Starting phenix.real_space_refine on Thu Sep 18 04:52:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rwy_19568/09_2025/8rwy_19568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rwy_19568/09_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_19568/09_2025/8rwy_19568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rwy_19568/09_2025/8rwy_19568.map" model { file = "/net/cci-nas-00/data/ceres_data/8rwy_19568/09_2025/8rwy_19568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rwy_19568/09_2025/8rwy_19568.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2} 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: 4.75, per 1000 atoms: 0.34 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: 0.85 Conformation dependent library (CDL) restraints added in 730.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.64 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: 1.99 Time building geometry restraints manager: 1.26 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 through 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 through 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 through 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 through 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 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.22 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.840 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 207 TYR 0.014 0.001 TYR C 186 PHE 0.008 0.001 PHE C 142 TRP 0.008 0.001 TRP D 71 HIS 0.002 0.000 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00291 (14452) covalent geometry : angle 0.48739 (19742) hydrogen bonds : bond 0.13123 ( 609) hydrogen bonds : angle 6.40730 ( 1968) 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 : 0.480 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: 0.1146 time to fit residues: 12.7282 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 : 0.477 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0010 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.9590 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.055074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.044012 restraints weight = 70867.095| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 4.21 r_work: 0.2417 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 14458 Z= 0.235 Angle : 0.575 7.959 19742 Z= 0.277 Chirality : 0.041 0.157 2170 Planarity : 0.003 0.046 2609 Dihedral : 8.283 85.182 2049 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1831 helix: 1.21 (0.23), residues: 524 sheet: 1.09 (0.24), residues: 435 loop : 0.52 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 265 TYR 0.016 0.001 TYR A 141 PHE 0.008 0.001 PHE D 52 TRP 0.009 0.001 TRP D 71 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00604 (14452) covalent geometry : angle 0.57539 (19742) hydrogen bonds : bond 0.03158 ( 609) hydrogen bonds : angle 4.78725 ( 1968) Misc. bond : bond 0.13672 ( 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 66 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.553 Fit side-chains REVERT: A 134 ASP cc_start: 0.8761 (t0) cc_final: 0.8341 (t0) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.1082 time to fit residues: 11.6483 Evaluate side-chains 61 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 0.0980 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.2928 r_free = 0.2928 target = 0.056715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.046153 restraints weight = 59921.441| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.94 r_work: 0.2504 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 14458 Z= 0.110 Angle : 0.505 6.628 19742 Z= 0.241 Chirality : 0.039 0.142 2170 Planarity : 0.003 0.034 2609 Dihedral : 7.948 83.068 2046 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 0.21 % Allowed : 4.00 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.20), residues: 1831 helix: 1.43 (0.24), residues: 524 sheet: 0.99 (0.24), residues: 441 loop : 0.61 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.008 0.001 TYR A 141 PHE 0.007 0.001 PHE A 116 TRP 0.009 0.001 TRP D 71 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00311 (14452) covalent geometry : angle 0.50498 (19742) hydrogen bonds : bond 0.02530 ( 609) hydrogen bonds : angle 4.38474 ( 1968) Misc. bond : bond 0.08486 ( 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: 3 poor density : 67 time to evaluate : 0.597 Fit side-chains REVERT: A 134 ASP cc_start: 0.8441 (t0) cc_final: 0.8200 (t0) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 0.1083 time to fit residues: 12.3204 Evaluate side-chains 69 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain E residue 140 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 134 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.2839 r_free = 0.2839 target = 0.053845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.042199 restraints weight = 101471.631| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 4.87 r_work: 0.2354 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2362 r_free = 0.2362 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2362 r_free = 0.2362 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.181 14458 Z= 0.294 Angle : 0.596 8.149 19742 Z= 0.286 Chirality : 0.042 0.152 2170 Planarity : 0.003 0.026 2609 Dihedral : 8.089 80.480 2046 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 0.49 % Allowed : 4.91 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.20), residues: 1831 helix: 0.99 (0.23), residues: 524 sheet: 0.77 (0.24), residues: 435 loop : 0.51 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.015 0.001 TYR A 141 PHE 0.012 0.001 PHE C 142 TRP 0.008 0.001 TRP D 71 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00741 (14452) covalent geometry : angle 0.59572 (19742) hydrogen bonds : bond 0.03198 ( 609) hydrogen bonds : angle 4.67422 ( 1968) Misc. bond : bond 0.16266 ( 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: 7 poor density : 59 time to evaluate : 0.555 Fit side-chains REVERT: A 134 ASP cc_start: 0.8689 (t0) cc_final: 0.8318 (t0) REVERT: D 141 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: E 55 GLN cc_start: 0.8433 (pp30) cc_final: 0.8210 (pm20) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.1095 time to fit residues: 11.7694 Evaluate side-chains 62 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 57 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 157 optimal weight: 0.0040 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.055362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.044014 restraints weight = 80268.874| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 4.57 r_work: 0.2428 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 14458 Z= 0.152 Angle : 0.521 6.818 19742 Z= 0.248 Chirality : 0.039 0.138 2170 Planarity : 0.003 0.025 2609 Dihedral : 8.043 81.832 2046 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 0.42 % Allowed : 5.54 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.20), residues: 1831 helix: 1.18 (0.23), residues: 524 sheet: 0.73 (0.24), residues: 435 loop : 0.55 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.008 0.001 TYR D 141 PHE 0.009 0.001 PHE C 116 TRP 0.010 0.001 TRP D 71 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00407 (14452) covalent geometry : angle 0.52134 (19742) hydrogen bonds : bond 0.02675 ( 609) hydrogen bonds : angle 4.40093 ( 1968) Misc. bond : bond 0.11404 ( 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 71 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.548 Fit side-chains REVERT: A 134 ASP cc_start: 0.8496 (t0) cc_final: 0.8257 (t0) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.1092 time to fit residues: 12.7070 Evaluate side-chains 68 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 E residue 166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 178 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.055290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.043384 restraints weight = 109613.917| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 5.23 r_work: 0.2394 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 14458 Z= 0.160 Angle : 0.523 6.680 19742 Z= 0.249 Chirality : 0.039 0.143 2170 Planarity : 0.003 0.023 2609 Dihedral : 8.032 81.634 2046 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 0.42 % Allowed : 6.73 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1831 helix: 1.22 (0.23), residues: 524 sheet: 0.69 (0.24), residues: 435 loop : 0.57 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.007 0.001 TYR D 141 PHE 0.008 0.001 PHE C 142 TRP 0.009 0.001 TRP D 71 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00429 (14452) covalent geometry : angle 0.52348 (19742) hydrogen bonds : bond 0.02650 ( 609) hydrogen bonds : angle 4.34746 ( 1968) Misc. bond : bond 0.11598 ( 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 69 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.558 Fit side-chains REVERT: A 134 ASP cc_start: 0.8577 (t0) cc_final: 0.8290 (t0) REVERT: D 141 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: F 141 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8089 (m-80) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1091 time to fit residues: 12.1782 Evaluate side-chains 68 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 176 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.2897 r_free = 0.2897 target = 0.055467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.043829 restraints weight = 96417.099| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 4.94 r_work: 0.2411 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 14458 Z= 0.151 Angle : 0.520 6.448 19742 Z= 0.248 Chirality : 0.039 0.157 2170 Planarity : 0.003 0.023 2609 Dihedral : 8.027 81.756 2046 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 0.56 % Allowed : 6.94 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.20), residues: 1831 helix: 1.27 (0.23), residues: 524 sheet: 0.70 (0.24), residues: 441 loop : 0.57 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.007 0.001 TYR D 141 PHE 0.008 0.001 PHE C 142 TRP 0.009 0.001 TRP D 71 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00409 (14452) covalent geometry : angle 0.52032 (19742) hydrogen bonds : bond 0.02591 ( 609) hydrogen bonds : angle 4.30505 ( 1968) Misc. bond : bond 0.11183 ( 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 72 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.561 Fit side-chains REVERT: A 134 ASP cc_start: 0.8489 (t0) cc_final: 0.8262 (t0) REVERT: D 141 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8364 (m-10) REVERT: E 55 GLN cc_start: 0.8386 (pp30) cc_final: 0.8095 (pm20) REVERT: F 141 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8140 (m-80) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1043 time to fit residues: 11.9310 Evaluate side-chains 68 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 144 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.2879 r_free = 0.2879 target = 0.054594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.043372 restraints weight = 78394.269| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 4.49 r_work: 0.2412 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.156 14458 Z= 0.205 Angle : 0.548 7.147 19742 Z= 0.261 Chirality : 0.040 0.158 2170 Planarity : 0.003 0.023 2609 Dihedral : 8.079 81.154 2046 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 0.70 % Allowed : 7.22 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.20), residues: 1831 helix: 1.14 (0.23), residues: 524 sheet: 0.60 (0.24), residues: 435 loop : 0.54 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 163 TYR 0.008 0.001 TYR D 141 PHE 0.008 0.001 PHE C 116 TRP 0.008 0.001 TRP D 71 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00534 (14452) covalent geometry : angle 0.54771 (19742) hydrogen bonds : bond 0.02801 ( 609) hydrogen bonds : angle 4.40928 ( 1968) Misc. bond : bond 0.13663 ( 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 70 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.475 Fit side-chains REVERT: A 134 ASP cc_start: 0.8473 (t0) cc_final: 0.8226 (t0) REVERT: D 141 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: F 141 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: F 210 MET cc_start: 0.8981 (mmm) cc_final: 0.8730 (mmm) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1104 time to fit residues: 12.2020 Evaluate side-chains 68 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 57 ASP 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 136 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 7 optimal weight: 0.0070 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 = 0.2856 r_free = 0.2856 target = 0.054589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.042896 restraints weight = 99205.065| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 4.93 r_work: 0.2367 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 14458 Z= 0.217 Angle : 0.554 7.347 19742 Z= 0.265 Chirality : 0.040 0.173 2170 Planarity : 0.003 0.023 2609 Dihedral : 8.120 81.074 2046 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 0.56 % Allowed : 7.36 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1831 helix: 1.10 (0.23), residues: 524 sheet: 0.55 (0.24), residues: 435 loop : 0.52 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.010 0.001 TYR D 141 PHE 0.009 0.001 PHE E 142 TRP 0.009 0.001 TRP D 71 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00561 (14452) covalent geometry : angle 0.55427 (19742) hydrogen bonds : bond 0.02847 ( 609) hydrogen bonds : angle 4.43370 ( 1968) Misc. bond : bond 0.14263 ( 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 67 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.591 Fit side-chains REVERT: A 134 ASP cc_start: 0.8631 (t0) cc_final: 0.8270 (t0) REVERT: D 141 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: E 55 GLN cc_start: 0.8329 (pp30) cc_final: 0.7993 (pm20) REVERT: F 141 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7974 (m-80) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.1083 time to fit residues: 11.5422 Evaluate side-chains 66 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 174 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 126 optimal weight: 0.0060 chunk 122 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.2927 r_free = 0.2927 target = 0.056643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.045475 restraints weight = 78122.723| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.52 r_work: 0.2469 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14458 Z= 0.099 Angle : 0.507 7.361 19742 Z= 0.241 Chirality : 0.039 0.167 2170 Planarity : 0.003 0.024 2609 Dihedral : 8.027 82.853 2046 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.56 % Allowed : 7.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 1831 helix: 1.42 (0.23), residues: 524 sheet: 0.67 (0.24), residues: 441 loop : 0.60 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 53 TYR 0.008 0.001 TYR A 186 PHE 0.006 0.001 PHE B 116 TRP 0.011 0.001 TRP D 71 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00282 (14452) covalent geometry : angle 0.50663 (19742) hydrogen bonds : bond 0.02311 ( 609) hydrogen bonds : angle 4.16424 ( 1968) Misc. bond : bond 0.07906 ( 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 77 residues out of total 1469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.580 Fit side-chains REVERT: A 134 ASP cc_start: 0.8378 (t0) cc_final: 0.8177 (t0) REVERT: D 42 ASP cc_start: 0.8711 (m-30) cc_final: 0.8483 (m-30) REVERT: D 141 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: D 210 MET cc_start: 0.9249 (mmm) cc_final: 0.8978 (mmm) REVERT: E 55 GLN cc_start: 0.8378 (pp30) cc_final: 0.8114 (pm20) REVERT: F 141 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: F 210 MET cc_start: 0.8971 (mmm) cc_final: 0.8767 (mmm) outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 0.1050 time to fit residues: 12.8438 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 : 0.562 ------------------------------------------------------------------------------- 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 174 optimal weight: 0.0170 chunk 115 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 172 optimal weight: 0.0040 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.6034 ------------------------------------------------------------------------------- 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 = 0.2883 r_free = 0.2883 target = 0.054791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.043590 restraints weight = 85418.549| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 4.63 r_work: 0.2411 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 14458 Z= 0.196 Angle : 0.549 6.883 19742 Z= 0.262 Chirality : 0.040 0.168 2170 Planarity : 0.003 0.024 2609 Dihedral : 8.071 81.123 2046 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 0.49 % Allowed : 7.50 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.20), residues: 1831 helix: 1.26 (0.23), residues: 524 sheet: 0.46 (0.25), residues: 405 loop : 0.60 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 163 TYR 0.009 0.001 TYR D 141 PHE 0.012 0.001 PHE A 52 TRP 0.007 0.001 TRP D 71 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00513 (14452) covalent geometry : angle 0.54918 (19742) hydrogen bonds : bond 0.02739 ( 609) hydrogen bonds : angle 4.30588 ( 1968) Misc. bond : bond 0.12858 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3280.69 seconds wall clock time: 57 minutes 8.44 seconds (3428.44 seconds total)