Starting phenix.real_space_refine on Sat Jan 20 06:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/01_2024/6n27_9325.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/01_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_9325/01_2024/6n27_9325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/01_2024/6n27_9325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/01_2024/6n27_9325.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n27_9325/01_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 7.70, per 1000 atoms: 0.55 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: 5.63 Conformation dependent library (CDL) restraints added in 2.5 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: 1.25 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: 3.84 Time building geometry restraints manager: 6.06 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.580 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.830 Find NCS groups from input model: 0.880 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.620 ------------------------------------------------------------------------------- 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 : 1.697 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: 1.3446 time to fit residues: 389.5133 Evaluate side-chains 141 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: