Starting phenix.real_space_refine on Fri Feb 16 08:47:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/02_2024/6n23_9321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/02_2024/6n23_9321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/02_2024/6n23_9321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/02_2024/6n23_9321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/02_2024/6n23_9321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/02_2024/6n23_9321.pdb" } resolution = 3.1 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= 0.000 sd= 0.004 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 9790 2.51 5 N 2430 2.21 5 O 2645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14935 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2986 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 344} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2986 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 344} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2986 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 344} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2986 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 344} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2986 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 344} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 7.85, per 1000 atoms: 0.53 Number of scatterers: 14935 At special positions: 0 Unit cell: (96.832, 97.92, 113.152, 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 2645 8.00 N 2430 7.00 C 9790 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=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.04 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: 5.50 Conformation dependent library (CDL) restraints added in 2.6 seconds 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.597A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.701A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 98 removed outlier: 3.653A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.699A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.783A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.939A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.546A pdb=" N PHE A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.595A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 53 removed outlier: 3.701A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 removed outlier: 3.653A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.700A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.784A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.532A pdb=" N SER B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.938A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.545A pdb=" N PHE B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.643A pdb=" N LEU B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.595A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.701A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 3.652A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.700A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.785A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.938A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.546A pdb=" N PHE C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS C 355 " --> pdb=" O ALA C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.595A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.700A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 3.653A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.848A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.701A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.784A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.939A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.546A pdb=" N PHE D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS D 355 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.596A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.648A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 53 removed outlier: 3.700A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.513A pdb=" N LEU E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 98 removed outlier: 3.652A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.700A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.785A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.938A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.545A pdb=" N PHE E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.816A pdb=" N LYS E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2370 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: 3.68 Time building geometry restraints manager: 5.98 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: 4624 1.34 - 1.47: 4141 1.47 - 1.59: 6500 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 15365 Sorted by residual: bond pdb=" CB TRP E 309 " pdb=" CG TRP E 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.41e+00 bond pdb=" CB TRP A 309 " pdb=" CG TRP A 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.40e+00 bond pdb=" CB TRP C 309 " pdb=" CG TRP C 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.37e+00 bond pdb=" CB TRP B 309 " pdb=" CG TRP B 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.36e+00 bond pdb=" CB TRP D 309 " pdb=" CG TRP D 309 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.29e+00 ... (remaining 15360 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 434 106.47 - 113.36: 8213 113.36 - 120.25: 6358 120.25 - 127.13: 5712 127.13 - 134.02: 208 Bond angle restraints: 20925 Sorted by residual: angle pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 112.96 106.53 6.43 1.00e+00 1.00e+00 4.13e+01 angle pdb=" N VAL B 186 " pdb=" CA VAL B 186 " pdb=" C VAL B 186 " ideal model delta sigma weight residual 112.96 106.54 6.42 1.00e+00 1.00e+00 4.12e+01 angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N VAL D 186 " pdb=" CA VAL D 186 " pdb=" C VAL D 186 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N VAL E 186 " pdb=" CA VAL E 186 " pdb=" C VAL E 186 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 ... (remaining 20920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 8600 14.94 - 29.87: 295 29.87 - 44.81: 105 44.81 - 59.74: 10 59.74 - 74.68: 10 Dihedral angle restraints: 9020 sinusoidal: 3625 harmonic: 5395 Sorted by residual: 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 -120.63 34.63 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " pdb=" CB CYS C 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.62 34.62 1 1.00e+01 1.00e-02 1.70e+01 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 -120.62 34.62 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1065 0.033 - 0.065: 815 0.065 - 0.098: 298 0.098 - 0.131: 90 0.131 - 0.164: 22 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE E 232 " pdb=" N ILE E 232 " pdb=" C ILE E 232 " pdb=" CB ILE E 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2287 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 287 " 0.030 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP D 287 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 287 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 287 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 287 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 287 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 287 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 287 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 287 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 287 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 287 " -0.030 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP A 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 287 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 287 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 287 " -0.030 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP B 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 287 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 287 " -0.005 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3462 2.76 - 3.30: 13161 3.30 - 3.83: 24541 3.83 - 4.37: 30586 4.37 - 4.90: 51416 Nonbonded interactions: 123166 Sorted by model distance: nonbonded pdb=" OD2 ASP C 203 " pdb=" OG SER D 204 " model vdw 2.231 2.440 nonbonded pdb=" OD2 ASP C 104 " pdb=" NH2 ARG D 218 " model vdw 2.278 2.520 nonbonded pdb=" OD2 ASP A 203 " pdb=" OG SER B 204 " model vdw 2.279 2.440 nonbonded pdb=" OD2 ASP B 203 " pdb=" OG SER C 204 " model vdw 2.328 2.440 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.329 2.520 ... (remaining 123161 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: 0.150 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: 1.640 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 38.930 Find NCS groups from input model: 0.870 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.008 0.067 15365 Z= 0.499 Angle : 0.785 7.861 20925 Z= 0.436 Chirality : 0.050 0.164 2290 Planarity : 0.006 0.040 2630 Dihedral : 9.584 74.678 5525 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -5.52 (0.13), residues: 1805 helix: -4.33 (0.06), residues: 1120 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP D 287 HIS 0.005 0.002 HIS A 168 PHE 0.022 0.003 PHE D 17 TYR 0.039 0.002 TYR C 236 ARG 0.009 0.001 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.950 Fit side-chains REVERT: E 320 MET cc_start: 0.8291 (ttt) cc_final: 0.7901 (ttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.3799 time to fit residues: 75.0498 Evaluate side-chains 60 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 7 ASN C 7 ASN C 293 GLN C 316 GLN D 7 ASN E 7 ASN E 293 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15365 Z= 0.163 Angle : 0.555 8.090 20925 Z= 0.294 Chirality : 0.041 0.389 2290 Planarity : 0.005 0.037 2630 Dihedral : 4.282 16.444 2020 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.28 % Allowed : 2.57 % Favored : 96.15 % 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: -1.94 (0.17), residues: 1805 helix: -1.01 (0.13), residues: 1170 sheet: None (None), residues: 0 loop : -1.56 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 287 HIS 0.001 0.000 HIS E 326 PHE 0.014 0.001 PHE C 17 TYR 0.015 0.001 TYR A 97 ARG 0.005 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.786 Fit side-chains REVERT: A 320 MET cc_start: 0.8483 (ttm) cc_final: 0.8227 (ttm) REVERT: E 320 MET cc_start: 0.7901 (ttt) cc_final: 0.7676 (ttp) outliers start: 21 outliers final: 12 residues processed: 100 average time/residue: 0.1941 time to fit residues: 34.2041 Evaluate side-chains 73 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 111 optimal weight: 0.2980 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15365 Z= 0.242 Angle : 0.532 8.686 20925 Z= 0.276 Chirality : 0.041 0.401 2290 Planarity : 0.004 0.035 2630 Dihedral : 3.958 19.049 2020 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.47 % Allowed : 4.53 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1805 helix: 0.74 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 287 HIS 0.003 0.001 HIS D 326 PHE 0.024 0.001 PHE D 80 TYR 0.018 0.001 TYR C 97 ARG 0.005 0.001 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.862 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 88 average time/residue: 0.1888 time to fit residues: 29.5747 Evaluate side-chains 64 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 251 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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: 0.8669 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15365 Z= 0.267 Angle : 0.522 7.917 20925 Z= 0.268 Chirality : 0.041 0.283 2290 Planarity : 0.003 0.036 2630 Dihedral : 3.881 22.886 2020 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.77 % Allowed : 5.38 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1805 helix: 1.48 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -0.79 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 287 HIS 0.002 0.001 HIS B 326 PHE 0.020 0.001 PHE D 80 TYR 0.016 0.001 TYR A 97 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 1.892 Fit side-chains REVERT: B 80 PHE cc_start: 0.7858 (m-80) cc_final: 0.7602 (m-80) REVERT: B 154 MET cc_start: 0.8639 (mmm) cc_final: 0.7967 (mmt) REVERT: E 80 PHE cc_start: 0.8053 (m-80) cc_final: 0.7831 (m-80) outliers start: 29 outliers final: 16 residues processed: 85 average time/residue: 0.2407 time to fit residues: 33.6648 Evaluate side-chains 67 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 251 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.0050 chunk 98 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15365 Z= 0.127 Angle : 0.456 9.030 20925 Z= 0.233 Chirality : 0.037 0.147 2290 Planarity : 0.003 0.036 2630 Dihedral : 3.728 22.957 2020 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.28 % Allowed : 6.12 % Favored : 92.60 % 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: 1.15 (0.20), residues: 1805 helix: 1.71 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -0.99 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 287 HIS 0.003 0.000 HIS C 168 PHE 0.011 0.001 PHE A 80 TYR 0.016 0.001 TYR D 284 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.773 Fit side-chains REVERT: C 75 LEU cc_start: 0.8442 (mp) cc_final: 0.8233 (mp) REVERT: E 80 PHE cc_start: 0.7840 (m-80) cc_final: 0.7593 (m-80) outliers start: 21 outliers final: 10 residues processed: 89 average time/residue: 0.2026 time to fit residues: 31.3787 Evaluate side-chains 65 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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: 0.8681 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15365 Z= 0.272 Angle : 0.518 9.722 20925 Z= 0.260 Chirality : 0.040 0.146 2290 Planarity : 0.003 0.036 2630 Dihedral : 3.729 24.899 2020 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.16 % Allowed : 6.42 % Favored : 92.42 % 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: 1.63 (0.20), residues: 1805 helix: 2.10 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -0.60 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 287 HIS 0.002 0.001 HIS A 326 PHE 0.026 0.001 PHE D 80 TYR 0.024 0.001 TYR D 284 ARG 0.005 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 1.760 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.2171 time to fit residues: 29.0839 Evaluate side-chains 66 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.8660 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15365 Z= 0.184 Angle : 0.485 10.390 20925 Z= 0.244 Chirality : 0.038 0.290 2290 Planarity : 0.003 0.036 2630 Dihedral : 3.689 23.111 2020 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.35 % Allowed : 6.36 % Favored : 92.29 % 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: 1.76 (0.20), residues: 1805 helix: 2.22 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -0.59 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.002 0.000 HIS A 326 PHE 0.014 0.001 PHE A 283 TYR 0.028 0.001 TYR D 284 ARG 0.002 0.000 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 1.923 Fit side-chains REVERT: E 80 PHE cc_start: 0.8046 (m-80) cc_final: 0.7789 (m-80) outliers start: 22 outliers final: 15 residues processed: 75 average time/residue: 0.2087 time to fit residues: 27.6554 Evaluate side-chains 68 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 overall best weight: 4.2386 ------------------------------------------------------------------------------- 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: 0.8686 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15365 Z= 0.276 Angle : 0.522 11.231 20925 Z= 0.261 Chirality : 0.040 0.145 2290 Planarity : 0.003 0.036 2630 Dihedral : 3.702 20.912 2020 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.28 % Allowed : 6.79 % Favored : 91.93 % 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: 1.78 (0.20), residues: 1805 helix: 2.23 (0.15), residues: 1105 sheet: None (None), residues: 0 loop : -0.57 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.002 0.001 HIS A 326 PHE 0.020 0.001 PHE A 80 TYR 0.020 0.001 TYR D 284 ARG 0.004 0.000 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 2.013 Fit side-chains REVERT: E 80 PHE cc_start: 0.8256 (m-80) cc_final: 0.8008 (m-80) outliers start: 21 outliers final: 19 residues processed: 76 average time/residue: 0.2090 time to fit residues: 27.6960 Evaluate side-chains 73 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8640 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15365 Z= 0.139 Angle : 0.469 12.072 20925 Z= 0.237 Chirality : 0.037 0.145 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.643 20.875 2020 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.22 % Allowed : 7.03 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.20), residues: 1805 helix: 2.30 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -0.84 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 94 HIS 0.002 0.000 HIS A 326 PHE 0.016 0.001 PHE A 80 TYR 0.024 0.001 TYR A 284 ARG 0.002 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 1.882 Fit side-chains REVERT: E 80 PHE cc_start: 0.8102 (m-80) cc_final: 0.7894 (m-80) outliers start: 20 outliers final: 17 residues processed: 77 average time/residue: 0.2055 time to fit residues: 27.8263 Evaluate side-chains 71 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.8658 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15365 Z= 0.195 Angle : 0.489 12.776 20925 Z= 0.244 Chirality : 0.038 0.289 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.620 20.426 2020 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.16 % Allowed : 7.16 % Favored : 91.68 % 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: 1.81 (0.20), residues: 1805 helix: 2.41 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -0.81 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.000 HIS A 326 PHE 0.022 0.001 PHE D 80 TYR 0.026 0.001 TYR A 284 ARG 0.003 0.000 ARG E 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 1.761 Fit side-chains REVERT: C 163 MET cc_start: 0.9218 (ttp) cc_final: 0.8852 (ttt) outliers start: 19 outliers final: 16 residues processed: 72 average time/residue: 0.2100 time to fit residues: 26.8686 Evaluate side-chains 72 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 ASN D 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.055306 restraints weight = 30502.779| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.97 r_work: 0.2563 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15365 Z= 0.131 Angle : 0.466 12.780 20925 Z= 0.234 Chirality : 0.037 0.238 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.553 20.439 2020 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.04 % Allowed : 7.28 % Favored : 91.68 % 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: 1.95 (0.20), residues: 1805 helix: 2.33 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.71 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.003 0.000 HIS A 326 PHE 0.026 0.001 PHE A 80 TYR 0.024 0.001 TYR A 284 ARG 0.002 0.000 ARG D 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.23 seconds wall clock time: 42 minutes 8.43 seconds (2528.43 seconds total)