Starting phenix.real_space_refine on Sun Jan 19 19:14:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rwy_19568/01_2025/8rwy_19568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rwy_19568/01_2025/8rwy_19568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rwy_19568/01_2025/8rwy_19568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rwy_19568/01_2025/8rwy_19568.map" model { file = "/net/cci-nas-00/data/ceres_data/8rwy_19568/01_2025/8rwy_19568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rwy_19568/01_2025/8rwy_19568.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 48 5.16 5 C 8925 2.51 5 N 2423 2.21 5 O 2707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14109 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2318 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 306, 2318 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2358 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2306 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2310 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2316 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 289} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2302 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 2290 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2284 Classifications: {'peptide': 306} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 306, 2284 Classifications: {'peptide': 306} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2326 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLN A 133 " occ=0.32 ... (16 atoms not shown) pdb=" NE2BGLN A 133 " occ=0.68 residue: pdb=" N ASER F 76 " occ=0.22 ... (10 atoms not shown) pdb=" OG BSER F 76 " occ=0.78 Time building chain proxies: 12.90, per 1000 atoms: 0.91 Number of scatterers: 14109 At special positions: 0 Unit cell: (107.58, 98.452, 94.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 48 16.00 O 2707 8.00 N 2423 7.00 C 8925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 2.6 seconds 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 27 sheets defined 35.8% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 32 through 52 removed outlier: 3.602A pdb=" N ASP A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.743A pdb=" N ASP A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.817A pdb=" N CYS A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.504A pdb=" N ALA A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.534A pdb=" N THR A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'B' and resid 32 through 53 removed outlier: 5.060A pdb=" N ALA B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.950A pdb=" N ASP B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.804A pdb=" N CYS B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 167 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.533A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 266 through 279 removed outlier: 4.502A pdb=" N THR B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 291 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'C' and resid 32 through 53 removed outlier: 4.924A pdb=" N ALA C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 4.002A pdb=" N ASP C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.824A pdb=" N CYS C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.556A pdb=" N THR C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 291 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.615A pdb=" N ARG D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 67 through 75 removed outlier: 3.707A pdb=" N ASP D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.811A pdb=" N CYS D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 167 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.571A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 266 through 279 removed outlier: 4.486A pdb=" N THR D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 291 Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'E' and resid 32 through 52 removed outlier: 5.031A pdb=" N ALA E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 75 removed outlier: 3.677A pdb=" N ASP E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 126 removed outlier: 3.712A pdb=" N CYS E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 167 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 189 through 194 Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 266 through 279 removed outlier: 4.499A pdb=" N THR E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'F' and resid 32 through 41 removed outlier: 3.613A pdb=" N SER F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 53 removed outlier: 4.234A pdb=" N ARG F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 111 through 126 removed outlier: 3.851A pdb=" N CYS F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 167 Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 267 through 279 Processing helix chain 'F' and resid 288 through 291 Processing helix chain 'F' and resid 305 through 311 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 139 removed outlier: 6.616A pdb=" N VAL A 25 " --> pdb=" O AGLN A 133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 135 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A 23 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N HIS A 137 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A 21 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS A 185 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY A 298 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 183 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 300 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA A 181 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 302 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 179 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE A 256 " --> pdb=" O HIS A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 139 removed outlier: 6.616A pdb=" N VAL A 25 " --> pdb=" O AGLN A 133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 135 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A 23 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N HIS A 137 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A 21 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS A 185 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY A 298 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 183 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 300 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA A 181 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 302 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 179 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE A 256 " --> pdb=" O HIS A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.577A pdb=" N LEU A 89 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 232 removed outlier: 4.756A pdb=" N VAL A 231 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 139 removed outlier: 6.744A pdb=" N VAL B 25 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B 135 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 23 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS B 137 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 21 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS B 185 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 298 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 183 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU B 300 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 181 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 302 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER B 179 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 256 " --> pdb=" O HIS B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 139 removed outlier: 6.744A pdb=" N VAL B 25 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B 135 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 23 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS B 137 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 21 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS B 185 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 298 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 183 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU B 300 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 181 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 302 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER B 179 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 256 " --> pdb=" O HIS B 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 removed outlier: 4.792A pdb=" N VAL B 231 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 66 Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB4, first strand: chain 'C' and resid 242 through 243 removed outlier: 5.258A pdb=" N PHE C 256 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER C 179 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE C 302 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 181 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU C 300 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 183 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY C 298 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS C 185 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 231 through 232 removed outlier: 4.660A pdb=" N VAL C 231 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.653A pdb=" N ALA D 21 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS D 137 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE D 23 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 135 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL D 25 " --> pdb=" O GLN D 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 90 Processing sheet with id=AB8, first strand: chain 'D' and resid 242 through 243 removed outlier: 5.086A pdb=" N PHE D 256 " --> pdb=" O HIS D 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 246 through 250 removed outlier: 5.086A pdb=" N PHE D 256 " --> pdb=" O HIS D 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 139 removed outlier: 6.677A pdb=" N VAL E 25 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU E 135 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE E 23 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS E 137 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA E 21 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS E 185 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY E 298 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 183 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU E 300 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA E 181 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE E 302 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER E 179 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE E 256 " --> pdb=" O HIS E 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 139 removed outlier: 6.677A pdb=" N VAL E 25 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU E 135 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE E 23 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS E 137 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA E 21 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS E 185 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY E 298 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 183 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU E 300 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA E 181 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE E 302 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER E 179 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE E 256 " --> pdb=" O HIS E 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 89 through 90 removed outlier: 3.521A pdb=" N LEU E 89 " --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 231 through 232 removed outlier: 4.753A pdb=" N VAL E 231 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 61 through 66 removed outlier: 6.514A pdb=" N ALA F 21 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N HIS F 137 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE F 23 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU F 135 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 25 " --> pdb=" O GLN F 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 89 through 90 removed outlier: 3.631A pdb=" N LEU F 89 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AC8, first strand: chain 'F' and resid 242 through 243 removed outlier: 5.091A pdb=" N PHE F 256 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER F 179 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE F 302 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA F 181 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU F 300 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL F 183 " --> pdb=" O GLY F 298 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY F 298 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS F 185 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 231 through 232 removed outlier: 4.457A pdb=" N VAL F 231 " --> pdb=" O LEU F 239 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 5413 1.38 - 1.54: 8890 1.54 - 1.71: 41 1.71 - 1.87: 84 1.87 - 2.04: 24 Bond restraints: 14452 Sorted by residual: bond pdb=" N GLU D 9 " pdb=" CA GLU D 9 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.86e+00 bond pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 1.235 1.214 0.022 1.30e-02 5.92e+03 2.75e+00 bond pdb=" C GLU D 9 " pdb=" N PRO D 10 " ideal model delta sigma weight residual 1.331 1.350 -0.020 1.31e-02 5.83e+03 2.24e+00 bond pdb=" N GLU D 7 " pdb=" CA GLU D 7 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.66e+00 bond pdb=" CA PRO D 8 " pdb=" C PRO D 8 " ideal model delta sigma weight residual 1.520 1.535 -0.015 1.42e-02 4.96e+03 1.12e+00 ... (remaining 14447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 19362 1.38 - 2.77: 253 2.77 - 4.15: 94 4.15 - 5.53: 27 5.53 - 6.91: 6 Bond angle restraints: 19742 Sorted by residual: angle pdb=" N GLN E 55 " pdb=" CA GLN E 55 " pdb=" C GLN E 55 " ideal model delta sigma weight residual 109.81 116.72 -6.91 2.21e+00 2.05e-01 9.79e+00 angle pdb=" N GLN D 55 " pdb=" CA GLN D 55 " pdb=" C GLN D 55 " ideal model delta sigma weight residual 109.81 116.02 -6.21 2.21e+00 2.05e-01 7.91e+00 angle pdb=" C GLU D 9 " pdb=" N PRO D 10 " pdb=" CA PRO D 10 " ideal model delta sigma weight residual 119.85 122.21 -2.36 1.01e+00 9.80e-01 5.45e+00 angle pdb=" C ALA D 54 " pdb=" N GLN D 55 " pdb=" CA GLN D 55 " ideal model delta sigma weight residual 121.80 126.90 -5.10 2.44e+00 1.68e-01 4.38e+00 angle pdb=" CA GLN E 55 " pdb=" C GLN E 55 " pdb=" N PRO E 56 " ideal model delta sigma weight residual 118.44 121.75 -3.31 1.59e+00 3.96e-01 4.33e+00 ... (remaining 19737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7727 17.25 - 34.51: 552 34.51 - 51.76: 108 51.76 - 69.01: 16 69.01 - 86.27: 27 Dihedral angle restraints: 8430 sinusoidal: 3237 harmonic: 5193 Sorted by residual: dihedral pdb=" CA LEU F 83 " pdb=" C LEU F 83 " pdb=" N HIS F 84 " pdb=" CA HIS F 84 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" C2A HEM C 401 " pdb=" CAA HEM C 401 " pdb=" CBA HEM C 401 " pdb=" CGA HEM C 401 " ideal model delta sinusoidal sigma weight residual 0.00 -86.27 86.27 2 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" C1A HEM C 401 " pdb=" C2A HEM C 401 " pdb=" CAA HEM C 401 " pdb=" CBA HEM C 401 " ideal model delta sinusoidal sigma weight residual 180.00 98.62 81.38 2 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1398 0.031 - 0.061: 545 0.061 - 0.092: 128 0.092 - 0.123: 98 0.123 - 0.153: 1 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CA GLN E 55 " pdb=" N GLN E 55 " pdb=" C GLN E 55 " pdb=" CB GLN E 55 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE F 107 " pdb=" N ILE F 107 " pdb=" C ILE F 107 " pdb=" CB ILE F 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 2167 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 55 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO E 56 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 56 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 56 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 79 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO F 80 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 80 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 80 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 55 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO D 56 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.014 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1972 2.75 - 3.29: 13351 3.29 - 3.83: 23903 3.83 - 4.36: 28544 4.36 - 4.90: 50000 Nonbonded interactions: 117770 Sorted by model distance: nonbonded pdb=" O ALA C 81 " pdb=" OH TYR C 180 " model vdw 2.218 3.040 nonbonded pdb=" O ALA A 81 " pdb=" OH TYR A 180 " model vdw 2.222 3.040 nonbonded pdb=" O ALA D 81 " pdb=" OH TYR D 180 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN F 184 " pdb=" OH TYR F 186 " model vdw 2.243 3.040 nonbonded pdb=" OG SER F 216 " pdb=" OD1 ASP F 218 " model vdw 2.244 3.040 ... (remaining 117765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 7 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 16 or (resid 17 and (name N or name CA or name C \ or name O )) or resid 18 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 75 or resid 77 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name NE )) or resid 96 through 132 or resid 134 through 139 or (resid 140 a \ nd (name N or name CA or name C or name O or name CB )) or resid 141 through 162 \ or (resid 163 and (name N or name CA or name C or name O or name CB or name CG \ )) or (resid 164 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or resid 165 through 193 or (resid 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 218 or (resid 219 and (name \ N or name CA or name C or name O or name CB )) or resid 220 through 234 or (res \ id 235 and (name N or name CA or name C or name O or name CB )) or resid 236 or \ (resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ through 243 or (resid 244 and (name N or name CA or name C or name O or name CB \ )) or resid 245 through 267 or (resid 268 and (name N or name CA or name C or n \ ame O or name CB )) or resid 269 through 309 or (resid 310 through 311 and (name \ N or name CA or name C or name O or name CB )) or resid 312 or resid 401)) selection = (chain 'B' and ((resid 7 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 16 or (resid 17 and (name N or name CA or name C \ or name O )) or resid 18 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 75 or resid 77 through 132 or res \ id 134 through 139 or (resid 140 and (name N or name CA or name C or name O or n \ ame CB )) or resid 141 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB or name CG )) or (resid 164 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 165 through 218 or (r \ esid 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 243 or (resid 244 and (name N or name CA or name C or name O or name CB ) \ ) or resid 245 through 309 or (resid 310 through 311 and (name N or name CA or n \ ame C or name O or name CB )) or resid 312 or resid 401)) selection = (chain 'C' and ((resid 7 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 16 or (resid 17 and (name N or name CA or name C \ or name O )) or resid 18 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 75 or resid 77 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name NE )) or resid 96 through 132 or resid 134 through 162 or (resid 163 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or (resid 164 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 165 through 193 or (resid 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 218 or (resid 219 and (name N or name CA or \ name C or name O or name CB )) or resid 220 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 243 or (res \ id 244 and (name N or name CA or name C or name O or name CB )) or resid 245 thr \ ough 267 or (resid 268 and (name N or name CA or name C or name O or name CB )) \ or resid 269 through 310 or (resid 311 and (name N or name CA or name C or name \ O or name CB )) or resid 312 or resid 401)) selection = (chain 'D' and ((resid 7 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 16 or (resid 17 and (name N or name CA or name C \ or name O )) or resid 18 through 75 or resid 77 through 94 or (resid 95 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ )) or resid 96 through 132 or resid 134 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB or name CG )) or (resid 164 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 165 \ through 193 or (resid 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 218 or (resid 219 and (name N or name CA or name C or na \ me O or name CB )) or resid 220 through 234 or (resid 235 and (name N or name CA \ or name C or name O or name CB )) or resid 236 or (resid 237 and (name N or nam \ e CA or name C or name O or name CB )) or resid 238 through 243 or (resid 244 an \ d (name N or name CA or name C or name O or name CB )) or resid 245 through 267 \ or (resid 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 309 or (resid 310 through 311 and (name N or name CA or name C or na \ me O or name CB )) or resid 312 or resid 401)) selection = (chain 'E' and ((resid 7 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 16 or (resid 17 and (name N or name CA or name C \ or name O )) or resid 18 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 75 or resid 77 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name NE )) or resid 96 through 132 or resid 134 through 139 or (resid 140 a \ nd (name N or name CA or name C or name O or name CB )) or resid 141 through 193 \ or (resid 194 and (name N or name CA or name C or name O or name CB )) or resid \ 195 through 243 or (resid 244 and (name N or name CA or name C or name O or nam \ e CB )) or resid 245 through 267 or (resid 268 and (name N or name CA or name C \ or name O or name CB )) or resid 269 through 310 or (resid 311 and (name N or na \ me CA or name C or name O or name CB )) or resid 312 or resid 401)) selection = (chain 'F' and (resid 7 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 75 or resid 77 through 94 or (resid \ 95 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE )) or resid 96 through 132 or resid 134 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB or name CG )) or (resid 164 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ resid 165 through 218 or (resid 219 and (name N or name CA or name C or name O \ or name CB )) or resid 220 through 234 or (resid 235 and (name N or name CA or n \ ame C or name O or name CB )) or resid 236 through 312 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.22 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.380 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14452 Z= 0.179 Angle : 0.487 6.914 19742 Z= 0.236 Chirality : 0.039 0.153 2170 Planarity : 0.003 0.035 2609 Dihedral : 13.418 86.265 5102 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 0.07 % Allowed : 0.00 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1831 helix: 1.68 (0.24), residues: 508 sheet: 1.17 (0.24), residues: 435 loop : 0.49 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 71 HIS 0.002 0.000 HIS C 137 PHE 0.008 0.001 PHE C 142 TYR 0.014 0.001 TYR C 186 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 1.754 Fit side-chains REVERT: C 42 ASP cc_start: 0.8393 (m-30) cc_final: 0.7930 (m-30) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.2590 time to fit residues: 28.9900 Evaluate side-chains 64 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS F 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.041213 restraints weight = 112463.814| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 5.38 r_work: 0.2297 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2308 r_free = 0.2308 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2308 r_free = 0.2308 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 14452 Z= 0.592 Angle : 0.663 9.363 19742 Z= 0.321 Chirality : 0.044 0.179 2170 Planarity : 0.004 0.045 2609 Dihedral : 8.452 85.742 2049 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1831 helix: 0.86 (0.23), residues: 524 sheet: 0.81 (0.24), residues: 451 loop : 0.44 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 71 HIS 0.010 0.001 HIS A 84 PHE 0.013 0.001 PHE C 142 TYR 0.024 0.002 TYR A 141 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 1.706 Fit side-chains REVERT: A 134 ASP cc_start: 0.8909 (t0) cc_final: 0.8235 (t0) REVERT: E 210 MET cc_start: 0.9211 (tpt) cc_final: 0.8814 (tpp) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.2680 time to fit residues: 26.9222 Evaluate side-chains 59 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain C residue 166 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.044629 restraints weight = 84250.631| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.65 r_work: 0.2439 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14452 Z= 0.213 Angle : 0.516 6.671 19742 Z= 0.247 Chirality : 0.039 0.146 2170 Planarity : 0.003 0.033 2609 Dihedral : 8.043 82.275 2046 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.08 % Rotamer: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1831 helix: 1.23 (0.23), residues: 524 sheet: 0.88 (0.24), residues: 441 loop : 0.52 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 71 HIS 0.004 0.001 HIS A 84 PHE 0.008 0.001 PHE A 116 TYR 0.008 0.001 TYR A 141 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 1.607 Fit side-chains REVERT: A 134 ASP cc_start: 0.8540 (t0) cc_final: 0.8271 (t0) REVERT: B 210 MET cc_start: 0.9127 (mmm) cc_final: 0.8922 (mmm) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.2382 time to fit residues: 27.5867 Evaluate side-chains 67 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 159 optimal weight: 0.0000 chunk 112 optimal weight: 0.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.055028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.043597 restraints weight = 90943.519| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 4.79 r_work: 0.2411 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14452 Z= 0.291 Angle : 0.529 7.003 19742 Z= 0.253 Chirality : 0.040 0.142 2170 Planarity : 0.003 0.028 2609 Dihedral : 8.043 81.462 2046 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 0.35 % Allowed : 5.82 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1831 helix: 1.20 (0.23), residues: 524 sheet: 0.80 (0.24), residues: 441 loop : 0.54 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 71 HIS 0.005 0.001 HIS A 84 PHE 0.010 0.001 PHE C 116 TYR 0.006 0.001 TYR F 263 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.647 Fit side-chains REVERT: A 134 ASP cc_start: 0.8545 (t0) cc_final: 0.8290 (t0) REVERT: B 210 MET cc_start: 0.9153 (mmm) cc_final: 0.8920 (tpp) REVERT: D 141 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: E 55 GLN cc_start: 0.8451 (pp30) cc_final: 0.8238 (pm20) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.2344 time to fit residues: 27.3271 Evaluate side-chains 68 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 57 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 114 optimal weight: 0.7980 chunk 178 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.044638 restraints weight = 104014.083| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 5.12 r_work: 0.2432 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14452 Z= 0.189 Angle : 0.497 6.429 19742 Z= 0.236 Chirality : 0.039 0.137 2170 Planarity : 0.003 0.027 2609 Dihedral : 7.985 82.427 2046 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Rotamer: Outliers : 0.56 % Allowed : 6.45 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1831 helix: 1.39 (0.23), residues: 524 sheet: 0.83 (0.24), residues: 441 loop : 0.58 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 71 HIS 0.003 0.000 HIS A 84 PHE 0.007 0.001 PHE C 116 TYR 0.007 0.001 TYR A 186 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3662 Ramachandran restraints generated. 1831 Oldfield, 0 Emsley, 1831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.560 Fit side-chains REVERT: A 134 ASP cc_start: 0.8527 (t0) cc_final: 0.8275 (t0) REVERT: B 210 MET cc_start: 0.9165 (mmm) cc_final: 0.8924 (tpp) REVERT: D 141 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: E 210 MET cc_start: 0.9170 (tpt) cc_final: 0.8859 (mmm) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.2352 time to fit residues: 27.7142 Evaluate side-chains 69 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain E residue 166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8761 > 50: distance: 0 - 1: 5.139 distance: 1 - 2: 7.568 distance: 1 - 4: 3.793 distance: 2 - 3: 5.569 distance: 2 - 5: 4.218 distance: 5 - 6: 6.688 distance: 6 - 7: 5.695 distance: 6 - 9: 9.827 distance: 7 - 8: 17.851 distance: 7 - 10: 12.157 distance: 10 - 11: 7.649 distance: 11 - 12: 11.891 distance: 11 - 14: 17.132 distance: 12 - 13: 22.403 distance: 12 - 15: 9.321 distance: 15 - 16: 4.328 distance: 15 - 21: 7.626 distance: 16 - 17: 4.477 distance: 16 - 19: 7.539 distance: 17 - 18: 12.322 distance: 17 - 22: 7.907 distance: 19 - 20: 7.710 distance: 20 - 21: 9.534 distance: 24 - 25: 8.448 distance: 24 - 31: 5.900 distance: 27 - 28: 3.934 distance: 31 - 32: 5.066 distance: 32 - 33: 8.683 distance: 32 - 35: 5.800 distance: 33 - 34: 21.909 distance: 33 - 36: 14.239 distance: 36 - 37: 6.223 distance: 37 - 38: 8.011 distance: 37 - 40: 7.184 distance: 38 - 39: 18.571 distance: 38 - 43: 10.399 distance: 40 - 41: 4.988 distance: 40 - 42: 6.051 distance: 43 - 44: 6.631 distance: 44 - 45: 15.630 distance: 44 - 47: 4.682 distance: 45 - 46: 9.640 distance: 45 - 51: 10.088 distance: 47 - 48: 6.550 distance: 48 - 49: 11.909 distance: 48 - 50: 9.178 distance: 51 - 52: 21.567 distance: 52 - 53: 8.966 distance: 52 - 55: 16.485 distance: 53 - 54: 15.691 distance: 53 - 57: 6.927 distance: 55 - 56: 18.918