Starting phenix.real_space_refine on Thu Sep 26 15:37:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/09_2024/6n27_9325.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/09_2024/6n27_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/09_2024/6n27_9325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/09_2024/6n27_9325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/09_2024/6n27_9325.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/09_2024/6n27_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-5461/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: 7.91, per 1000 atoms: 0.57 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 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: 1.15 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: 3.62 Time building geometry restraints manager: 3.44 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.130 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- 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 14315 Z= 0.463 Angle : 0.877 9.068 19495 Z= 0.505 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.580 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: 1.3714 time to fit residues: 397.4108 Evaluate side-chains 141 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 14315 Z= 0.156 Angle : 0.499 6.100 19495 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 *********************** 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 fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.603 Fit side-chains REVERT: A 30 LYS cc_start: 0.9066 (tttt) cc_final: 0.8776 (ttpp) REVERT: A 41 SER cc_start: 0.8958 (m) cc_final: 0.8731 (m) REVERT: B 272 PHE cc_start: 0.8483 (m-10) cc_final: 0.7994 (m-80) REVERT: B 293 GLN cc_start: 0.8604 (tt0) cc_final: 0.8376 (tt0) REVERT: B 334 LYS cc_start: 0.8667 (mttm) cc_final: 0.8451 (mttm) REVERT: C 8 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7900 (mtm-85) REVERT: C 41 SER cc_start: 0.8833 (m) cc_final: 0.8586 (m) REVERT: C 149 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8193 (mtmt) REVERT: C 334 LYS cc_start: 0.8927 (mttp) cc_final: 0.8572 (mttm) REVERT: D 30 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8767 (ttpp) REVERT: D 41 SER cc_start: 0.8859 (m) cc_final: 0.8651 (m) REVERT: D 119 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: D 293 GLN cc_start: 0.8607 (tt0) cc_final: 0.8377 (tt0) REVERT: D 320 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8202 (ttt) REVERT: E 6 THR cc_start: 0.8674 (m) cc_final: 0.8473 (p) REVERT: E 41 SER cc_start: 0.8912 (m) cc_final: 0.8679 (m) REVERT: E 46 ILE cc_start: 0.8816 (mt) cc_final: 0.8501 (mt) REVERT: E 149 LYS cc_start: 0.8466 (mttm) cc_final: 0.8143 (mtpt) outliers start: 27 outliers final: 9 residues processed: 187 average time/residue: 1.2065 time to fit residues: 249.0062 Evaluate side-chains 143 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14315 Z= 0.188 Angle : 0.496 6.619 19495 Z= 0.257 Chirality : 0.038 0.156 2155 Planarity : 0.004 0.043 2440 Dihedral : 3.734 11.752 1880 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 10.26 % Favored : 86.84 % 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: 0.21 (0.20), residues: 1685 helix: 1.16 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 287 HIS 0.002 0.000 HIS C 178 PHE 0.017 0.002 PHE A 80 TYR 0.018 0.001 TYR B 97 ARG 0.003 0.000 ARG E 223 *********************** 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 179 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.436 Fit side-chains REVERT: A 30 LYS cc_start: 0.9116 (tttt) cc_final: 0.8809 (ttpp) REVERT: A 41 SER cc_start: 0.8933 (m) cc_final: 0.8673 (t) REVERT: C 41 SER cc_start: 0.8805 (m) cc_final: 0.8556 (m) REVERT: C 149 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8225 (mtpt) REVERT: C 324 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: D 30 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8776 (ttpp) REVERT: D 41 SER cc_start: 0.8836 (m) cc_final: 0.8625 (m) REVERT: D 119 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: D 293 GLN cc_start: 0.8719 (tt0) cc_final: 0.8441 (tt0) REVERT: D 320 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8261 (ttt) REVERT: E 37 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8426 (mm) REVERT: E 41 SER cc_start: 0.8863 (m) cc_final: 0.8623 (m) REVERT: E 42 LEU cc_start: 0.8525 (mt) cc_final: 0.8272 (mp) REVERT: E 46 ILE cc_start: 0.8792 (mt) cc_final: 0.8393 (mt) outliers start: 44 outliers final: 18 residues processed: 164 average time/residue: 1.0556 time to fit residues: 193.5053 Evaluate side-chains 146 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 6 THR 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 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 119 GLU 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 37 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 14315 Z= 0.307 Angle : 0.556 8.406 19495 Z= 0.287 Chirality : 0.042 0.155 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.788 12.587 1880 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.49 % Allowed : 10.92 % Favored : 85.59 % 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: 0.46 (0.21), residues: 1685 helix: 1.29 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 287 HIS 0.003 0.001 HIS C 178 PHE 0.021 0.002 PHE C 80 TYR 0.021 0.002 TYR E 236 ARG 0.003 0.001 ARG E 196 *********************** 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 179 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 126 time to evaluate : 1.730 Fit side-chains REVERT: A 41 SER cc_start: 0.8929 (m) cc_final: 0.8694 (t) REVERT: A 136 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 324 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 136 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8718 (p) REVERT: B 203 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: C 8 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7951 (mtm-85) REVERT: C 41 SER cc_start: 0.8795 (m) cc_final: 0.8551 (m) REVERT: C 324 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: C 334 LYS cc_start: 0.8909 (mttp) cc_final: 0.8530 (mttm) REVERT: D 30 LYS cc_start: 0.9123 (ttmm) cc_final: 0.8811 (ttpp) REVERT: D 41 SER cc_start: 0.8879 (m) cc_final: 0.8636 (m) REVERT: D 293 GLN cc_start: 0.8789 (tt0) cc_final: 0.8464 (tt0) REVERT: D 320 MET cc_start: 0.8641 (ttm) cc_final: 0.8439 (ttp) REVERT: E 37 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8457 (mm) REVERT: E 41 SER cc_start: 0.8830 (m) cc_final: 0.8593 (m) REVERT: E 119 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: E 149 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8139 (mtpt) outliers start: 53 outliers final: 25 residues processed: 164 average time/residue: 1.0342 time to fit residues: 189.7079 Evaluate side-chains 158 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 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 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 E residue 22 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 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 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14315 Z= 0.207 Angle : 0.500 7.361 19495 Z= 0.258 Chirality : 0.039 0.153 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.688 14.023 1880 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.29 % Allowed : 11.25 % 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: 1.50 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.99 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 94 HIS 0.002 0.000 HIS C 178 PHE 0.019 0.002 PHE C 80 TYR 0.018 0.001 TYR A 97 ARG 0.002 0.000 ARG E 223 *********************** 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 180 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 1.627 Fit side-chains REVERT: A 30 LYS cc_start: 0.9026 (tttm) cc_final: 0.8713 (ttpp) REVERT: A 41 SER cc_start: 0.8921 (m) cc_final: 0.8699 (t) REVERT: A 324 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: C 8 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7869 (mtm-85) REVERT: C 41 SER cc_start: 0.8792 (m) cc_final: 0.8556 (m) REVERT: C 303 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6642 (t0) REVERT: C 324 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: C 334 LYS cc_start: 0.8911 (mttp) cc_final: 0.8534 (mttm) REVERT: D 30 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8857 (ttpp) REVERT: D 41 SER cc_start: 0.8873 (m) cc_final: 0.8621 (m) REVERT: D 75 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7608 (mt) REVERT: D 293 GLN cc_start: 0.8772 (tt0) cc_final: 0.8462 (tt0) REVERT: D 334 LYS cc_start: 0.8886 (mttm) cc_final: 0.8646 (mttm) REVERT: E 37 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8454 (mm) REVERT: E 41 SER cc_start: 0.8870 (m) cc_final: 0.8637 (m) REVERT: E 149 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8136 (mtpt) outliers start: 50 outliers final: 20 residues processed: 164 average time/residue: 1.0447 time to fit residues: 192.2053 Evaluate side-chains 151 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 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 37 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14315 Z= 0.195 Angle : 0.498 6.704 19495 Z= 0.256 Chirality : 0.039 0.152 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.625 12.931 1880 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.76 % Allowed : 11.97 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.21), residues: 1685 helix: 1.62 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.96 (0.28), residues: 520 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 0.016 0.001 PHE C 80 TYR 0.018 0.001 TYR B 97 ARG 0.002 0.000 ARG E 223 *********************** 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 174 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.596 Fit side-chains REVERT: A 30 LYS cc_start: 0.9033 (tttm) cc_final: 0.8789 (ttpp) REVERT: A 324 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 119 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: C 8 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: C 41 SER cc_start: 0.8791 (m) cc_final: 0.8561 (m) REVERT: C 303 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6641 (t0) REVERT: C 324 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: C 334 LYS cc_start: 0.8871 (mttp) cc_final: 0.8481 (mttm) REVERT: D 30 LYS cc_start: 0.9076 (ttmm) cc_final: 0.8852 (ttpp) REVERT: D 41 SER cc_start: 0.8900 (m) cc_final: 0.8681 (m) REVERT: D 75 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7612 (mt) REVERT: D 293 GLN cc_start: 0.8796 (tt0) cc_final: 0.8477 (tt0) REVERT: D 334 LYS cc_start: 0.8824 (mttm) cc_final: 0.8595 (mttm) REVERT: E 37 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8454 (mm) REVERT: E 41 SER cc_start: 0.8828 (m) cc_final: 0.8592 (m) REVERT: E 149 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8130 (mtpt) outliers start: 42 outliers final: 23 residues processed: 161 average time/residue: 1.0497 time to fit residues: 188.8440 Evaluate side-chains 150 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 48 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14315 Z= 0.302 Angle : 0.553 7.050 19495 Z= 0.283 Chirality : 0.041 0.153 2155 Planarity : 0.004 0.046 2440 Dihedral : 3.710 13.363 1880 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.03 % Allowed : 12.24 % 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: 0.79 (0.21), residues: 1685 helix: 1.53 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.89 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 94 HIS 0.004 0.000 HIS C 178 PHE 0.018 0.002 PHE C 80 TYR 0.020 0.001 TYR B 97 ARG 0.002 0.000 ARG B 105 *********************** 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 168 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 1.634 Fit side-chains REVERT: A 30 LYS cc_start: 0.9055 (tttm) cc_final: 0.8770 (ttpp) REVERT: A 136 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8890 (p) REVERT: A 324 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 119 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 324 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: C 8 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7961 (mtm-85) REVERT: C 41 SER cc_start: 0.8796 (m) cc_final: 0.8565 (m) REVERT: C 324 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: C 334 LYS cc_start: 0.8952 (mttp) cc_final: 0.8541 (mttm) REVERT: D 30 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8880 (ttpp) REVERT: D 41 SER cc_start: 0.8898 (m) cc_final: 0.8651 (m) REVERT: D 75 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7851 (mt) REVERT: D 293 GLN cc_start: 0.8802 (tt0) cc_final: 0.8472 (tt0) REVERT: E 37 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8433 (mm) REVERT: E 41 SER cc_start: 0.8854 (m) cc_final: 0.8621 (m) REVERT: E 119 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: E 149 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8148 (mtpt) outliers start: 46 outliers final: 23 residues processed: 154 average time/residue: 1.0723 time to fit residues: 184.4461 Evaluate side-chains 151 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 37 LEU Chi-restraints excluded: chain C residue 75 LEU 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 37 LEU Chi-restraints excluded: chain E residue 49 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 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14315 Z= 0.243 Angle : 0.525 7.291 19495 Z= 0.270 Chirality : 0.040 0.153 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.690 13.123 1880 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.63 % Allowed : 12.63 % 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: 0.85 (0.21), residues: 1685 helix: 1.56 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.84 (0.29), 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 0.018 0.002 PHE C 80 TYR 0.019 0.001 TYR A 97 ARG 0.002 0.000 ARG C 196 *********************** 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 163 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.519 Fit side-chains REVERT: A 30 LYS cc_start: 0.9047 (tttm) cc_final: 0.8781 (ttpp) REVERT: A 136 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8871 (p) REVERT: A 324 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 119 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: B 203 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: C 8 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7891 (mtm-85) REVERT: C 41 SER cc_start: 0.8796 (m) cc_final: 0.8560 (m) REVERT: C 324 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: C 334 LYS cc_start: 0.8945 (mttp) cc_final: 0.8544 (mttm) REVERT: D 30 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8870 (ttpp) REVERT: D 41 SER cc_start: 0.8901 (m) cc_final: 0.8658 (m) REVERT: D 75 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7790 (mt) REVERT: D 293 GLN cc_start: 0.8814 (tt0) cc_final: 0.8487 (tt0) REVERT: D 334 LYS cc_start: 0.8786 (mttm) cc_final: 0.8554 (mttm) REVERT: E 37 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8456 (mm) REVERT: E 41 SER cc_start: 0.8831 (m) cc_final: 0.8598 (m) REVERT: E 149 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8138 (mtpt) REVERT: E 334 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8568 (mtpm) outliers start: 40 outliers final: 23 residues processed: 153 average time/residue: 1.1143 time to fit residues: 191.7514 Evaluate side-chains 152 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 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 75 LEU 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 37 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14315 Z= 0.138 Angle : 0.473 8.393 19495 Z= 0.242 Chirality : 0.037 0.152 2155 Planarity : 0.004 0.044 2440 Dihedral : 3.534 14.606 1880 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.43 % Allowed : 13.09 % Favored : 84.47 % 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: 1.72 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.77 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 182 HIS 0.001 0.000 HIS C 178 PHE 0.013 0.001 PHE B 80 TYR 0.014 0.001 TYR B 97 ARG 0.002 0.000 ARG E 223 *********************** 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 172 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.680 Fit side-chains REVERT: A 30 LYS cc_start: 0.8961 (tttm) cc_final: 0.8695 (ttpp) REVERT: B 334 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8419 (mttm) REVERT: C 41 SER cc_start: 0.8789 (m) cc_final: 0.8557 (m) REVERT: C 64 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8637 (mptp) REVERT: C 324 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: C 325 MET cc_start: 0.9389 (mtp) cc_final: 0.9188 (mtm) REVERT: C 334 LYS cc_start: 0.8878 (mttp) cc_final: 0.8498 (mttm) REVERT: D 30 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8831 (ttpp) REVERT: D 41 SER cc_start: 0.8900 (m) cc_final: 0.8684 (m) REVERT: D 75 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7564 (mt) REVERT: D 293 GLN cc_start: 0.8738 (tt0) cc_final: 0.8433 (tt0) REVERT: D 334 LYS cc_start: 0.8813 (mttm) cc_final: 0.8575 (mttm) REVERT: E 41 SER cc_start: 0.8829 (m) cc_final: 0.8606 (m) REVERT: E 149 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8092 (mtpt) REVERT: E 334 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8571 (mtpm) outliers start: 37 outliers final: 17 residues processed: 161 average time/residue: 1.0235 time to fit residues: 184.6852 Evaluate side-chains 151 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 64 LYS 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 49 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU 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 156 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14315 Z= 0.256 Angle : 0.535 7.989 19495 Z= 0.274 Chirality : 0.040 0.165 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.619 13.377 1880 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.24 % Allowed : 13.36 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1685 helix: 1.61 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 182 HIS 0.003 0.000 HIS C 178 PHE 0.017 0.002 PHE C 80 TYR 0.019 0.001 TYR A 97 ARG 0.005 0.000 ARG C 8 ********************** 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 160 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.600 Fit side-chains REVERT: A 30 LYS cc_start: 0.9036 (tttm) cc_final: 0.8776 (ttpp) REVERT: A 136 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 324 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: B 30 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8970 (ttpp) REVERT: B 334 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8475 (mttm) REVERT: C 41 SER cc_start: 0.8798 (m) cc_final: 0.8566 (m) REVERT: C 324 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: C 334 LYS cc_start: 0.8926 (mttp) cc_final: 0.8495 (mttm) REVERT: D 30 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8847 (ttpp) REVERT: D 41 SER cc_start: 0.8897 (m) cc_final: 0.8681 (m) REVERT: D 75 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7815 (mt) REVERT: D 293 GLN cc_start: 0.8784 (tt0) cc_final: 0.8452 (tt0) REVERT: E 41 SER cc_start: 0.8844 (m) cc_final: 0.8615 (m) REVERT: E 149 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8095 (mtpt) REVERT: E 334 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8545 (mtpm) outliers start: 34 outliers final: 20 residues processed: 150 average time/residue: 1.0651 time to fit residues: 178.9219 Evaluate side-chains 150 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 37 LEU 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 49 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 329 LEU 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 139 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 115 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 = 0.3155 r_free = 0.3155 target = 0.101536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.079971 restraints weight = 18948.910| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.69 r_work: 0.2689 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14315 Z= 0.223 Angle : 0.520 8.431 19495 Z= 0.267 Chirality : 0.040 0.167 2155 Planarity : 0.004 0.045 2440 Dihedral : 3.627 13.938 1880 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 13.49 % Favored : 84.54 % 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: 0.95 (0.21), residues: 1685 helix: 1.63 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.79 (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 0.027 0.002 PHE C 80 TYR 0.018 0.001 TYR B 97 ARG 0.004 0.000 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.69 seconds wall clock time: 71 minutes 5.97 seconds (4265.97 seconds total)