Starting phenix.real_space_refine on Thu Jul 31 12:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n27_9325/07_2025/6n27_9325.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n27_9325/07_2025/6n27_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_9325/07_2025/6n27_9325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n27_9325/07_2025/6n27_9325.map" model { file = "/net/cci-nas-00/data/ceres_data/6n27_9325/07_2025/6n27_9325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n27_9325/07_2025/6n27_9325.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLU:plan': 2, 'ARG:plan': 1} 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: 8.57, per 1000 atoms: 0.62 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: 3.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.16 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: 4.11 Time building geometry restraints manager: 3.55 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.069 0.005 TRP D 287 HIS 0.006 0.002 HIS D 326 PHE 0.031 0.004 PHE E 80 TYR 0.037 0.002 TYR B 236 ARG 0.006 0.001 ARG E 313 Details of bonding type rmsd hydrogen bonds : bond 0.15350 ( 860) hydrogen bonds : angle 5.37973 ( 2535) SS BOND : bond 0.01699 ( 5) SS BOND : angle 3.47092 ( 10) covalent geometry : bond 0.00735 (14315) covalent geometry : angle 0.87651 (19495) *********************** 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 : 1.538 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: 1.3414 time to fit residues: 388.8552 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 : 1.664 ------------------------------------------------------------------------------- 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 139 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3219 r_free = 0.3219 target = 0.105760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.085527 restraints weight = 18848.740| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.60 r_work: 0.2788 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14320 Z= 0.121 Angle : 0.500 6.100 19505 Z= 0.263 Chirality : 0.038 0.160 2155 Planarity : 0.004 0.041 2440 Dihedral : 4.021 12.510 1882 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.78 % Allowed : 8.68 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1685 helix: 0.41 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 287 HIS 0.001 0.000 HIS C 178 PHE 0.012 0.001 PHE C 80 TYR 0.016 0.001 TYR B 97 ARG 0.006 0.001 ARG E 223 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 860) hydrogen bonds : angle 3.88085 ( 2535) SS BOND : bond 0.00404 ( 5) SS BOND : angle 1.15339 ( 10) covalent geometry : bond 0.00248 (14315) covalent geometry : angle 0.49928 (19495) *********************** 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 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.544 Fit side-chains REVERT: A 30 LYS cc_start: 0.9255 (tttt) cc_final: 0.8995 (ttpp) REVERT: A 41 SER cc_start: 0.9089 (m) cc_final: 0.8877 (m) REVERT: B 272 PHE cc_start: 0.8672 (m-10) cc_final: 0.8238 (m-80) REVERT: B 334 LYS cc_start: 0.8691 (mttm) cc_final: 0.8487 (mttm) REVERT: C 8 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8098 (mtm-85) REVERT: C 41 SER cc_start: 0.9072 (m) cc_final: 0.8858 (m) REVERT: C 149 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8419 (mtmt) REVERT: C 334 LYS cc_start: 0.8969 (mttp) cc_final: 0.8621 (mttm) REVERT: D 30 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8994 (ttpp) REVERT: D 119 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: D 320 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8537 (ttt) REVERT: E 6 THR cc_start: 0.8772 (m) cc_final: 0.8562 (p) REVERT: E 46 ILE cc_start: 0.9050 (mt) cc_final: 0.8693 (mt) REVERT: E 149 LYS cc_start: 0.8685 (mttm) cc_final: 0.8388 (mtpt) outliers start: 27 outliers final: 9 residues processed: 187 average time/residue: 1.2565 time to fit residues: 258.4821 Evaluate side-chains 140 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3144 r_free = 0.3144 target = 0.100567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.079000 restraints weight = 19254.425| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.71 r_work: 0.2673 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14320 Z= 0.185 Angle : 0.548 7.342 19505 Z= 0.284 Chirality : 0.041 0.157 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.837 13.155 1880 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.36 % Allowed : 10.39 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1685 helix: 1.11 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 287 HIS 0.004 0.001 HIS C 178 PHE 0.017 0.002 PHE A 80 TYR 0.022 0.002 TYR D 236 ARG 0.003 0.001 ARG E 223 Details of bonding type rmsd hydrogen bonds : bond 0.06641 ( 860) hydrogen bonds : angle 3.93632 ( 2535) SS BOND : bond 0.00658 ( 5) SS BOND : angle 1.52132 ( 10) covalent geometry : bond 0.00438 (14315) covalent geometry : angle 0.54737 (19495) *********************** 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: 51 poor density : 124 time to evaluate : 1.424 Fit side-chains REVERT: A 30 LYS cc_start: 0.9336 (tttt) cc_final: 0.9030 (ttpp) REVERT: A 41 SER cc_start: 0.9116 (m) cc_final: 0.8876 (t) REVERT: A 136 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.9061 (p) REVERT: A 149 LYS cc_start: 0.8597 (mttm) cc_final: 0.8369 (mtpt) REVERT: B 203 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (m-30) REVERT: B 320 MET cc_start: 0.9022 (ttt) cc_final: 0.8740 (ttm) REVERT: C 8 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8015 (mtm-85) REVERT: C 41 SER cc_start: 0.9005 (m) cc_final: 0.8785 (m) REVERT: C 149 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8464 (mtpt) REVERT: C 324 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 30 LYS cc_start: 0.9252 (ttmm) cc_final: 0.9000 (ttpp) REVERT: D 320 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8676 (ttt) REVERT: E 42 LEU cc_start: 0.8791 (mt) cc_final: 0.8480 (mp) REVERT: E 46 ILE cc_start: 0.8965 (mt) cc_final: 0.8606 (mt) REVERT: E 324 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7560 (mp0) outliers start: 51 outliers final: 21 residues processed: 159 average time/residue: 1.1411 time to fit residues: 201.7587 Evaluate side-chains 145 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 B residue 6 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 107 MET 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 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 61 MET 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 320 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 48 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 81 optimal weight: 0.0060 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.083512 restraints weight = 18905.017| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.65 r_work: 0.2746 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14320 Z= 0.114 Angle : 0.468 6.040 19505 Z= 0.242 Chirality : 0.037 0.153 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.628 12.829 1880 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.03 % Allowed : 11.51 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1685 helix: 1.48 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 94 HIS 0.002 0.000 HIS C 178 PHE 0.014 0.001 PHE C 80 TYR 0.016 0.001 TYR B 97 ARG 0.003 0.000 ARG E 223 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 860) hydrogen bonds : angle 3.69646 ( 2535) SS BOND : bond 0.00393 ( 5) SS BOND : angle 0.96142 ( 10) covalent geometry : bond 0.00241 (14315) covalent geometry : angle 0.46772 (19495) *********************** 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 180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.468 Fit side-chains REVERT: A 30 LYS cc_start: 0.9332 (tttt) cc_final: 0.9065 (ttpp) REVERT: B 324 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: B 334 LYS cc_start: 0.8690 (mttm) cc_final: 0.8441 (mttm) REVERT: C 8 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: C 41 SER cc_start: 0.9009 (m) cc_final: 0.8806 (m) REVERT: C 324 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: D 320 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8629 (ttm) REVERT: E 46 ILE cc_start: 0.8971 (mt) cc_final: 0.8710 (mm) REVERT: E 149 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8381 (mtpt) REVERT: E 324 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7547 (mt-10) outliers start: 46 outliers final: 19 residues processed: 166 average time/residue: 1.0487 time to fit residues: 194.7088 Evaluate side-chains 150 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 107 MET 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 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 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 320 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 141 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.078800 restraints weight = 19274.761| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.70 r_work: 0.2668 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14320 Z= 0.179 Angle : 0.531 8.578 19505 Z= 0.273 Chirality : 0.041 0.153 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.665 12.595 1880 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.03 % Allowed : 11.51 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1685 helix: 1.53 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -2.05 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 94 HIS 0.004 0.000 HIS C 178 PHE 0.014 0.002 PHE C 80 TYR 0.020 0.001 TYR A 97 ARG 0.002 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.06386 ( 860) hydrogen bonds : angle 3.85985 ( 2535) SS BOND : bond 0.00628 ( 5) SS BOND : angle 1.40202 ( 10) covalent geometry : bond 0.00423 (14315) covalent geometry : angle 0.53029 (19495) *********************** 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 171 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.727 Fit side-chains REVERT: A 30 LYS cc_start: 0.9285 (tttt) cc_final: 0.8988 (ttpp) REVERT: A 136 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.9086 (p) REVERT: A 324 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: B 119 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: B 324 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 334 LYS cc_start: 0.8716 (mttm) cc_final: 0.8481 (mttm) REVERT: C 8 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8026 (mtm-85) REVERT: C 41 SER cc_start: 0.8998 (m) cc_final: 0.8792 (m) REVERT: C 303 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.6930 (t0) REVERT: C 324 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: D 75 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7792 (mt) REVERT: E 46 ILE cc_start: 0.8964 (mt) cc_final: 0.8741 (mm) REVERT: E 119 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: E 149 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8342 (mtpt) REVERT: E 324 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7609 (mt-10) outliers start: 46 outliers final: 18 residues processed: 158 average time/residue: 1.1956 time to fit residues: 209.3700 Evaluate side-chains 148 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 107 MET 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.080075 restraints weight = 19135.612| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.69 r_work: 0.2690 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14320 Z= 0.151 Angle : 0.511 7.891 19505 Z= 0.261 Chirality : 0.039 0.153 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.636 12.808 1880 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.29 % Allowed : 11.58 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1685 helix: 1.58 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 94 HIS 0.003 0.000 HIS C 178 PHE 0.015 0.002 PHE C 80 TYR 0.019 0.001 TYR B 97 ARG 0.002 0.000 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.05878 ( 860) hydrogen bonds : angle 3.78238 ( 2535) SS BOND : bond 0.00526 ( 5) SS BOND : angle 1.21347 ( 10) covalent geometry : bond 0.00349 (14315) covalent geometry : angle 0.51052 (19495) *********************** 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 176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 1.685 Fit side-chains REVERT: A 30 LYS cc_start: 0.9282 (tttt) cc_final: 0.8990 (ttpp) REVERT: A 136 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.9102 (p) REVERT: A 324 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 119 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: B 203 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: B 334 LYS cc_start: 0.8705 (mttm) cc_final: 0.8369 (mttm) REVERT: C 8 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8026 (mtm-85) REVERT: C 41 SER cc_start: 0.8995 (m) cc_final: 0.8794 (m) REVERT: C 324 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: C 334 LYS cc_start: 0.8874 (mttp) cc_final: 0.8591 (mttm) REVERT: D 75 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7705 (mt) REVERT: E 46 ILE cc_start: 0.8918 (mt) cc_final: 0.8648 (mm) REVERT: E 119 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: E 149 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8328 (mtpt) outliers start: 50 outliers final: 23 residues processed: 160 average time/residue: 1.4692 time to fit residues: 262.1313 Evaluate side-chains 151 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 107 MET 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 C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG 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 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 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 131 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 17 optimal weight: 0.0020 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.083856 restraints weight = 18950.575| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.65 r_work: 0.2753 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14320 Z= 0.109 Angle : 0.476 7.595 19505 Z= 0.243 Chirality : 0.037 0.150 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.509 12.277 1880 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.24 % Allowed : 13.03 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1685 helix: 1.76 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 94 HIS 0.001 0.000 HIS C 178 PHE 0.012 0.001 PHE C 80 TYR 0.015 0.001 TYR B 97 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 860) hydrogen bonds : angle 3.65039 ( 2535) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.91024 ( 10) covalent geometry : bond 0.00229 (14315) covalent geometry : angle 0.47601 (19495) *********************** 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 172 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.772 Fit side-chains REVERT: A 30 LYS cc_start: 0.9292 (tttt) cc_final: 0.9032 (ttpp) REVERT: A 324 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 334 LYS cc_start: 0.8637 (mttm) cc_final: 0.8298 (mttm) REVERT: C 303 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.6740 (t0) REVERT: C 324 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: C 334 LYS cc_start: 0.8796 (mttp) cc_final: 0.8562 (mttm) REVERT: D 75 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7578 (mt) REVERT: E 46 ILE cc_start: 0.8941 (mt) cc_final: 0.8669 (mm) REVERT: E 149 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8336 (mtpt) outliers start: 34 outliers final: 19 residues processed: 158 average time/residue: 1.4144 time to fit residues: 249.6428 Evaluate side-chains 150 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 107 MET 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.081181 restraints weight = 19013.729| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.70 r_work: 0.2708 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14320 Z= 0.140 Angle : 0.508 10.985 19505 Z= 0.259 Chirality : 0.039 0.150 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.524 11.958 1880 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.37 % Allowed : 13.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1685 helix: 1.77 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.86 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 94 HIS 0.003 0.000 HIS C 178 PHE 0.015 0.002 PHE C 80 TYR 0.018 0.001 TYR B 97 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 860) hydrogen bonds : angle 3.72519 ( 2535) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.12972 ( 10) covalent geometry : bond 0.00320 (14315) covalent geometry : angle 0.50762 (19495) *********************** 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 169 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 2.341 Fit side-chains REVERT: A 30 LYS cc_start: 0.9233 (tttt) cc_final: 0.8945 (ttpp) REVERT: A 136 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.9086 (p) REVERT: A 324 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 334 LYS cc_start: 0.8647 (mttm) cc_final: 0.8291 (mttm) REVERT: C 303 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6693 (t0) REVERT: C 324 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 334 LYS cc_start: 0.8831 (mttp) cc_final: 0.8551 (mttm) REVERT: D 75 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7630 (mt) REVERT: E 46 ILE cc_start: 0.8924 (mt) cc_final: 0.8663 (mm) REVERT: E 149 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8272 (mtpt) outliers start: 36 outliers final: 20 residues processed: 157 average time/residue: 1.6964 time to fit residues: 299.8746 Evaluate side-chains 153 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 107 MET 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 136 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.083992 restraints weight = 18896.020| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.65 r_work: 0.2754 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14320 Z= 0.113 Angle : 0.487 7.805 19505 Z= 0.249 Chirality : 0.038 0.162 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.466 11.823 1880 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 14.21 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1685 helix: 1.79 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.78 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 94 HIS 0.001 0.000 HIS C 178 PHE 0.022 0.001 PHE C 80 TYR 0.015 0.001 TYR B 97 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 860) hydrogen bonds : angle 3.65072 ( 2535) SS BOND : bond 0.00354 ( 5) SS BOND : angle 0.93241 ( 10) covalent geometry : bond 0.00242 (14315) covalent geometry : angle 0.48711 (19495) *********************** 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 163 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 2.892 Fit side-chains REVERT: A 30 LYS cc_start: 0.9240 (tttt) cc_final: 0.8993 (ttpp) REVERT: B 30 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8969 (ttpp) REVERT: B 334 LYS cc_start: 0.8633 (mttm) cc_final: 0.8289 (mttm) REVERT: C 324 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: D 75 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7629 (mt) REVERT: E 30 LYS cc_start: 0.9298 (ttmm) cc_final: 0.8960 (ttpp) REVERT: E 46 ILE cc_start: 0.8935 (mt) cc_final: 0.8669 (mm) REVERT: E 149 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8321 (mtpt) outliers start: 27 outliers final: 19 residues processed: 154 average time/residue: 1.9762 time to fit residues: 342.2884 Evaluate side-chains 152 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 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 75 LEU Chi-restraints excluded: chain C residue 136 SER 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 E residue 22 LEU Chi-restraints excluded: chain E residue 48 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.077237 restraints weight = 19014.688| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.72 r_work: 0.2632 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14320 Z= 0.241 Angle : 0.611 11.968 19505 Z= 0.312 Chirality : 0.044 0.184 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.716 13.636 1880 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.97 % Allowed : 14.21 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1685 helix: 1.56 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 182 HIS 0.004 0.001 HIS C 178 PHE 0.021 0.002 PHE A 80 TYR 0.023 0.002 TYR E 236 ARG 0.004 0.001 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.07100 ( 860) hydrogen bonds : angle 3.96350 ( 2535) SS BOND : bond 0.00788 ( 5) SS BOND : angle 1.75452 ( 10) covalent geometry : bond 0.00587 (14315) covalent geometry : angle 0.61031 (19495) ********************** 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 157 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.319 Fit side-chains REVERT: B 203 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: B 334 LYS cc_start: 0.8748 (mttm) cc_final: 0.8414 (mttm) REVERT: C 324 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: D 75 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (mt) REVERT: E 149 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8266 (mtpt) REVERT: E 334 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8477 (mtpm) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 1.5085 time to fit residues: 247.9542 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 : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 107 MET 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 136 SER 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 E residue 22 LEU Chi-restraints excluded: chain E residue 48 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 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 31 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.083804 restraints weight = 18831.113| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.70 r_work: 0.2749 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14320 Z= 0.115 Angle : 0.498 8.760 19505 Z= 0.255 Chirality : 0.038 0.165 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.568 14.586 1880 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.64 % Allowed : 14.80 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1685 helix: 1.75 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.78 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 182 HIS 0.001 0.000 HIS C 178 PHE 0.018 0.001 PHE C 80 TYR 0.015 0.001 TYR B 97 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 860) hydrogen bonds : angle 3.68807 ( 2535) SS BOND : bond 0.00361 ( 5) SS BOND : angle 0.97961 ( 10) covalent geometry : bond 0.00244 (14315) covalent geometry : angle 0.49804 (19495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8527.84 seconds wall clock time: 158 minutes 21.78 seconds (9501.78 seconds total)