Starting phenix.real_space_refine on Thu Jun 12 17:31:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rwy_19568/06_2025/8rwy_19568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rwy_19568/06_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_19568/06_2025/8rwy_19568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rwy_19568/06_2025/8rwy_19568.map" model { file = "/net/cci-nas-00/data/ceres_data/8rwy_19568/06_2025/8rwy_19568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rwy_19568/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.39, per 1000 atoms: 0.95 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: 3.26 Conformation dependent library (CDL) restraints added in 2.3 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: 1.76 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: 4.77 Time building geometry restraints manager: 3.85 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: 8.340 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.020 ------------------------------------------------------------------------------- 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 0.084 14458 Z= 0.106 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 Details of bonding type rmsd hydrogen bonds : bond 0.13123 ( 609) hydrogen bonds : angle 6.40730 ( 1968) covalent geometry : bond 0.00291 (14452) covalent geometry : angle 0.48739 (19742) Misc. bond : bond 0.06962 ( 6) *********************** 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 : 1.767 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: 0.2650 time to fit residues: 29.3123 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 : 1.661 ------------------------------------------------------------------------------- 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: 7.9990 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 = 0.053367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.041200 restraints weight = 112501.721| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 5.37 r_work: 0.2299 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2307 r_free = 0.2307 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: 0.8609 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 : 0.010 0.200 14458 Z= 0.369 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 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 609) hydrogen bonds : angle 5.01012 ( 1968) covalent geometry : bond 0.00913 (14452) covalent geometry : angle 0.66304 (19742) Misc. bond : bond 0.18492 ( 6) *********************** 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 : 1.481 Fit side-chains REVERT: A 134 ASP cc_start: 0.8910 (t0) cc_final: 0.8237 (t0) REVERT: E 210 MET cc_start: 0.9210 (tpt) cc_final: 0.8813 (tpp) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.2306 time to fit residues: 23.3638 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 : 1.479 ------------------------------------------------------------------------------- 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: 0.0980 chunk 156 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 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: 0.7980 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 = 0.2911 r_free = 0.2911 target = 0.056084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.044717 restraints weight = 84183.134| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 4.64 r_work: 0.2444 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 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 = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 14458 Z= 0.112 Angle : 0.515 6.628 19742 Z= 0.246 Chirality : 0.039 0.144 2170 Planarity : 0.003 0.032 2609 Dihedral : 8.048 82.351 2046 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.92 % Favored : 98.03 % Rotamer: Outliers : 0.14 % Allowed : 4.42 % Favored : 95.44 % 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: 1.15 (0.20), residues: 1831 helix: 1.26 (0.23), residues: 524 sheet: 0.88 (0.24), residues: 441 loop : 0.54 (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 0.007 0.001 TYR A 186 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02649 ( 609) hydrogen bonds : angle 4.46457 ( 1968) covalent geometry : bond 0.00311 (14452) covalent geometry : angle 0.51505 (19742) Misc. bond : bond 0.09272 ( 6) *********************** 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 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.645 Fit side-chains REVERT: A 134 ASP cc_start: 0.8535 (t0) cc_final: 0.8275 (t0) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.2277 time to fit residues: 26.2303 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 : 1.502 ------------------------------------------------------------------------------- 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: 2.9990 chunk 176 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.2864 r_free = 0.2864 target = 0.054087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.042630 restraints weight = 91467.829| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 4.76 r_work: 0.2384 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2391 r_free = 0.2391 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2391 r_free = 0.2391 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.166 14458 Z= 0.239 Angle : 0.568 7.761 19742 Z= 0.272 Chirality : 0.041 0.148 2170 Planarity : 0.003 0.027 2609 Dihedral : 8.102 80.787 2046 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 0.49 % Allowed : 5.96 % Favored : 93.55 % 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: 0.96 (0.20), residues: 1831 helix: 1.06 (0.23), residues: 524 sheet: 0.71 (0.24), residues: 435 loop : 0.51 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 71 HIS 0.006 0.001 HIS A 84 PHE 0.011 0.001 PHE C 142 TYR 0.014 0.001 TYR A 141 ARG 0.002 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 609) hydrogen bonds : angle 4.59671 ( 1968) covalent geometry : bond 0.00614 (14452) covalent geometry : angle 0.56752 (19742) Misc. bond : bond 0.14881 ( 6) *********************** 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 67 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.594 Fit side-chains REVERT: A 134 ASP cc_start: 0.8579 (t0) cc_final: 0.8288 (t0) REVERT: D 141 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: E 55 GLN cc_start: 0.8466 (pp30) cc_final: 0.8240 (pm20) outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 0.2339 time to fit residues: 25.6696 Evaluate side-chains 66 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 TYR 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 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: 4.9990 chunk 81 optimal weight: 0.1980 chunk 35 optimal weight: 0.0010 chunk 114 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.2925 r_free = 0.2925 target = 0.056603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.044837 restraints weight = 104162.163| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 5.12 r_work: 0.2438 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 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 = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14458 Z= 0.101 Angle : 0.497 6.462 19742 Z= 0.237 Chirality : 0.039 0.137 2170 Planarity : 0.003 0.027 2609 Dihedral : 8.015 82.948 2046 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.08 % Rotamer: Outliers : 0.49 % Allowed : 6.66 % Favored : 92.85 % 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: 1.19 (0.20), residues: 1831 helix: 1.37 (0.23), residues: 524 sheet: 0.79 (0.24), residues: 441 loop : 0.58 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 71 HIS 0.003 0.000 HIS A 84 PHE 0.007 0.001 PHE B 116 TYR 0.007 0.001 TYR A 186 ARG 0.003 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02364 ( 609) hydrogen bonds : angle 4.24049 ( 1968) covalent geometry : bond 0.00285 (14452) covalent geometry : angle 0.49698 (19742) Misc. bond : bond 0.07897 ( 6) *********************** 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 72 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.492 Fit side-chains REVERT: A 134 ASP cc_start: 0.8496 (t0) cc_final: 0.8278 (t0) REVERT: D 141 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: E 210 MET cc_start: 0.9157 (tpt) cc_final: 0.8856 (mmm) REVERT: F 141 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8193 (m-80) outliers start: 7 outliers final: 2 residues processed: 70 average time/residue: 0.2282 time to fit residues: 26.0119 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 : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 178 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 = 0.2915 r_free = 0.2915 target = 0.056130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.044722 restraints weight = 87525.305| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 4.74 r_work: 0.2445 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2458 r_free = 0.2458 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2458 r_free = 0.2458 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 14458 Z= 0.125 Angle : 0.504 6.433 19742 Z= 0.240 Chirality : 0.039 0.140 2170 Planarity : 0.003 0.026 2609 Dihedral : 7.989 82.149 2046 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.75 % Rotamer: Outliers : 0.49 % Allowed : 7.29 % Favored : 92.22 % 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: 1.40 (0.23), residues: 524 sheet: 0.78 (0.24), residues: 441 loop : 0.60 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 71 HIS 0.003 0.000 HIS A 84 PHE 0.006 0.001 PHE B 116 TYR 0.006 0.001 TYR A 186 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02422 ( 609) hydrogen bonds : angle 4.20732 ( 1968) covalent geometry : bond 0.00348 (14452) covalent geometry : angle 0.50421 (19742) Misc. bond : bond 0.09240 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 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 74 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.490 Fit side-chains REVERT: A 134 ASP cc_start: 0.8455 (t0) cc_final: 0.8237 (t0) REVERT: D 42 ASP cc_start: 0.8736 (m-30) cc_final: 0.8433 (m-30) REVERT: D 141 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: F 141 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8186 (m-80) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.2821 time to fit residues: 32.5418 Evaluate side-chains 71 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 141 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 102 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 111 optimal weight: 0.0010 chunk 48 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.043750 restraints weight = 95709.122| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 4.92 r_work: 0.2414 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 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 = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 14458 Z= 0.163 Angle : 0.522 6.405 19742 Z= 0.249 Chirality : 0.039 0.156 2170 Planarity : 0.003 0.025 2609 Dihedral : 8.023 81.645 2046 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 0.63 % Allowed : 7.43 % Favored : 91.94 % 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: 1.15 (0.20), residues: 1831 helix: 1.33 (0.23), residues: 524 sheet: 0.75 (0.24), residues: 441 loop : 0.59 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 71 HIS 0.004 0.001 HIS A 84 PHE 0.010 0.001 PHE A 52 TYR 0.007 0.001 TYR D 141 ARG 0.002 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.02612 ( 609) hydrogen bonds : angle 4.28071 ( 1968) covalent geometry : bond 0.00435 (14452) covalent geometry : angle 0.52153 (19742) Misc. bond : bond 0.11437 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 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: 9 poor density : 64 time to evaluate : 1.499 Fit side-chains REVERT: A 134 ASP cc_start: 0.8543 (t0) cc_final: 0.8257 (t0) REVERT: D 141 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: E 55 GLN cc_start: 0.8361 (pp30) cc_final: 0.8067 (pm20) REVERT: F 141 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8198 (m-80) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.2210 time to fit residues: 25.7716 Evaluate side-chains 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 D residue 166 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 141 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 0.0570 chunk 166 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 162 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 88 optimal weight: 0.9980 overall best weight: 0.3452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.057284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.045759 restraints weight = 97291.918| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 4.93 r_work: 0.2471 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14458 Z= 0.091 Angle : 0.491 6.233 19742 Z= 0.234 Chirality : 0.038 0.152 2170 Planarity : 0.003 0.026 2609 Dihedral : 7.964 83.009 2046 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 0.42 % Allowed : 7.85 % Favored : 91.73 % 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: 1.32 (0.20), residues: 1831 helix: 1.54 (0.23), residues: 524 sheet: 0.83 (0.24), residues: 441 loop : 0.64 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 71 HIS 0.002 0.000 HIS C 137 PHE 0.009 0.001 PHE A 52 TYR 0.008 0.001 TYR A 186 ARG 0.001 0.000 ARG F 288 Details of bonding type rmsd hydrogen bonds : bond 0.02158 ( 609) hydrogen bonds : angle 4.06465 ( 1968) covalent geometry : bond 0.00261 (14452) covalent geometry : angle 0.49055 (19742) Misc. bond : bond 0.06155 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 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 76 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 1.732 Fit side-chains REVERT: A 140 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8493 (tmtt) REVERT: D 42 ASP cc_start: 0.8660 (m-30) cc_final: 0.8354 (m-30) REVERT: D 141 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: E 55 GLN cc_start: 0.8409 (pp30) cc_final: 0.8136 (pm20) REVERT: F 141 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: F 210 MET cc_start: 0.8941 (mmm) cc_final: 0.8736 (mmm) outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 0.2735 time to fit residues: 33.3198 Evaluate side-chains 71 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 141 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.2804 r_free = 0.2804 target = 0.052887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.040820 restraints weight = 111433.743| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 5.36 r_work: 0.2286 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2295 r_free = 0.2295 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2295 r_free = 0.2295 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.206 14458 Z= 0.377 Angle : 0.656 8.619 19742 Z= 0.318 Chirality : 0.044 0.161 2170 Planarity : 0.004 0.033 2609 Dihedral : 8.231 80.085 2046 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 0.56 % Allowed : 7.99 % Favored : 91.44 % 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: 0.75 (0.20), residues: 1831 helix: 0.88 (0.23), residues: 524 sheet: 0.40 (0.25), residues: 405 loop : 0.49 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 193 HIS 0.007 0.001 HIS A 84 PHE 0.014 0.001 PHE E 142 TYR 0.011 0.001 TYR D 141 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 609) hydrogen bonds : angle 4.66138 ( 1968) covalent geometry : bond 0.00936 (14452) covalent geometry : angle 0.65648 (19742) Misc. bond : bond 0.18751 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 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 66 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.616 Fit side-chains REVERT: D 141 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8139 (m-10) REVERT: F 141 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7947 (m-80) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.2277 time to fit residues: 23.9346 Evaluate side-chains 65 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 141 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 81 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.056078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.044214 restraints weight = 115554.025| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 5.33 r_work: 0.2414 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 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 = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 14458 Z= 0.105 Angle : 0.517 6.701 19742 Z= 0.248 Chirality : 0.039 0.169 2170 Planarity : 0.003 0.028 2609 Dihedral : 8.075 83.128 2046 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 0.42 % Allowed : 7.99 % Favored : 91.58 % 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: 1.09 (0.20), residues: 1831 helix: 1.31 (0.23), residues: 524 sheet: 0.67 (0.24), residues: 441 loop : 0.55 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 71 HIS 0.003 0.001 HIS A 84 PHE 0.007 0.001 PHE A 52 TYR 0.008 0.001 TYR A 186 ARG 0.002 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.02387 ( 609) hydrogen bonds : angle 4.21109 ( 1968) covalent geometry : bond 0.00298 (14452) covalent geometry : angle 0.51669 (19742) Misc. bond : bond 0.08811 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 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 69 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 3.672 Fit side-chains REVERT: D 141 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: E 55 GLN cc_start: 0.8348 (pp30) cc_final: 0.8031 (pm20) REVERT: F 141 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: F 210 MET cc_start: 0.9063 (mmm) cc_final: 0.8861 (mmm) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.2831 time to fit residues: 31.7672 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 : 3.560 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 141 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.0570 chunk 158 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.0470 chunk 167 optimal weight: 0.8980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.057640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.045906 restraints weight = 112624.615| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 5.24 r_work: 0.2476 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14458 Z= 0.092 Angle : 0.502 6.712 19742 Z= 0.240 Chirality : 0.038 0.160 2170 Planarity : 0.003 0.032 2609 Dihedral : 7.972 82.585 2046 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 0.42 % Allowed : 8.06 % Favored : 91.51 % 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: 1.32 (0.20), residues: 1831 helix: 1.58 (0.23), residues: 524 sheet: 0.81 (0.24), residues: 441 loop : 0.63 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 71 HIS 0.002 0.000 HIS C 137 PHE 0.009 0.001 PHE A 52 TYR 0.007 0.001 TYR F 263 ARG 0.002 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.02112 ( 609) hydrogen bonds : angle 3.99183 ( 1968) covalent geometry : bond 0.00265 (14452) covalent geometry : angle 0.50191 (19742) Misc. bond : bond 0.05767 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7365.26 seconds wall clock time: 130 minutes 47.51 seconds (7847.51 seconds total)