Starting phenix.real_space_refine on Fri May 16 07:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rwy_19568/05_2025/8rwy_19568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rwy_19568/05_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_19568/05_2025/8rwy_19568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rwy_19568/05_2025/8rwy_19568.map" model { file = "/net/cci-nas-00/data/ceres_data/8rwy_19568/05_2025/8rwy_19568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rwy_19568/05_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-5687/modules/chem_data/mon_lib" Total number of atoms: 14109 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2318 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 306, 2318 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2358 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2306 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2310 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2316 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 289} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2302 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 2290 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2284 Classifications: {'peptide': 306} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 306, 2284 Classifications: {'peptide': 306} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 288} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2326 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLN A 133 " occ=0.32 ... (16 atoms not shown) pdb=" NE2BGLN A 133 " occ=0.68 residue: pdb=" N ASER F 76 " occ=0.22 ... (10 atoms not shown) pdb=" OG BSER F 76 " occ=0.78 Time building chain proxies: 12.43, per 1000 atoms: 0.88 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: 3.28 Conformation dependent library (CDL) restraints added in 2.2 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: 1.79 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: 4.65 Time building geometry restraints manager: 3.86 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: 0.010 Normalize map: mean=0, sd=1: 6.680 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.570 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.320 ------------------------------------------------------------------------------- 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 : 1.509 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: 0.2514 time to fit residues: 27.7376 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 : 1.517 ------------------------------------------------------------------------------- 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 = 0.053383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.041213 restraints weight = 112463.814| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 5.38 r_work: 0.2297 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2308 r_free = 0.2308 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2308 r_free = 0.2308 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 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 5.01011 ( 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 : 1.703 Fit side-chains REVERT: A 134 ASP cc_start: 0.8909 (t0) cc_final: 0.8235 (t0) REVERT: E 210 MET cc_start: 0.9211 (tpt) cc_final: 0.8814 (tpp) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.2407 time to fit residues: 24.4873 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 : 1.642 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2906 r_free = 0.2906 target = 0.055872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.044544 restraints weight = 84271.971| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.63 r_work: 0.2441 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2445 r_free = 0.2445 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 = 0.2445 r_free = 0.2445 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 14458 Z= 0.118 Angle : 0.518 6.688 19742 Z= 0.248 Chirality : 0.039 0.145 2170 Planarity : 0.003 0.032 2609 Dihedral : 8.060 82.265 2046 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1831 helix: 1.22 (0.23), residues: 524 sheet: 0.87 (0.24), residues: 441 loop : 0.53 (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 0.007 0.001 PHE A 116 TYR 0.009 0.001 TYR A 141 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 609) hydrogen bonds : angle 4.49119 ( 1968) covalent geometry : bond 0.00324 (14452) covalent geometry : angle 0.51810 (19742) Misc. bond : bond 0.09471 ( 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 : 1.686 Fit side-chains REVERT: A 134 ASP cc_start: 0.8600 (t0) cc_final: 0.8285 (t0) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.2304 time to fit residues: 26.5058 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 : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 111 optimal weight: 0.0030 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 = 0.2865 r_free = 0.2865 target = 0.054147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.042663 restraints weight = 91395.431| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.77 r_work: 0.2386 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2395 r_free = 0.2395 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 = 0.2395 r_free = 0.2395 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 14458 Z= 0.238 Angle : 0.564 7.687 19742 Z= 0.270 Chirality : 0.041 0.149 2170 Planarity : 0.003 0.026 2609 Dihedral : 8.094 80.793 2046 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 0.42 % Allowed : 6.10 % Favored : 93.48 % 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: 0.70 (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 0.010 0.001 PHE C 142 TYR 0.015 0.001 TYR A 141 ARG 0.002 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 609) hydrogen bonds : angle 4.58339 ( 1968) covalent geometry : bond 0.00612 (14452) covalent geometry : angle 0.56360 (19742) Misc. bond : bond 0.14557 ( 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 66 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.613 Fit side-chains REVERT: A 134 ASP cc_start: 0.8579 (t0) cc_final: 0.8288 (t0) REVERT: D 141 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: E 55 GLN cc_start: 0.8465 (pp30) cc_final: 0.8242 (pm20) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.2330 time to fit residues: 25.2798 Evaluate side-chains 65 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 57 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 35 optimal weight: 0.0040 chunk 114 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4972 ------------------------------------------------------------------------------- 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 = 0.2924 r_free = 0.2924 target = 0.056575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.044836 restraints weight = 104082.224| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 5.12 r_work: 0.2441 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- 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: 0.8928 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 14458 Z= 0.100 Angle : 0.496 6.509 19742 Z= 0.237 Chirality : 0.039 0.137 2170 Planarity : 0.003 0.026 2609 Dihedral : 8.011 82.890 2046 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.08 % Rotamer: Outliers : 0.49 % Allowed : 6.59 % Favored : 92.92 % 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: 1.38 (0.23), residues: 524 sheet: 0.78 (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 0.006 0.001 PHE B 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 0.02353 ( 609) hydrogen bonds : angle 4.23960 ( 1968) covalent geometry : bond 0.00284 (14452) covalent geometry : angle 0.49649 (19742) Misc. bond : bond 0.07650 ( 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 : 1.488 Fit side-chains REVERT: A 134 ASP cc_start: 0.8553 (t0) cc_final: 0.8276 (t0) REVERT: D 141 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: E 210 MET cc_start: 0.9158 (tpt) cc_final: 0.8846 (mmm) REVERT: F 141 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8145 (m-80) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.2340 time to fit residues: 27.0375 Evaluate side-chains 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 178 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.055957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.044524 restraints weight = 87493.842| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.75 r_work: 0.2441 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- 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: 0.9019 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 0.115 14458 Z= 0.133 Angle : 0.508 6.679 19742 Z= 0.241 Chirality : 0.039 0.140 2170 Planarity : 0.003 0.025 2609 Dihedral : 7.988 81.983 2046 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 0.49 % Allowed : 7.08 % Favored : 92.43 % 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: 1.18 (0.20), residues: 1831 helix: 1.38 (0.23), residues: 524 sheet: 0.76 (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 0.003 0.001 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 0.02458 ( 609) hydrogen bonds : angle 4.21930 ( 1968) covalent geometry : bond 0.00368 (14452) covalent geometry : angle 0.50764 (19742) Misc. bond : bond 0.09686 ( 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 73 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.495 Fit side-chains REVERT: A 134 ASP cc_start: 0.8465 (t0) cc_final: 0.8247 (t0) REVERT: D 42 ASP cc_start: 0.8738 (m-30) cc_final: 0.8447 (m-30) REVERT: D 141 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: F 141 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8187 (m-80) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.2350 time to fit residues: 27.1377 Evaluate side-chains 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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: 4.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 166 optimal weight: 0.0170 chunk 17 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- 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 = 0.2889 r_free = 0.2889 target = 0.055121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.043518 restraints weight = 95895.511| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 4.91 r_work: 0.2409 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2415 r_free = 0.2415 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 = 0.2415 r_free = 0.2415 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 14458 Z= 0.172 Angle : 0.524 6.525 19742 Z= 0.250 Chirality : 0.040 0.156 2170 Planarity : 0.003 0.025 2609 Dihedral : 8.026 81.588 2046 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 0.63 % Allowed : 7.50 % Favored : 91.87 % 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: 1.11 (0.20), residues: 1831 helix: 1.29 (0.23), residues: 524 sheet: 0.71 (0.24), residues: 441 loop : 0.57 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 71 HIS 0.004 0.001 HIS A 84 PHE 0.011 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 0.02641 ( 609) hydrogen bonds : angle 4.29923 ( 1968) covalent geometry : bond 0.00458 (14452) covalent geometry : angle 0.52439 (19742) Misc. bond : bond 0.11893 ( 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 : 1.629 Fit side-chains REVERT: A 134 ASP cc_start: 0.8557 (t0) cc_final: 0.8266 (t0) REVERT: D 141 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: E 55 GLN cc_start: 0.8359 (pp30) cc_final: 0.8051 (pm20) REVERT: F 141 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8198 (m-80) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.2298 time to fit residues: 26.8518 Evaluate side-chains 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.2890 r_free = 0.2890 target = 0.055095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.043552 restraints weight = 97858.611| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 4.95 r_work: 0.2402 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2414 r_free = 0.2414 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 = 0.2414 r_free = 0.2414 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 14458 Z= 0.166 Angle : 0.524 6.477 19742 Z= 0.250 Chirality : 0.039 0.155 2170 Planarity : 0.003 0.025 2609 Dihedral : 8.044 81.664 2046 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.75 % Rotamer: Outliers : 0.56 % Allowed : 7.64 % Favored : 91.80 % 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: 1.28 (0.23), residues: 524 sheet: 0.68 (0.24), residues: 441 loop : 0.57 (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 0.02614 ( 609) hydrogen bonds : angle 4.28684 ( 1968) covalent geometry : bond 0.00442 (14452) covalent geometry : angle 0.52356 (19742) Misc. bond : bond 0.11727 ( 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 71 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.756 Fit side-chains REVERT: A 134 ASP cc_start: 0.8499 (t0) cc_final: 0.8258 (t0) REVERT: D 141 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: F 141 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: F 210 MET cc_start: 0.9040 (mmm) cc_final: 0.8803 (mmm) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.2341 time to fit residues: 26.5758 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 : 1.721 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.2876 r_free = 0.2876 target = 0.054510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.042786 restraints weight = 112852.533| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 5.21 r_work: 0.2378 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2386 r_free = 0.2386 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 = 0.2386 r_free = 0.2386 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 14458 Z= 0.201 Angle : 0.545 7.017 19742 Z= 0.261 Chirality : 0.040 0.172 2170 Planarity : 0.003 0.024 2609 Dihedral : 8.092 81.273 2046 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 0.56 % Allowed : 7.78 % Favored : 91.65 % 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: 1.18 (0.23), residues: 524 sheet: 0.45 (0.25), residues: 405 loop : 0.57 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 71 HIS 0.005 0.001 HIS A 84 PHE 0.010 0.001 PHE A 52 TYR 0.009 0.001 TYR D 141 ARG 0.002 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 609) hydrogen bonds : angle 4.38311 ( 1968) covalent geometry : bond 0.00524 (14452) covalent geometry : angle 0.54531 (19742) Misc. bond : bond 0.13557 ( 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 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 1.477 Fit side-chains REVERT: A 134 ASP cc_start: 0.8550 (t0) cc_final: 0.8290 (t0) REVERT: D 141 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: E 55 GLN cc_start: 0.8400 (pp30) cc_final: 0.8090 (pm20) REVERT: F 141 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8194 (m-80) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.2277 time to fit residues: 25.0718 Evaluate side-chains 69 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.2908 r_free = 0.2908 target = 0.055775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.043872 restraints weight = 115784.158| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 5.35 r_work: 0.2408 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 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 = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 14458 Z= 0.121 Angle : 0.511 6.635 19742 Z= 0.243 Chirality : 0.039 0.166 2170 Planarity : 0.003 0.024 2609 Dihedral : 8.038 82.401 2046 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 0.56 % Allowed : 7.64 % Favored : 91.80 % 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: 1.13 (0.20), residues: 1831 helix: 1.35 (0.23), residues: 524 sheet: 0.67 (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 0.009 0.001 PHE A 52 TYR 0.007 0.001 TYR D 141 ARG 0.001 0.000 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.02434 ( 609) hydrogen bonds : angle 4.20923 ( 1968) covalent geometry : bond 0.00339 (14452) covalent geometry : angle 0.51105 (19742) Misc. bond : bond 0.09738 ( 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 73 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.545 Fit side-chains REVERT: A 134 ASP cc_start: 0.8550 (t0) cc_final: 0.8249 (t0) REVERT: D 141 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: D 210 MET cc_start: 0.9272 (mmm) cc_final: 0.9067 (mmm) REVERT: E 55 GLN cc_start: 0.8390 (pp30) cc_final: 0.8095 (pm20) REVERT: F 141 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: F 210 MET cc_start: 0.9071 (mmm) cc_final: 0.8854 (mmm) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.2193 time to fit residues: 25.6134 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 : 1.433 ------------------------------------------------------------------------------- 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=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: 1.9990 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.2901 r_free = 0.2901 target = 0.055512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.043624 restraints weight = 112996.816| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 5.28 r_work: 0.2404 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 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 = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 14458 Z= 0.146 Angle : 0.525 7.920 19742 Z= 0.249 Chirality : 0.039 0.165 2170 Planarity : 0.003 0.023 2609 Dihedral : 8.037 81.871 2046 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 0.49 % Allowed : 7.92 % 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: 1.12 (0.20), residues: 1831 helix: 1.34 (0.23), residues: 524 sheet: 0.66 (0.24), residues: 441 loop : 0.58 (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 0.001 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.02523 ( 609) hydrogen bonds : angle 4.22566 ( 1968) covalent geometry : bond 0.00398 (14452) covalent geometry : angle 0.52468 (19742) Misc. bond : bond 0.10701 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6170.94 seconds wall clock time: 108 minutes 20.23 seconds (6500.23 seconds total)