Starting phenix.real_space_refine on Thu Sep 26 23:59:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/09_2024/6n23_9321.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/09_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_9321/09_2024/6n23_9321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/09_2024/6n23_9321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/09_2024/6n23_9321.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n23_9321/09_2024/6n23_9321.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14935 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 6.16, per 1000 atoms: 0.41 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.9 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: 1.27 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: 4.81 Time building geometry restraints manager: 3.73 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: 0.00 - 1.57: 19912 1.57 - 3.14: 839 3.14 - 4.72: 104 4.72 - 6.29: 40 6.29 - 7.86: 30 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: 8596 14.94 - 29.87: 291 29.87 - 44.81: 101 44.81 - 59.74: 10 59.74 - 74.68: 10 Dihedral angle restraints: 9008 sinusoidal: 3613 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=" CA TRP D 287 " pdb=" C TRP D 287 " pdb=" N LEU D 288 " pdb=" CA LEU D 288 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TRP B 287 " pdb=" C TRP B 287 " pdb=" N LEU B 288 " pdb=" CA LEU B 288 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9005 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: 2.04 - 2.61: 134 2.61 - 3.18: 12404 3.18 - 3.76: 22833 3.76 - 4.33: 33385 4.33 - 4.90: 54422 Nonbonded interactions: 123178 Sorted by model distance: nonbonded pdb=" SG CYS B 135 " pdb=" SG CYS B 185 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 185 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " model vdw 2.041 3.760 nonbonded pdb=" OD2 ASP C 203 " pdb=" OG SER D 204 " model vdw 2.231 3.040 ... (remaining 123173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.820 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- 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= 0.496 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 : 2.040 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 : 1.762 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: 0.3879 time to fit residues: 77.0420 Evaluate side-chains 60 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8585 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15365 Z= 0.197 Angle : 0.586 8.106 20925 Z= 0.313 Chirality : 0.043 0.412 2290 Planarity : 0.005 0.038 2630 Dihedral : 4.318 16.104 2020 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.41 % Allowed : 2.75 % Favored : 95.84 % 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: -1.79 (0.18), residues: 1805 helix: -0.87 (0.13), residues: 1165 sheet: None (None), residues: 0 loop : -1.55 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 287 HIS 0.002 0.001 HIS E 178 PHE 0.015 0.001 PHE D 17 TYR 0.018 0.001 TYR A 97 ARG 0.005 0.001 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 100 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.736 Fit side-chains REVERT: A 80 PHE cc_start: 0.7890 (m-80) cc_final: 0.7641 (m-80) REVERT: A 320 MET cc_start: 0.8505 (ttm) cc_final: 0.8233 (ttm) REVERT: E 320 MET cc_start: 0.7956 (ttt) cc_final: 0.7709 (ttp) outliers start: 23 outliers final: 13 residues processed: 96 average time/residue: 0.1897 time to fit residues: 32.1193 Evaluate side-chains 70 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 D residue 87 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 0.1980 chunk 45 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15365 Z= 0.145 Angle : 0.487 9.371 20925 Z= 0.254 Chirality : 0.039 0.411 2290 Planarity : 0.004 0.038 2630 Dihedral : 3.882 18.175 2020 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.10 % Allowed : 4.95 % Favored : 93.94 % 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: -0.10 (0.19), residues: 1805 helix: 0.61 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 287 HIS 0.003 0.000 HIS D 326 PHE 0.019 0.001 PHE D 80 TYR 0.013 0.001 TYR C 97 ARG 0.004 0.000 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 97 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.639 Fit side-chains REVERT: A 80 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: A 320 MET cc_start: 0.8567 (ttm) cc_final: 0.8276 (ttm) REVERT: E 80 PHE cc_start: 0.7868 (m-80) cc_final: 0.7622 (m-80) REVERT: E 320 MET cc_start: 0.8030 (ttt) cc_final: 0.7798 (ttp) outliers start: 18 outliers final: 10 residues processed: 92 average time/residue: 0.1847 time to fit residues: 29.8724 Evaluate side-chains 68 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2750 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= 0.165 Angle : 0.466 6.727 20925 Z= 0.241 Chirality : 0.038 0.151 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.743 24.244 2020 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.35 % Allowed : 5.81 % 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: 0.67 (0.20), residues: 1805 helix: 1.32 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.16 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 287 HIS 0.002 0.000 HIS D 178 PHE 0.009 0.001 PHE A 171 TYR 0.015 0.001 TYR C 97 ARG 0.004 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 90 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 1.897 Fit side-chains REVERT: A 80 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: A 320 MET cc_start: 0.8629 (ttm) cc_final: 0.8317 (ttm) REVERT: E 80 PHE cc_start: 0.7934 (m-80) cc_final: 0.7706 (m-80) REVERT: E 320 MET cc_start: 0.8112 (ttt) cc_final: 0.7887 (ttp) outliers start: 22 outliers final: 13 residues processed: 84 average time/residue: 0.1950 time to fit residues: 28.5322 Evaluate side-chains 75 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 351 THR 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 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 351 THR 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 D residue 351 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 71 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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: 0.8643 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15365 Z= 0.200 Angle : 0.487 9.026 20925 Z= 0.247 Chirality : 0.038 0.151 2290 Planarity : 0.004 0.041 2630 Dihedral : 3.688 24.350 2020 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.10 % Allowed : 6.85 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1805 helix: 1.75 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.05 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 287 HIS 0.002 0.001 HIS A 326 PHE 0.020 0.001 PHE D 80 TYR 0.015 0.001 TYR A 97 ARG 0.003 0.000 ARG C 150 *********************** 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 82 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.740 Fit side-chains REVERT: A 80 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 320 MET cc_start: 0.8728 (ttm) cc_final: 0.8379 (ttm) REVERT: E 80 PHE cc_start: 0.7957 (m-80) cc_final: 0.7698 (m-80) REVERT: E 320 MET cc_start: 0.8259 (ttt) cc_final: 0.8046 (ttp) outliers start: 18 outliers final: 13 residues processed: 81 average time/residue: 0.2141 time to fit residues: 30.1958 Evaluate side-chains 72 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER 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 240 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER 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: 9.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 91 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: 0.8649 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15365 Z= 0.198 Angle : 0.485 9.385 20925 Z= 0.246 Chirality : 0.039 0.324 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.652 26.931 2020 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.65 % Allowed : 6.73 % Favored : 91.62 % 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: 1.41 (0.20), residues: 1805 helix: 2.00 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.00 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 287 HIS 0.003 0.001 HIS A 326 PHE 0.011 0.001 PHE A 283 TYR 0.022 0.001 TYR D 284 ARG 0.003 0.000 ARG B 218 *********************** 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 93 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 1.818 Fit side-chains REVERT: A 80 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: A 320 MET cc_start: 0.8695 (ttm) cc_final: 0.8365 (ttm) REVERT: E 80 PHE cc_start: 0.7976 (m-80) cc_final: 0.7691 (m-80) outliers start: 27 outliers final: 16 residues processed: 90 average time/residue: 0.2169 time to fit residues: 32.7559 Evaluate side-chains 77 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER 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 351 THR Chi-restraints excluded: chain D residue 61 MET 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 E residue 18 SER Chi-restraints excluded: chain E residue 87 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: 0.9990 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 0.0270 chunk 108 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3380 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= 0.150 Angle : 0.465 10.965 20925 Z= 0.235 Chirality : 0.038 0.231 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.567 21.540 2020 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.04 % Allowed : 7.34 % Favored : 91.62 % 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: 1.64 (0.20), residues: 1805 helix: 2.25 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.06 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 94 HIS 0.003 0.000 HIS A 326 PHE 0.014 0.001 PHE D 80 TYR 0.020 0.001 TYR A 284 ARG 0.003 0.000 ARG B 218 *********************** 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 85 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 1.738 Fit side-chains REVERT: A 320 MET cc_start: 0.8707 (ttm) cc_final: 0.8358 (ttm) REVERT: E 80 PHE cc_start: 0.7954 (m-80) cc_final: 0.7680 (m-80) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.1999 time to fit residues: 28.5807 Evaluate side-chains 76 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 351 THR 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 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 87 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: 0.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3467 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= 0.179 Angle : 0.483 11.486 20925 Z= 0.243 Chirality : 0.038 0.203 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.572 22.837 2020 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.16 % Allowed : 7.03 % Favored : 91.80 % 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: 1.84 (0.20), residues: 1805 helix: 2.40 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -0.93 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.002 0.001 HIS A 326 PHE 0.013 0.001 PHE D 283 TYR 0.026 0.001 TYR D 284 ARG 0.003 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 86 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.579 Fit side-chains REVERT: A 320 MET cc_start: 0.8724 (ttm) cc_final: 0.8370 (ttm) REVERT: E 80 PHE cc_start: 0.7926 (m-80) cc_final: 0.7610 (m-80) outliers start: 19 outliers final: 16 residues processed: 85 average time/residue: 0.2214 time to fit residues: 32.3067 Evaluate side-chains 80 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER 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 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8651 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15365 Z= 0.190 Angle : 0.487 12.229 20925 Z= 0.244 Chirality : 0.038 0.149 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.552 22.149 2020 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.10 % Allowed : 7.52 % Favored : 91.38 % 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: 1.93 (0.20), residues: 1805 helix: 2.41 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.81 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.002 0.001 HIS A 326 PHE 0.019 0.001 PHE D 80 TYR 0.025 0.001 TYR D 284 ARG 0.003 0.000 ARG E 150 *********************** 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 88 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.664 Fit side-chains REVERT: A 320 MET cc_start: 0.8727 (ttm) cc_final: 0.8431 (ttm) REVERT: E 80 PHE cc_start: 0.7994 (m-80) cc_final: 0.7686 (m-80) outliers start: 18 outliers final: 16 residues processed: 86 average time/residue: 0.2106 time to fit residues: 30.7057 Evaluate side-chains 77 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 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 61 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 351 THR 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: 9.9990 chunk 104 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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: 0.8661 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15365 Z= 0.213 Angle : 0.503 12.650 20925 Z= 0.251 Chirality : 0.039 0.188 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.586 23.900 2020 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.92 % Allowed : 8.01 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 1805 helix: 2.40 (0.15), residues: 1145 sheet: None (None), residues: 0 loop : -0.79 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 287 HIS 0.002 0.001 HIS A 326 PHE 0.024 0.001 PHE A 80 TYR 0.023 0.001 TYR D 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 80 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 1.742 Fit side-chains REVERT: E 80 PHE cc_start: 0.8151 (m-80) cc_final: 0.7882 (m-80) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.2112 time to fit residues: 28.6600 Evaluate side-chains 77 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 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 61 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL 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: 7.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN C 133 ASN D 293 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.055128 restraints weight = 31329.486| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.90 r_work: 0.2565 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15365 Z= 0.127 Angle : 0.463 12.705 20925 Z= 0.233 Chirality : 0.037 0.200 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.492 20.151 2020 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 8.07 % Favored : 90.95 % 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: 2.05 (0.20), residues: 1805 helix: 2.46 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.78 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.003 0.001 HIS A 326 PHE 0.023 0.001 PHE D 283 TYR 0.036 0.001 TYR D 284 ARG 0.002 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.19 seconds wall clock time: 40 minutes 36.01 seconds (2436.01 seconds total)