18:09:09 core.init: Rosetta extras: [] core.init: command: PyRosetta -constant_seed -include_sugars -database /Volumes/scratch/w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.7-arm64-arm-64bit/clang-14.0.0/python-3.9/minsizerel/build/pyrosetta/database 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.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 1647 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.822453 seconds. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/maltotriose.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/isomaltose.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose: by appending by jump... core.conformation.Conformation: appending residue by a chemical bond in the foldtree: 3 ->4)-alpha-L-Fucp:non-reducing_end anchor: O3 1 root: C1 core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/Lex.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc1 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Gal2 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Fuc3 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 3 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-L-Fucp:non-reducing_end 3. Returning BOGUS ID instead. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/N-linked_14-mer_glycan.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc6 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc7 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man8 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man9 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man10 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man11 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc12 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc13 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc14 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man15 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man16 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man17 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man18 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Man19 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 6 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 15 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 18 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 6. Returning BOGUS ID instead. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->3)-alpha-D-Manp:->6)-branch 15. Returning BOGUS ID instead. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->2)-alpha-D-Manp 18. Returning BOGUS ID instead. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.import_pose.import_pose: File '../test/data/carbohydrates/O_glycan.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] Glc4 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 4 H1 that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-alpha-D-Glcp:non-reducing_end 4. Returning BOGUS ID instead. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->4)-alpha-D-Glcp:non-reducing_end anchor: OG 2 root: C1 core.pose.carbohydrates.util: Glycosylated pose with a(n) Glcp-OGSER2 bond. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose.carbohydrates.util: Idealizing glycosidic torsions. core.conformation.Conformation: appending residue by a chemical bond in the foldtree: 4 ->3)-alpha-D-Galp:2-AcNH anchor: OG 2 root: C1 core.pose.carbohydrates.util: Glycosylated pose with a(n) a-D-GalpNAc-(1->3)-a-D-GalpNAc--OGSER2 bond. core.conformation.carbohydrates.GlycanTreeSet: Setting up Glycan Trees core.conformation.carbohydrates.GlycanTreeSet: Found 1 glycan trees. core.pose.carbohydrates.util: Idealizing glycosidic torsions. /Volumes/scratch/w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.7-arm64-arm-64bit/clang-14.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:21: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.core.pose import pose_from_saccharide_sequence /Volumes/scratch/w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.7-arm64-arm-64bit/clang-14.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:42: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for res in lactose: print( res.seqpos(), res.name() ) /Volumes/scratch/w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.7-arm64-arm-64bit/clang-14.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:43: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for res in maltotriose: print( res.seqpos(), res.name() ) /Volumes/scratch/w/rosetta/commits/rosetta/source/build/PyRosetta/macOS-12.7-arm64-arm-64bit/clang-14.0.0/python-3.9/minsizerel/build/test/C001_Carbohydrates_Demo01.py:128: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. for res in Lex: print( res ) Finished C001_Carbohydrates_Demo01 in 0:00:02.278234