Starting phenix.real_space_refine on Sat Sep 12 03:35:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n27_9325/09_2026/6n27_9325.cif" } resolution = 3.0 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= 0.001 sd= 0.012 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 Ca 5 9.91 5 S 65 5.16 5 C 9135 2.51 5 N 2260 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13930 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2785 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2785 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2785 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2785 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2785 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 325} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.09, per 1000 atoms: 0.22 Number of scatterers: 13930 At special positions: 0 Unit cell: (93.568, 93.568, 114.24, 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) Ca 5 19.99 S 65 16.00 O 2465 8.00 N 2260 7.00 C 9135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.05 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.05 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.05 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.05 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=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 608.8 milliseconds 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 74.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 Processing helix chain 'A' and resid 75 through 98 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.773A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.767A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.577A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.212A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.685A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.067A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.609A pdb=" N LEU A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.784A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.772A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.767A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.577A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.213A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.686A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 4.068A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.609A pdb=" N LEU B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 Processing helix chain 'C' and resid 75 through 98 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.772A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.768A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.578A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.211A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.685A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.068A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 255 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.610A pdb=" N LEU C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 Processing helix chain 'D' and resid 75 through 98 Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.772A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.767A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.577A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.213A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.684A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 4.067A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG D 255 " --> pdb=" O CYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.535A pdb=" N LYS D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.514A pdb=" N PHE D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.610A pdb=" N LEU D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.509A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 Processing helix chain 'E' and resid 75 through 98 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.773A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.768A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.576A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.213A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.685A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 4.067A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 255 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS E 262 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.609A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2535 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: 2.13 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4320 1.34 - 1.47: 3906 1.47 - 1.59: 5989 1.59 - 1.72: 0 1.72 - 1.84: 100 Bond restraints: 14315 Sorted by residual: bond pdb=" C TRP A 102 " pdb=" N PRO A 103 " ideal model delta sigma weight residual 1.331 1.316 0.016 7.90e-03 1.60e+04 3.93e+00 bond pdb=" C TRP C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 1.331 1.316 0.015 7.90e-03 1.60e+04 3.84e+00 bond pdb=" C TRP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.331 1.316 0.015 7.90e-03 1.60e+04 3.79e+00 bond pdb=" C TRP B 102 " pdb=" N PRO B 103 " ideal model delta sigma weight residual 1.331 1.316 0.015 7.90e-03 1.60e+04 3.71e+00 bond pdb=" C TRP D 102 " pdb=" N PRO D 103 " ideal model delta sigma weight residual 1.331 1.317 0.015 7.90e-03 1.60e+04 3.57e+00 ... (remaining 14310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 18642 1.81 - 3.63: 728 3.63 - 5.44: 88 5.44 - 7.25: 17 7.25 - 9.07: 20 Bond angle restraints: 19495 Sorted by residual: angle pdb=" N VAL B 186 " pdb=" CA VAL B 186 " pdb=" C VAL B 186 " ideal model delta sigma weight residual 111.81 107.71 4.10 8.60e-01 1.35e+00 2.28e+01 angle pdb=" N VAL E 186 " pdb=" CA VAL E 186 " pdb=" C VAL E 186 " ideal model delta sigma weight residual 111.81 107.72 4.09 8.60e-01 1.35e+00 2.26e+01 angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 111.81 107.74 4.07 8.60e-01 1.35e+00 2.24e+01 angle pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 111.81 107.75 4.06 8.60e-01 1.35e+00 2.23e+01 angle pdb=" N VAL D 186 " pdb=" CA VAL D 186 " pdb=" C VAL D 186 " ideal model delta sigma weight residual 111.81 107.77 4.04 8.60e-01 1.35e+00 2.20e+01 ... (remaining 19490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 7920 15.08 - 30.15: 320 30.15 - 45.23: 110 45.23 - 60.30: 5 60.30 - 75.38: 5 Dihedral angle restraints: 8360 sinusoidal: 3325 harmonic: 5035 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " pdb=" CB CYS D 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.74 34.74 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 185 " pdb=" CB CYS E 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.74 34.74 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.70 34.70 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1203 0.042 - 0.084: 735 0.084 - 0.126: 179 0.126 - 0.168: 28 0.168 - 0.210: 10 Chirality restraints: 2155 Sorted by residual: chirality pdb=" CB VAL D 81 " pdb=" CA VAL D 81 " pdb=" CG1 VAL D 81 " pdb=" CG2 VAL D 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 81 " pdb=" CA VAL A 81 " pdb=" CG1 VAL A 81 " pdb=" CG2 VAL A 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL B 81 " pdb=" CA VAL B 81 " pdb=" CG1 VAL B 81 " pdb=" CG2 VAL B 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2152 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 287 " 0.036 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP D 287 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP D 287 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 287 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 287 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 287 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 287 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 287 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 287 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 287 " -0.036 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP A 287 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 287 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 287 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 287 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 287 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 287 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 287 " 0.035 2.00e-02 2.50e+03 2.57e-02 1.66e+01 pdb=" CG TRP E 287 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP E 287 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 287 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 287 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 287 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 287 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 287 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 287 " 0.004 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 4296 2.82 - 3.34: 12829 3.34 - 3.86: 23881 3.86 - 4.38: 27578 4.38 - 4.90: 47783 Nonbonded interactions: 116367 Sorted by model distance: nonbonded pdb=" NH2 ARG A 218 " pdb=" OD2 ASP E 104 " model vdw 2.305 3.120 nonbonded pdb=" OG1 THR D 6 " pdb=" OG SER E 231 " model vdw 2.306 3.040 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.306 3.120 nonbonded pdb=" OG1 THR B 6 " pdb=" OG SER C 231 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR C 6 " pdb=" OG SER D 231 " model vdw 2.316 3.040 ... (remaining 116362 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 13.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.007 0.053 14320 Z= 0.312 Angle : 0.880 9.068 19505 Z= 0.506 Chirality : 0.054 0.210 2155 Planarity : 0.007 0.050 2440 Dihedral : 9.609 75.376 5095 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 are not related in a simple way. whole: -2.91 (0.16), residues: 1685 helix: -1.56 (0.12), residues: 1150 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 313 TYR 0.037 0.002 TYR B 236 PHE 0.031 0.004 PHE E 80 TRP 0.069 0.005 TRP D 287 HIS 0.006 0.002 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.31 (14315) covalent geometry : angle 0.87651 / 0.50 (19495) SS BOND : bond 0.01699 / 0.91 ( 5) SS BOND : angle 3.47092 / 2.11 ( 10) hydrogen bonds : bond 0.15350 / 9.77 ( 860) hydrogen bonds : angle 5.37973 / 3.86 ( 2535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.605 Fit side-chains REVERT: A 30 LYS cc_start: 0.9114 (tttt) cc_final: 0.8909 (ttpp) REVERT: A 41 SER cc_start: 0.8938 (m) cc_final: 0.8679 (m) REVERT: C 41 SER cc_start: 0.8874 (m) cc_final: 0.8601 (m) REVERT: C 320 MET cc_start: 0.8188 (ttt) cc_final: 0.7926 (ttm) REVERT: C 325 MET cc_start: 0.9435 (mtp) cc_final: 0.9225 (mtm) REVERT: D 41 SER cc_start: 0.8917 (m) cc_final: 0.8717 (m) REVERT: E 41 SER cc_start: 0.8847 (m) cc_final: 0.8620 (m) REVERT: E 46 ILE cc_start: 0.8873 (mt) cc_final: 0.8643 (mt) outliers start: 0 outliers final: 1 residues processed: 266 average time/residue: 0.6221 time to fit residues: 180.4705 Evaluate side-chains 141 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN A 326 HIS B 326 HIS C 326 HIS D 326 HIS E 175 ASN E 326 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.082985 restraints weight = 19010.586| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.63 r_work: 0.2745 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14320 Z= 0.139 Angle : 0.521 6.561 19505 Z= 0.274 Chirality : 0.039 0.161 2155 Planarity : 0.005 0.042 2440 Dihedral : 4.062 12.741 1882 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.84 % Allowed : 8.88 % Favored : 89.28 % 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 are not related in a simple way. whole: -0.68 (0.19), residues: 1685 helix: 0.39 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 223 TYR 0.018 0.001 TYR B 97 PHE 0.012 0.001 PHE C 80 TRP 0.033 0.002 TRP D 287 HIS 0.002 0.000 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14315) covalent geometry : angle 0.52054 / 0.27 (19495) SS BOND : bond 0.00499 / 0.26 ( 5) SS BOND : angle 1.44199 / 0.86 ( 10) hydrogen bonds : bond 0.05985 / 3.89 ( 860) hydrogen bonds : angle 3.93822 / 2.84 ( 2535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.564 Fit side-chains REVERT: A 30 LYS cc_start: 0.9308 (tttt) cc_final: 0.9081 (ttpp) REVERT: A 41 SER cc_start: 0.9097 (m) cc_final: 0.8874 (m) REVERT: B 272 PHE cc_start: 0.8672 (m-10) cc_final: 0.8216 (m-80) REVERT: C 8 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8082 (mtm-85) REVERT: C 41 SER cc_start: 0.9064 (m) cc_final: 0.8849 (m) REVERT: C 149 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8400 (mtmt) REVERT: D 30 LYS cc_start: 0.9264 (ttmm) cc_final: 0.9052 (ttpp) REVERT: D 119 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: D 293 GLN cc_start: 0.9021 (tt0) cc_final: 0.8818 (tt0) REVERT: D 320 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (ttt) REVERT: E 46 ILE cc_start: 0.9024 (mt) cc_final: 0.8634 (mt) REVERT: E 149 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8383 (mtpt) REVERT: E 320 MET cc_start: 0.8825 (ttt) cc_final: 0.8589 (ttm) outliers start: 28 outliers final: 10 residues processed: 168 average time/residue: 0.5917 time to fit residues: 109.5976 Evaluate side-chains 132 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.077032 restraints weight = 19364.680| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.70 r_work: 0.2641 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 14320 Z= 0.226 Angle : 0.587 7.473 19505 Z= 0.304 Chirality : 0.043 0.159 2155 Planarity : 0.005 0.045 2440 Dihedral : 3.946 13.798 1880 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.16 % Allowed : 9.74 % Favored : 87.11 % 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 are not related in a simple way. whole: 0.10 (0.20), residues: 1685 helix: 1.04 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -2.21 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 223 TYR 0.023 0.002 TYR E 236 PHE 0.020 0.002 PHE C 80 TRP 0.024 0.003 TRP A 287 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (14315) covalent geometry : angle 0.58550 / 0.30 (19495) SS BOND : bond 0.00804 / 0.42 ( 5) SS BOND : angle 1.81384 / 1.07 ( 10) hydrogen bonds : bond 0.07297 / 4.74 ( 860) hydrogen bonds : angle 4.03778 / 2.91 ( 2535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.542 Fit side-chains REVERT: A 41 SER cc_start: 0.9107 (m) cc_final: 0.8856 (t) REVERT: A 136 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.9064 (p) REVERT: A 149 LYS cc_start: 0.8705 (mttm) cc_final: 0.8504 (mtpt) REVERT: A 324 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 30 LYS cc_start: 0.9362 (ttmm) cc_final: 0.9133 (ttpp) REVERT: B 136 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8971 (p) REVERT: B 203 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8496 (m-30) REVERT: B 320 MET cc_start: 0.9026 (ttt) cc_final: 0.8759 (ttm) REVERT: B 334 LYS cc_start: 0.8749 (mttm) cc_final: 0.8500 (mttm) REVERT: C 8 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8021 (mtm-85) REVERT: C 41 SER cc_start: 0.9005 (m) cc_final: 0.8790 (m) REVERT: C 149 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8471 (mtpt) REVERT: C 324 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: C 334 LYS cc_start: 0.8957 (mttp) cc_final: 0.8537 (mttm) REVERT: D 30 LYS cc_start: 0.9286 (ttmm) cc_final: 0.9027 (ttpp) REVERT: D 75 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7815 (mt) REVERT: D 293 GLN cc_start: 0.9120 (tt0) cc_final: 0.8870 (tt0) REVERT: E 42 LEU cc_start: 0.8825 (mt) cc_final: 0.8604 (mp) REVERT: E 119 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: E 149 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8351 (mtpt) REVERT: E 324 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7708 (mp0) outliers start: 48 outliers final: 19 residues processed: 160 average time/residue: 0.5406 time to fit residues: 96.2245 Evaluate side-chains 151 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.079015 restraints weight = 19184.141| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.69 r_work: 0.2677 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14320 Z= 0.159 Angle : 0.519 7.679 19505 Z= 0.268 Chirality : 0.040 0.155 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.790 14.372 1880 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.22 % Allowed : 10.79 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1685 helix: 1.35 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 223 TYR 0.018 0.001 TYR A 97 PHE 0.017 0.002 PHE C 80 TRP 0.016 0.002 TRP E 287 HIS 0.003 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14315) covalent geometry : angle 0.51812 / 0.27 (19495) SS BOND : bond 0.00577 / 0.30 ( 5) SS BOND : angle 1.27875 / 0.74 ( 10) hydrogen bonds : bond 0.06122 / 3.98 ( 860) hydrogen bonds : angle 3.84966 / 2.77 ( 2535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.610 Fit side-chains REVERT: A 30 LYS cc_start: 0.9244 (tttm) cc_final: 0.8926 (tttt) REVERT: A 41 SER cc_start: 0.9100 (m) cc_final: 0.8872 (t) REVERT: A 136 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.9058 (p) REVERT: A 149 LYS cc_start: 0.8681 (mttm) cc_final: 0.8472 (mtpt) REVERT: A 324 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 119 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: B 334 LYS cc_start: 0.8693 (mttm) cc_final: 0.8314 (mttm) REVERT: C 8 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7996 (mtm-85) REVERT: C 41 SER cc_start: 0.8998 (m) cc_final: 0.8791 (m) REVERT: C 149 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8509 (mtpt) REVERT: C 303 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7016 (t70) REVERT: C 324 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: C 334 LYS cc_start: 0.8956 (mttp) cc_final: 0.8556 (mttm) REVERT: D 60 LEU cc_start: 0.8545 (tt) cc_final: 0.8328 (tp) REVERT: D 75 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7679 (mt) REVERT: D 293 GLN cc_start: 0.9148 (tt0) cc_final: 0.8879 (tt0) REVERT: E 149 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8339 (mtpt) outliers start: 49 outliers final: 17 residues processed: 162 average time/residue: 0.5170 time to fit residues: 93.2608 Evaluate side-chains 146 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 164 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 128 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 2.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.080309 restraints weight = 19149.504| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.69 r_work: 0.2701 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14320 Z= 0.136 Angle : 0.495 7.147 19505 Z= 0.255 Chirality : 0.039 0.154 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.649 13.203 1880 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.89 % Allowed : 11.84 % Favored : 85.26 % 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 are not related in a simple way. whole: 0.79 (0.21), residues: 1685 helix: 1.59 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -2.03 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 223 TYR 0.018 0.001 TYR B 97 PHE 0.019 0.001 PHE C 80 TRP 0.014 0.002 TRP E 94 HIS 0.002 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14315) covalent geometry : angle 0.49485 / 0.25 (19495) SS BOND : bond 0.00502 / 0.26 ( 5) SS BOND : angle 1.11451 / 0.64 ( 10) hydrogen bonds : bond 0.05649 / 3.67 ( 860) hydrogen bonds : angle 3.76559 / 2.71 ( 2535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.585 Fit side-chains REVERT: A 30 LYS cc_start: 0.9234 (tttm) cc_final: 0.8913 (tttt) REVERT: A 149 LYS cc_start: 0.8633 (mttm) cc_final: 0.8416 (mtpt) REVERT: A 324 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 119 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: B 334 LYS cc_start: 0.8660 (mttm) cc_final: 0.8329 (mttm) REVERT: C 8 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7997 (mtm-85) REVERT: C 41 SER cc_start: 0.8997 (m) cc_final: 0.8795 (m) REVERT: C 149 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8492 (mtpt) REVERT: C 334 LYS cc_start: 0.8929 (mttp) cc_final: 0.8501 (mttm) REVERT: D 75 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7648 (mt) REVERT: D 293 GLN cc_start: 0.9167 (tt0) cc_final: 0.8895 (tt0) REVERT: D 334 LYS cc_start: 0.8856 (mttm) cc_final: 0.8607 (mttm) REVERT: E 149 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8290 (mtpt) outliers start: 44 outliers final: 18 residues processed: 162 average time/residue: 0.4822 time to fit residues: 87.9487 Evaluate side-chains 152 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 124 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.077497 restraints weight = 19169.051| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.71 r_work: 0.2653 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14320 Z= 0.184 Angle : 0.537 6.992 19505 Z= 0.275 Chirality : 0.041 0.154 2155 Planarity : 0.004 0.046 2440 Dihedral : 3.693 13.013 1880 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.16 % Allowed : 11.78 % Favored : 85.07 % 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 are not related in a simple way. whole: 0.78 (0.21), residues: 1685 helix: 1.55 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.98 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 196 TYR 0.019 0.001 TYR A 97 PHE 0.018 0.002 PHE C 80 TRP 0.014 0.002 TRP E 94 HIS 0.003 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (14315) covalent geometry : angle 0.53581 / 0.27 (19495) SS BOND : bond 0.00646 / 0.34 ( 5) SS BOND : angle 1.37117 / 0.81 ( 10) hydrogen bonds : bond 0.06477 / 4.20 ( 860) hydrogen bonds : angle 3.87030 / 2.79 ( 2535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.605 Fit side-chains REVERT: A 30 LYS cc_start: 0.9250 (tttm) cc_final: 0.8970 (ttpp) REVERT: A 136 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9113 (p) REVERT: A 149 LYS cc_start: 0.8651 (mttm) cc_final: 0.8423 (mtpt) REVERT: A 324 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 119 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: B 203 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: B 324 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: B 334 LYS cc_start: 0.8705 (mttm) cc_final: 0.8376 (mttm) REVERT: C 8 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7997 (mtm-85) REVERT: C 41 SER cc_start: 0.9006 (m) cc_final: 0.8802 (m) REVERT: C 149 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8508 (mtpt) REVERT: C 324 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: C 334 LYS cc_start: 0.8994 (mttp) cc_final: 0.8540 (mttm) REVERT: D 75 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7853 (mt) REVERT: D 293 GLN cc_start: 0.9176 (tt0) cc_final: 0.8901 (tt0) REVERT: E 119 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: E 149 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: E 324 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: E 334 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8573 (mtpm) outliers start: 48 outliers final: 20 residues processed: 155 average time/residue: 0.5552 time to fit residues: 95.6746 Evaluate side-chains 155 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.080946 restraints weight = 19015.037| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.66 r_work: 0.2701 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14320 Z= 0.132 Angle : 0.491 8.255 19505 Z= 0.252 Chirality : 0.038 0.152 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.603 13.512 1880 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.70 % Allowed : 12.37 % Favored : 84.93 % 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 are not related in a simple way. whole: 0.92 (0.21), residues: 1685 helix: 1.65 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 223 TYR 0.017 0.001 TYR B 97 PHE 0.020 0.001 PHE C 80 TRP 0.014 0.001 TRP E 94 HIS 0.002 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14315) covalent geometry : angle 0.49101 / 0.25 (19495) SS BOND : bond 0.00467 / 0.25 ( 5) SS BOND : angle 1.07752 / 0.62 ( 10) hydrogen bonds : bond 0.05578 / 3.62 ( 860) hydrogen bonds : angle 3.75021 / 2.70 ( 2535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.536 Fit side-chains REVERT: A 30 LYS cc_start: 0.9235 (tttm) cc_final: 0.9017 (ttpt) REVERT: A 149 LYS cc_start: 0.8627 (mttm) cc_final: 0.8412 (mtpt) REVERT: B 324 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: B 334 LYS cc_start: 0.8677 (mttm) cc_final: 0.8318 (mttm) REVERT: C 8 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8066 (mtm-85) REVERT: C 149 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8475 (mtpt) REVERT: C 303 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.6936 (t0) REVERT: C 324 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: C 325 MET cc_start: 0.9394 (mtp) cc_final: 0.9126 (mtm) REVERT: C 334 LYS cc_start: 0.8933 (mttp) cc_final: 0.8487 (mttm) REVERT: D 75 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7792 (mt) REVERT: D 293 GLN cc_start: 0.9171 (tt0) cc_final: 0.8912 (tt0) REVERT: D 334 LYS cc_start: 0.8844 (mttm) cc_final: 0.8637 (mttm) REVERT: E 30 LYS cc_start: 0.9347 (ttmm) cc_final: 0.8952 (ttpp) REVERT: E 119 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: E 149 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8304 (mtpt) REVERT: E 324 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: E 334 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8546 (mtpm) outliers start: 41 outliers final: 21 residues processed: 154 average time/residue: 0.5146 time to fit residues: 88.1358 Evaluate side-chains 154 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.075828 restraints weight = 19287.555| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.71 r_work: 0.2608 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14320 Z= 0.261 Angle : 0.598 7.408 19505 Z= 0.306 Chirality : 0.044 0.152 2155 Planarity : 0.005 0.047 2440 Dihedral : 3.795 14.049 1880 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.09 % Allowed : 12.30 % Favored : 84.61 % 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 are not related in a simple way. whole: 0.74 (0.21), residues: 1685 helix: 1.47 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 92 TYR 0.022 0.002 TYR B 97 PHE 0.021 0.002 PHE C 80 TRP 0.014 0.002 TRP E 94 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.26 (14315) covalent geometry : angle 0.59650 / 0.31 (19495) SS BOND : bond 0.00847 / 0.45 ( 5) SS BOND : angle 1.80012 / 1.07 ( 10) hydrogen bonds : bond 0.07351 / 4.77 ( 860) hydrogen bonds : angle 4.01551 / 2.90 ( 2535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.523 Fit side-chains REVERT: A 30 LYS cc_start: 0.9260 (tttm) cc_final: 0.8971 (ttpp) REVERT: A 136 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9158 (p) REVERT: A 149 LYS cc_start: 0.8692 (mttm) cc_final: 0.8450 (mtpt) REVERT: A 324 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: B 30 LYS cc_start: 0.9378 (ttmm) cc_final: 0.8946 (tttm) REVERT: B 119 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: B 203 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8545 (m-30) REVERT: B 324 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: C 8 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8018 (mtm-85) REVERT: C 119 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: C 149 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8516 (mtpt) REVERT: C 324 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: C 334 LYS cc_start: 0.9055 (mttp) cc_final: 0.8567 (mttm) REVERT: D 75 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8115 (mt) REVERT: D 293 GLN cc_start: 0.9216 (tt0) cc_final: 0.8930 (tt0) REVERT: E 119 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: E 149 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: E 324 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: E 334 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8562 (mtpm) outliers start: 47 outliers final: 20 residues processed: 153 average time/residue: 0.5558 time to fit residues: 94.5235 Evaluate side-chains 154 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.082663 restraints weight = 19055.673| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.66 r_work: 0.2729 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14320 Z= 0.112 Angle : 0.488 9.545 19505 Z= 0.250 Chirality : 0.038 0.153 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.606 14.356 1880 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.04 % Allowed : 13.68 % Favored : 84.28 % 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 are not related in a simple way. whole: 1.02 (0.21), residues: 1685 helix: 1.71 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 223 TYR 0.015 0.001 TYR B 97 PHE 0.022 0.001 PHE C 80 TRP 0.014 0.001 TRP D 94 HIS 0.002 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (14315) covalent geometry : angle 0.48733 / 0.25 (19495) SS BOND : bond 0.00362 / 0.19 ( 5) SS BOND : angle 0.95016 / 0.53 ( 10) hydrogen bonds : bond 0.05056 / 3.29 ( 860) hydrogen bonds : angle 3.71149 / 2.67 ( 2535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.449 Fit side-chains REVERT: A 30 LYS cc_start: 0.9214 (tttm) cc_final: 0.9002 (ttpt) REVERT: A 149 LYS cc_start: 0.8623 (mttm) cc_final: 0.8402 (mtpt) REVERT: A 324 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 8 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8065 (mtm-85) REVERT: C 149 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8520 (mtpt) REVERT: C 325 MET cc_start: 0.9389 (mtp) cc_final: 0.9135 (mtm) REVERT: C 334 LYS cc_start: 0.8943 (mttp) cc_final: 0.8523 (mttm) REVERT: D 75 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7783 (mt) REVERT: D 293 GLN cc_start: 0.9106 (tt0) cc_final: 0.8848 (tt0) REVERT: D 334 LYS cc_start: 0.8833 (mttm) cc_final: 0.8595 (mttm) REVERT: E 149 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (mtpt) REVERT: E 320 MET cc_start: 0.9010 (ttm) cc_final: 0.8766 (ttm) REVERT: E 324 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: E 334 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8555 (mtpm) outliers start: 31 outliers final: 17 residues processed: 146 average time/residue: 0.5189 time to fit residues: 84.6469 Evaluate side-chains 149 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.084694 restraints weight = 18916.752| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.65 r_work: 0.2766 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14320 Z= 0.105 Angle : 0.475 9.236 19505 Z= 0.242 Chirality : 0.037 0.151 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.448 13.739 1880 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.64 % Allowed : 14.14 % Favored : 84.21 % 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 are not related in a simple way. whole: 1.16 (0.21), residues: 1685 helix: 1.83 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 223 TYR 0.013 0.001 TYR D 97 PHE 0.013 0.001 PHE C 171 TRP 0.014 0.001 TRP E 94 HIS 0.001 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (14315) covalent geometry : angle 0.47477 / 0.24 (19495) SS BOND : bond 0.00293 / 0.15 ( 5) SS BOND : angle 0.84760 / 0.46 ( 10) hydrogen bonds : bond 0.04680 / 3.04 ( 860) hydrogen bonds : angle 3.63296 / 2.62 ( 2535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.555 Fit side-chains REVERT: A 30 LYS cc_start: 0.9175 (tttm) cc_final: 0.8907 (ttpp) REVERT: A 149 LYS cc_start: 0.8567 (mttm) cc_final: 0.8353 (mtpt) REVERT: C 64 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (mptp) REVERT: C 149 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8452 (mtpt) REVERT: C 325 MET cc_start: 0.9387 (mtp) cc_final: 0.9136 (mtm) REVERT: C 334 LYS cc_start: 0.8886 (mttp) cc_final: 0.8467 (mttm) REVERT: D 75 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7701 (mt) REVERT: D 293 GLN cc_start: 0.9102 (tt0) cc_final: 0.8864 (tt0) REVERT: D 334 LYS cc_start: 0.8832 (mttm) cc_final: 0.8608 (mttm) REVERT: E 149 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8272 (mtpt) REVERT: E 324 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7424 (mp0) outliers start: 25 outliers final: 14 residues processed: 156 average time/residue: 0.5310 time to fit residues: 92.4842 Evaluate side-chains 147 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.083063 restraints weight = 18786.905| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.69 r_work: 0.2736 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14320 Z= 0.124 Angle : 0.506 10.284 19505 Z= 0.258 Chirality : 0.038 0.149 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.464 13.350 1880 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 14.67 % Favored : 83.88 % 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 are not related in a simple way. whole: 1.15 (0.21), residues: 1685 helix: 1.81 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 223 TYR 0.015 0.001 TYR B 97 PHE 0.016 0.001 PHE C 80 TRP 0.014 0.001 TRP E 94 HIS 0.002 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14315) covalent geometry : angle 0.50539 / 0.26 (19495) SS BOND : bond 0.00389 / 0.21 ( 5) SS BOND : angle 0.97104 / 0.55 ( 10) hydrogen bonds : bond 0.05108 / 3.32 ( 860) hydrogen bonds : angle 3.69317 / 2.66 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.98 seconds wall clock time: 62 minutes 25.19 seconds (3745.19 seconds total)