Starting phenix.real_space_refine on Fri Feb 16 01:18:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/02_2024/6n27_9325.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/02_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_9325/02_2024/6n27_9325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/02_2024/6n27_9325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/02_2024/6n27_9325.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/02_2024/6n27_9325.pdb" } 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 Residue "A ARG 59": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.22, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 5.32 Conformation dependent library (CDL) restraints added in 2.3 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: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 Processing helix chain 'A' and resid 75 through 98 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.773A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.767A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.577A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.212A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.685A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.067A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.609A pdb=" N LEU A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.784A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.772A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.767A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.577A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.213A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.686A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 4.068A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.609A pdb=" N LEU B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 Processing helix chain 'C' and resid 75 through 98 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.772A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.768A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.578A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.211A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.685A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.068A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 255 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.610A pdb=" N LEU C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.508A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 Processing helix chain 'D' and resid 75 through 98 Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.772A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.767A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.577A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.213A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.684A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 4.067A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG D 255 " --> pdb=" O CYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.535A pdb=" N LYS D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.514A pdb=" N PHE D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.610A pdb=" N LEU D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.509A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 3.783A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 Processing helix chain 'E' and resid 75 through 98 Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.773A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.768A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.576A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.213A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.685A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 4.067A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 255 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS E 262 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.515A pdb=" N PHE E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.609A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 5.76 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: 99.47 - 106.37: 353 106.37 - 113.28: 7517 113.28 - 120.19: 5881 120.19 - 127.10: 5554 127.10 - 134.01: 190 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 2.520 nonbonded pdb=" OG1 THR D 6 " pdb=" OG SER E 231 " model vdw 2.306 2.440 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.306 2.520 nonbonded pdb=" OG1 THR B 6 " pdb=" OG SER C 231 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR C 6 " pdb=" OG SER D 231 " model vdw 2.316 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.000 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.750 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- 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 : 1.542 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: 1.3885 time to fit residues: 401.8493 Evaluate side-chains 141 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 2.075 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8277 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14315 Z= 0.145 Angle : 0.491 6.028 19495 Z= 0.258 Chirality : 0.037 0.156 2155 Planarity : 0.004 0.040 2440 Dihedral : 3.951 12.696 1882 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.78 % Allowed : 9.14 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.19), residues: 1685 helix: 0.40 (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 0.030 0.002 TRP D 287 HIS 0.001 0.000 HIS C 178 PHE 0.010 0.001 PHE B 272 TYR 0.015 0.001 TYR B 97 ARG 0.005 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 183 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.465 Fit side-chains REVERT: A 30 LYS cc_start: 0.9113 (tttt) cc_final: 0.8881 (ttpp) REVERT: A 41 SER cc_start: 0.8958 (m) cc_final: 0.8732 (m) REVERT: B 272 PHE cc_start: 0.8474 (m-10) cc_final: 0.7970 (m-80) REVERT: B 293 GLN cc_start: 0.8590 (tt0) cc_final: 0.8375 (tt0) REVERT: C 41 SER cc_start: 0.8834 (m) cc_final: 0.8588 (m) REVERT: C 149 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8188 (mtmt) REVERT: D 30 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8781 (ttpp) REVERT: D 41 SER cc_start: 0.8858 (m) cc_final: 0.8654 (m) REVERT: D 119 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: D 293 GLN cc_start: 0.8596 (tt0) cc_final: 0.8371 (tt0) REVERT: D 320 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8209 (ttt) REVERT: E 41 SER cc_start: 0.8911 (m) cc_final: 0.8674 (m) REVERT: E 42 LEU cc_start: 0.8482 (mt) cc_final: 0.8234 (mp) REVERT: E 46 ILE cc_start: 0.8820 (mt) cc_final: 0.8513 (mt) REVERT: E 149 LYS cc_start: 0.8475 (mttm) cc_final: 0.8117 (mtpt) outliers start: 27 outliers final: 9 residues processed: 176 average time/residue: 1.3040 time to fit residues: 250.8929 Evaluate side-chains 138 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.2009 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= 0.192 Angle : 0.491 6.542 19495 Z= 0.255 Chirality : 0.038 0.152 2155 Planarity : 0.004 0.041 2440 Dihedral : 3.701 11.997 1880 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.63 % Allowed : 10.00 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1685 helix: 1.17 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 287 HIS 0.002 0.000 HIS C 178 PHE 0.017 0.002 PHE A 80 TYR 0.019 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 170 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.745 Fit side-chains REVERT: A 30 LYS cc_start: 0.9125 (tttt) cc_final: 0.8818 (ttpp) REVERT: A 41 SER cc_start: 0.8951 (m) cc_final: 0.8697 (t) REVERT: B 334 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8498 (mttm) REVERT: C 41 SER cc_start: 0.8805 (m) cc_final: 0.8557 (m) REVERT: C 149 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8166 (mtmt) REVERT: C 324 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: D 30 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8824 (ttpp) REVERT: D 41 SER cc_start: 0.8838 (m) cc_final: 0.8627 (m) REVERT: D 154 MET cc_start: 0.9065 (mmt) cc_final: 0.8850 (mmt) REVERT: D 293 GLN cc_start: 0.8718 (tt0) cc_final: 0.8430 (tt0) REVERT: D 320 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7739 (ttt) REVERT: D 324 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: E 37 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8429 (mm) REVERT: E 41 SER cc_start: 0.8818 (m) cc_final: 0.8595 (m) REVERT: E 42 LEU cc_start: 0.8494 (mt) cc_final: 0.8257 (mp) REVERT: E 46 ILE cc_start: 0.8796 (mt) cc_final: 0.8500 (mt) REVERT: E 149 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8058 (mtpt) outliers start: 40 outliers final: 14 residues processed: 155 average time/residue: 1.0516 time to fit residues: 182.0411 Evaluate side-chains 140 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL 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 273 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP 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 D residue 324 GLU Chi-restraints excluded: chain E residue 37 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 0.0000 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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: 0.8262 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14315 Z= 0.122 Angle : 0.439 7.804 19495 Z= 0.226 Chirality : 0.036 0.150 2155 Planarity : 0.003 0.039 2440 Dihedral : 3.449 11.880 1880 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.76 % Allowed : 10.79 % Favored : 86.45 % 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: 0.75 (0.21), residues: 1685 helix: 1.59 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -2.13 (0.27), 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 0.014 0.001 PHE C 80 TYR 0.014 0.001 TYR B 97 ARG 0.003 0.000 ARG E 223 *********************** 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 186 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.649 Fit side-chains REVERT: A 30 LYS cc_start: 0.9107 (tttt) cc_final: 0.8824 (ttpp) REVERT: B 334 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8534 (mttm) REVERT: C 41 SER cc_start: 0.8807 (m) cc_final: 0.8570 (m) REVERT: C 149 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8133 (mtmt) REVERT: C 324 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: D 30 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8736 (ttpp) REVERT: D 41 SER cc_start: 0.8895 (m) cc_final: 0.8682 (m) REVERT: D 293 GLN cc_start: 0.8696 (tt0) cc_final: 0.8441 (tt0) REVERT: D 320 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8207 (ttm) REVERT: E 41 SER cc_start: 0.8883 (m) cc_final: 0.8662 (m) REVERT: E 149 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7925 (mtpt) outliers start: 42 outliers final: 16 residues processed: 172 average time/residue: 1.0385 time to fit residues: 200.0221 Evaluate side-chains 146 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 48 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS 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 335 ASP 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 149 LYS Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 14315 Z= 0.114 Angle : 0.433 6.854 19495 Z= 0.221 Chirality : 0.036 0.148 2155 Planarity : 0.003 0.039 2440 Dihedral : 3.303 11.624 1880 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.04 % Allowed : 12.17 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.21), residues: 1685 helix: 1.78 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 520 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 0.020 0.001 PHE A 80 TYR 0.013 0.001 TYR B 97 ARG 0.003 0.000 ARG A 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 174 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.757 Fit side-chains REVERT: A 30 LYS cc_start: 0.9093 (tttt) cc_final: 0.8821 (ttpp) REVERT: B 320 MET cc_start: 0.8500 (ttt) cc_final: 0.8178 (ttt) REVERT: B 334 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8504 (mttm) REVERT: C 41 SER cc_start: 0.8768 (m) cc_final: 0.8532 (m) REVERT: C 149 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8108 (mtmt) REVERT: C 324 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: C 325 MET cc_start: 0.9425 (mtp) cc_final: 0.9078 (mtm) REVERT: C 334 LYS cc_start: 0.8609 (mttp) cc_final: 0.8254 (mttm) REVERT: D 30 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8686 (ttpp) REVERT: D 41 SER cc_start: 0.8896 (m) cc_final: 0.8691 (m) REVERT: D 293 GLN cc_start: 0.8679 (tt0) cc_final: 0.8448 (tt0) REVERT: E 41 SER cc_start: 0.8892 (m) cc_final: 0.8659 (m) REVERT: E 149 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8006 (mtpt) outliers start: 31 outliers final: 9 residues processed: 160 average time/residue: 1.1423 time to fit residues: 202.7119 Evaluate side-chains 137 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8299 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14315 Z= 0.159 Angle : 0.459 7.034 19495 Z= 0.235 Chirality : 0.037 0.147 2155 Planarity : 0.003 0.040 2440 Dihedral : 3.328 11.567 1880 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.17 % Allowed : 12.89 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.21), residues: 1685 helix: 1.78 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.91 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 94 HIS 0.002 0.000 HIS C 178 PHE 0.011 0.001 PHE C 171 TYR 0.017 0.001 TYR B 97 ARG 0.003 0.000 ARG B 59 *********************** 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 171 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.916 Fit side-chains REVERT: A 30 LYS cc_start: 0.9097 (tttt) cc_final: 0.8814 (ttpp) REVERT: B 334 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8570 (mttm) REVERT: C 41 SER cc_start: 0.8777 (m) cc_final: 0.8536 (m) REVERT: C 149 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8143 (mtmt) REVERT: C 324 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: C 334 LYS cc_start: 0.8669 (mttp) cc_final: 0.8293 (mttm) REVERT: D 30 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8816 (ttpp) REVERT: D 41 SER cc_start: 0.8895 (m) cc_final: 0.8689 (m) REVERT: D 293 GLN cc_start: 0.8733 (tt0) cc_final: 0.8499 (tt0) REVERT: E 37 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8379 (mm) REVERT: E 41 SER cc_start: 0.8845 (m) cc_final: 0.8610 (m) REVERT: E 149 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7950 (mtpt) outliers start: 33 outliers final: 13 residues processed: 157 average time/residue: 1.1309 time to fit residues: 197.7033 Evaluate side-chains 148 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 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 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: 0.8980 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.2477 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= 0.289 Angle : 0.535 7.092 19495 Z= 0.275 Chirality : 0.041 0.147 2155 Planarity : 0.004 0.041 2440 Dihedral : 3.568 13.163 1880 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.11 % Allowed : 12.83 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.21), residues: 1685 helix: 1.65 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.89 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 94 HIS 0.004 0.001 HIS C 178 PHE 0.019 0.002 PHE C 80 TYR 0.021 0.002 TYR B 97 ARG 0.003 0.000 ARG C 59 *********************** 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 161 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.508 Fit side-chains REVERT: A 136 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 203 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: B 334 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8662 (mttm) REVERT: C 41 SER cc_start: 0.8806 (m) cc_final: 0.8568 (m) REVERT: C 149 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8150 (mtmt) REVERT: C 324 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: D 30 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8863 (ttpp) REVERT: D 41 SER cc_start: 0.8917 (m) cc_final: 0.8696 (m) REVERT: D 293 GLN cc_start: 0.8781 (tt0) cc_final: 0.8468 (tt0) REVERT: E 37 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8431 (mm) REVERT: E 41 SER cc_start: 0.8867 (m) cc_final: 0.8639 (m) REVERT: E 46 ILE cc_start: 0.8735 (mt) cc_final: 0.8414 (mm) REVERT: E 149 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8033 (mtpt) outliers start: 32 outliers final: 12 residues processed: 151 average time/residue: 1.1639 time to fit residues: 194.8754 Evaluate side-chains 144 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 B residue 22 LEU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 324 GLU 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 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: 0.9980 chunk 94 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 144 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14315 Z= 0.249 Angle : 0.519 7.138 19495 Z= 0.266 Chirality : 0.040 0.149 2155 Planarity : 0.004 0.041 2440 Dihedral : 3.622 15.558 1880 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.24 % Allowed : 13.49 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.83 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 94 HIS 0.003 0.000 HIS C 178 PHE 0.020 0.002 PHE C 80 TYR 0.020 0.001 TYR B 97 ARG 0.003 0.000 ARG C 59 *********************** 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 155 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.772 Fit side-chains REVERT: A 30 LYS cc_start: 0.9044 (tttm) cc_final: 0.8722 (tttt) REVERT: B 320 MET cc_start: 0.8639 (ttt) cc_final: 0.8387 (ttt) REVERT: B 334 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8666 (mttm) REVERT: C 41 SER cc_start: 0.8805 (m) cc_final: 0.8563 (m) REVERT: C 149 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8166 (mtmt) REVERT: C 324 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: C 334 LYS cc_start: 0.8776 (mttp) cc_final: 0.8453 (mttm) REVERT: D 30 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8846 (ttpp) REVERT: D 41 SER cc_start: 0.8915 (m) cc_final: 0.8672 (m) REVERT: D 246 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.9008 (p) REVERT: D 293 GLN cc_start: 0.8790 (tt0) cc_final: 0.8484 (tt0) REVERT: E 37 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (mm) REVERT: E 41 SER cc_start: 0.8859 (m) cc_final: 0.8627 (m) REVERT: E 149 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8053 (mtpt) outliers start: 34 outliers final: 16 residues processed: 144 average time/residue: 1.0953 time to fit residues: 176.7614 Evaluate side-chains 141 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 246 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8367 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14315 Z= 0.256 Angle : 0.525 7.741 19495 Z= 0.270 Chirality : 0.040 0.149 2155 Planarity : 0.004 0.041 2440 Dihedral : 3.647 13.784 1880 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.91 % Allowed : 13.49 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.83 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 94 HIS 0.003 0.000 HIS C 178 PHE 0.021 0.002 PHE C 80 TYR 0.021 0.001 TYR A 97 ARG 0.002 0.000 ARG C 59 *********************** 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 147 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.565 Fit side-chains REVERT: A 30 LYS cc_start: 0.9070 (tttm) cc_final: 0.8820 (ttpt) REVERT: B 320 MET cc_start: 0.8610 (ttt) cc_final: 0.8372 (ttt) REVERT: B 334 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8666 (mttm) REVERT: C 41 SER cc_start: 0.8802 (m) cc_final: 0.8560 (m) REVERT: C 149 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8169 (mtmt) REVERT: C 324 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: C 334 LYS cc_start: 0.8787 (mttp) cc_final: 0.8469 (mttm) REVERT: D 30 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8848 (ttpp) REVERT: D 41 SER cc_start: 0.8908 (m) cc_final: 0.8664 (m) REVERT: D 246 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.9008 (p) REVERT: D 293 GLN cc_start: 0.8797 (tt0) cc_final: 0.8495 (tt0) REVERT: D 335 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7745 (p0) REVERT: E 37 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (mm) REVERT: E 41 SER cc_start: 0.8850 (m) cc_final: 0.8611 (m) REVERT: E 149 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8052 (mtpt) outliers start: 29 outliers final: 16 residues processed: 140 average time/residue: 1.0924 time to fit residues: 170.3701 Evaluate side-chains 138 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 335 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14315 Z= 0.187 Angle : 0.496 9.537 19495 Z= 0.253 Chirality : 0.038 0.151 2155 Planarity : 0.004 0.041 2440 Dihedral : 3.565 13.680 1880 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.91 % Allowed : 13.68 % 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: 1.06 (0.21), residues: 1685 helix: 1.71 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 515 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 0.019 0.002 PHE C 80 TYR 0.018 0.001 TYR B 97 ARG 0.002 0.000 ARG C 59 ********************** 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 154 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.801 Fit side-chains REVERT: A 30 LYS cc_start: 0.9044 (tttm) cc_final: 0.8717 (tttt) REVERT: B 320 MET cc_start: 0.8566 (ttt) cc_final: 0.8331 (ttt) REVERT: B 334 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: C 41 SER cc_start: 0.8798 (m) cc_final: 0.8560 (m) REVERT: C 149 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8152 (mtmt) REVERT: C 324 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: C 334 LYS cc_start: 0.8746 (mttp) cc_final: 0.8458 (mttm) REVERT: D 30 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8835 (ttpp) REVERT: D 41 SER cc_start: 0.8911 (m) cc_final: 0.8691 (m) REVERT: D 293 GLN cc_start: 0.8756 (tt0) cc_final: 0.8472 (tt0) REVERT: D 335 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7745 (p0) REVERT: E 37 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8402 (mm) REVERT: E 41 SER cc_start: 0.8850 (m) cc_final: 0.8624 (m) REVERT: E 149 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8028 (mtpt) outliers start: 29 outliers final: 14 residues processed: 145 average time/residue: 1.1124 time to fit residues: 179.5558 Evaluate side-chains 142 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 335 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 54 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 = 0.3163 r_free = 0.3163 target = 0.102769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.080775 restraints weight = 18738.621| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.69 r_work: 0.2695 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2642 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= 0.238 Angle : 0.519 8.342 19495 Z= 0.267 Chirality : 0.040 0.159 2155 Planarity : 0.004 0.041 2440 Dihedral : 3.600 12.815 1880 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.71 % Allowed : 13.88 % 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: 1.02 (0.21), residues: 1685 helix: 1.66 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.72 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 94 HIS 0.003 0.000 HIS C 178 PHE 0.018 0.002 PHE C 80 TYR 0.020 0.001 TYR A 97 ARG 0.002 0.000 ARG C 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3969.81 seconds wall clock time: 71 minutes 47.59 seconds (4307.59 seconds total)