Starting phenix.real_space_refine on Fri Jul 3 09:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyd_29565/07_2026/8fyd_29565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyd_29565/07_2026/8fyd_29565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2026/8fyd_29565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2026/8fyd_29565.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2026/8fyd_29565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2026/8fyd_29565.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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 P 154 5.49 5 S 32 5.16 5 C 8107 2.51 5 N 2481 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13612 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1005 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2163 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2261 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2188 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "G" Number of atoms: 1330 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 1308 Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} Conformer: "B" Number of residues, atoms: 64, 1308 Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} bond proxies already assigned to first conformer: 1440 Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DG G 29 " occ=0.61 ... (42 atoms not shown) pdb=" C4 B DG G 29 " occ=0.39 Time building chain proxies: 3.51, per 1000 atoms: 0.26 Number of scatterers: 13612 At special positions: 0 Unit cell: (115.96, 95.89, 154.985, 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) S 32 16.00 P 154 15.00 O 2838 8.00 N 2481 7.00 C 8107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.17 Conformation dependent library (CDL) restraints added in 614.6 milliseconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2446 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 52.8% alpha, 12.8% beta 61 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 68 through 76 removed outlier: 3.629A pdb=" N ASP B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.253A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 removed outlier: 3.519A pdb=" N TYR B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 162 removed outlier: 3.730A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 4.271A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.879A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.793A pdb=" N ALA B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.536A pdb=" N LYS B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 271 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.930A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.551A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.670A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.808A pdb=" N ARG C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 163 removed outlier: 3.553A pdb=" N ARG C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 204 removed outlier: 3.829A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.519A pdb=" N TYR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.949A pdb=" N ILE C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 266 removed outlier: 3.518A pdb=" N ASP C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'D' and resid 12 through 19 removed outlier: 3.537A pdb=" N ARG D 16 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.551A pdb=" N ARG D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 77 removed outlier: 3.556A pdb=" N LEU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.611A pdb=" N ARG E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 removed outlier: 4.354A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 139 through 162 removed outlier: 3.549A pdb=" N HIS E 146 " --> pdb=" O GLN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 205 removed outlier: 3.518A pdb=" N ALA E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.525A pdb=" N ASP E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.912A pdb=" N ALA E 262 " --> pdb=" O ARG E 258 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.550A pdb=" N LYS E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 17 through 21 removed outlier: 4.018A pdb=" N ARG F 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 67 through 78 removed outlier: 3.938A pdb=" N VAL F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.747A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 4.169A pdb=" N TYR F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 163 removed outlier: 3.586A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 205 removed outlier: 3.885A pdb=" N GLN F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA F 185 " --> pdb=" O PRO F 181 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 229 removed outlier: 3.588A pdb=" N ASP F 227 " --> pdb=" O TYR F 223 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 removed outlier: 3.517A pdb=" N ILE F 237 " --> pdb=" O ILE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 267 removed outlier: 3.893A pdb=" N LEU F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.679A pdb=" N VAL F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.910A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 71 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.608A pdb=" N ARG E 34 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 5.979A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 22 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.840A pdb=" N LYS B 31 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 65 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 32 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 67 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 34 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27 removed outlier: 6.353A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 80 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.211A pdb=" N GLU D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL D 32 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D 56 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 73 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 60 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 293 removed outlier: 6.571A pdb=" N ALA E 22 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU E 293 " --> pdb=" O ALA E 22 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE E 24 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU E 81 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY F 85 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 58 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL F 84 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU F 60 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 25 " --> pdb=" O VAL F 57 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 157 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.61 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: 3797 1.34 - 1.46: 3112 1.46 - 1.57: 6912 1.57 - 1.69: 308 1.69 - 1.81: 62 Bond restraints: 14191 Sorted by residual: bond pdb=" C3' DG J 26 " pdb=" C2' DG J 26 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DA H 1 " pdb=" C2' DA H 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC H 10 " pdb=" C2' DC H 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG G 60 " pdb=" C2' DG G 60 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG G 8 " pdb=" C2' DG G 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.67e+00 ... (remaining 14186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 18865 1.43 - 2.86: 894 2.86 - 4.29: 87 4.29 - 5.72: 23 5.72 - 7.15: 5 Bond angle restraints: 19874 Sorted by residual: angle pdb=" N3 DT G 5 " pdb=" C4 DT G 5 " pdb=" O4 DT G 5 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT G 32 " pdb=" C4 DT G 32 " pdb=" O4 DT G 32 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT G 4 " pdb=" C4 DT G 4 " pdb=" O4 DT G 4 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT G 17 " pdb=" C4 DT G 17 " pdb=" O4 DT G 17 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 19869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 7393 35.88 - 71.75: 673 71.75 - 107.63: 19 107.63 - 143.50: 3 143.50 - 179.38: 4 Dihedral angle restraints: 8092 sinusoidal: 4276 harmonic: 3816 Sorted by residual: dihedral pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " pdb=" O3' DA J 32 " pdb=" P DA J 33 " ideal model delta sinusoidal sigma weight residual -140.00 39.38 -179.38 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 31 " pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " pdb=" P DA J 32 " ideal model delta sinusoidal sigma weight residual -140.00 38.42 -178.42 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG G 38 " pdb=" C3' DG G 38 " pdb=" O3' DG G 38 " pdb=" P DC G 39 " ideal model delta sinusoidal sigma weight residual -140.00 34.60 -174.60 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1385 0.034 - 0.068: 584 0.068 - 0.101: 190 0.101 - 0.135: 60 0.135 - 0.169: 14 Chirality restraints: 2233 Sorted by residual: chirality pdb=" P DC J 21 " pdb=" OP1 DC J 21 " pdb=" OP2 DC J 21 " pdb=" O5' DC J 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.50 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" C3' DC J 21 " pdb=" C4' DC J 21 " pdb=" O3' DC J 21 " pdb=" C2' DC J 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" C3' DG J 34 " pdb=" C4' DG J 34 " pdb=" O3' DG J 34 " pdb=" C2' DG J 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2230 not shown) Planarity restraints: 2009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 8 " 0.028 2.00e-02 2.50e+03 1.17e-02 4.11e+00 pdb=" N9 DG J 8 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J 8 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG J 8 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG J 8 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 8 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 8 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG J 8 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 8 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG J 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 8 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 8 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 37 " 0.024 2.00e-02 2.50e+03 1.12e-02 3.48e+00 pdb=" N9 DA J 37 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA J 37 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 37 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 37 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 37 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA J 37 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA J 37 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA J 37 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA J 37 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA J 37 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 1 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 2 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 2 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 2 " -0.025 5.00e-02 4.00e+02 ... (remaining 2006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1115 2.74 - 3.28: 14284 3.28 - 3.82: 25857 3.82 - 4.36: 29081 4.36 - 4.90: 45125 Nonbonded interactions: 115462 Sorted by model distance: nonbonded pdb=" OH TYR B 91 " pdb=" OG SER B 94 " model vdw 2.196 3.040 nonbonded pdb=" O ASN F 33 " pdb=" OG1 THR F 40 " model vdw 2.235 3.040 nonbonded pdb=" NE2 GLN E 277 " pdb=" O ILE E 288 " model vdw 2.247 3.120 nonbonded pdb=" OG SER B 159 " pdb=" O VAL B 164 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG A 46 " pdb=" OG SER C 10 " model vdw 2.259 3.120 ... (remaining 115457 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 'D' } ncs_group { reference = (chain 'B' and (resid 20 through 129 or resid 134 through 279)) selection = (chain 'C' and (resid 20 through 129 or resid 134 through 279)) selection = (chain 'E' and resid 20 through 279) selection = (chain 'F' and (resid 20 through 129 or resid 134 through 279)) } 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.490 Find NCS groups from input model: 0.240 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.004 0.036 14191 Z= 0.363 Angle : 0.659 7.149 19874 Z= 0.500 Chirality : 0.044 0.169 2233 Planarity : 0.004 0.044 2009 Dihedral : 22.389 179.381 5646 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1311 helix: 0.80 (0.21), residues: 597 sheet: -0.24 (0.37), residues: 191 loop : -0.83 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 90 TYR 0.021 0.001 TYR B 91 PHE 0.014 0.001 PHE A 35 TRP 0.028 0.002 TRP C 166 HIS 0.008 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.36 (14191) covalent geometry : angle 0.65933 / 0.50 (19874) hydrogen bonds : bond 0.22576 / 24.76 ( 670) hydrogen bonds : angle 7.03387 / 9.24 ( 1781) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.425 Fit side-chains REVERT: A 34 ASN cc_start: 0.7529 (m-40) cc_final: 0.6416 (m110) REVERT: B 32 ILE cc_start: 0.8858 (pt) cc_final: 0.8608 (pt) REVERT: B 54 MET cc_start: 0.8246 (mtp) cc_final: 0.8005 (mtp) REVERT: B 91 TYR cc_start: 0.7625 (t80) cc_final: 0.7311 (t80) REVERT: B 128 MET cc_start: 0.9255 (mpp) cc_final: 0.9030 (mpp) REVERT: C 157 GLU cc_start: 0.9159 (pp20) cc_final: 0.8920 (pp20) REVERT: C 183 ASN cc_start: 0.8867 (m110) cc_final: 0.8427 (m110) REVERT: D 60 PHE cc_start: 0.8180 (p90) cc_final: 0.7938 (p90) REVERT: F 116 ARG cc_start: 0.8270 (tmm-80) cc_final: 0.8037 (tmm-80) REVERT: F 239 PHE cc_start: 0.8719 (t80) cc_final: 0.8296 (t80) REVERT: F 265 ASP cc_start: 0.6901 (m-30) cc_final: 0.6573 (t0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1064 time to fit residues: 42.6511 Evaluate side-chains 205 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.2980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 HIS C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 87 GLN F 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.127278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087153 restraints weight = 36619.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089691 restraints weight = 19998.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091309 restraints weight = 14048.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092278 restraints weight = 11472.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092587 restraints weight = 10245.225| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14191 Z= 0.227 Angle : 0.710 8.897 19874 Z= 0.399 Chirality : 0.046 0.241 2233 Planarity : 0.005 0.069 2009 Dihedral : 25.547 177.267 3174 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.94 % Allowed : 12.40 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.22), residues: 1311 helix: 0.77 (0.20), residues: 628 sheet: -0.50 (0.37), residues: 181 loop : -0.95 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 156 TYR 0.028 0.002 TYR E 194 PHE 0.015 0.002 PHE F 176 TRP 0.014 0.002 TRP C 166 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (14191) covalent geometry : angle 0.71004 / 0.40 (19874) hydrogen bonds : bond 0.06549 / 7.21 ( 670) hydrogen bonds : angle 5.00272 / 6.67 ( 1781) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.435 Fit side-chains REVERT: A 23 MET cc_start: 0.8802 (mmt) cc_final: 0.7663 (mmt) REVERT: B 91 TYR cc_start: 0.7906 (t80) cc_final: 0.7566 (t80) REVERT: B 272 MET cc_start: 0.8608 (mpp) cc_final: 0.8311 (mpp) REVERT: C 54 MET cc_start: 0.9459 (mmt) cc_final: 0.9022 (mmt) REVERT: C 127 GLN cc_start: 0.8067 (pp30) cc_final: 0.7633 (pp30) REVERT: C 128 MET cc_start: 0.8600 (mmm) cc_final: 0.8113 (mmm) REVERT: C 157 GLU cc_start: 0.9167 (pp20) cc_final: 0.8910 (pp20) REVERT: C 183 ASN cc_start: 0.9092 (m110) cc_final: 0.8716 (m-40) REVERT: D 58 MET cc_start: 0.7714 (ppp) cc_final: 0.7192 (ppp) REVERT: D 60 PHE cc_start: 0.8578 (p90) cc_final: 0.8258 (p90) REVERT: E 194 TYR cc_start: 0.8584 (m-80) cc_final: 0.8093 (m-80) REVERT: E 305 TYR cc_start: 0.8216 (m-10) cc_final: 0.7988 (m-10) REVERT: F 114 ASN cc_start: 0.7887 (t0) cc_final: 0.7603 (t0) REVERT: F 171 TYR cc_start: 0.4128 (t80) cc_final: 0.3920 (t80) REVERT: F 190 HIS cc_start: 0.8242 (m170) cc_final: 0.7659 (m90) REVERT: F 265 ASP cc_start: 0.7329 (m-30) cc_final: 0.6843 (t0) outliers start: 21 outliers final: 16 residues processed: 226 average time/residue: 0.0963 time to fit residues: 32.8132 Evaluate side-chains 205 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 174 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.0980 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 119 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN B 146 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.129446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088071 restraints weight = 52466.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.091250 restraints weight = 23961.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093292 restraints weight = 15265.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094585 restraints weight = 11768.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095317 restraints weight = 10123.444| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14191 Z= 0.153 Angle : 0.651 8.498 19874 Z= 0.366 Chirality : 0.045 0.257 2233 Planarity : 0.005 0.052 2009 Dihedral : 25.514 177.605 3174 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.76 % Allowed : 14.99 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1311 helix: 0.82 (0.20), residues: 626 sheet: -0.42 (0.38), residues: 181 loop : -0.95 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 124 TYR 0.026 0.002 TYR E 194 PHE 0.018 0.001 PHE F 239 TRP 0.010 0.001 TRP C 166 HIS 0.011 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14191) covalent geometry : angle 0.65124 / 0.37 (19874) hydrogen bonds : bond 0.05503 / 6.09 ( 670) hydrogen bonds : angle 4.57708 / 6.09 ( 1781) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8650 (mmt) cc_final: 0.7950 (mmt) REVERT: A 35 PHE cc_start: 0.8593 (m-10) cc_final: 0.8040 (m-10) REVERT: B 91 TYR cc_start: 0.7954 (t80) cc_final: 0.7282 (t80) REVERT: B 94 SER cc_start: 0.8465 (p) cc_final: 0.8131 (p) REVERT: C 54 MET cc_start: 0.9453 (mmt) cc_final: 0.9003 (mmt) REVERT: C 67 SER cc_start: 0.8985 (t) cc_final: 0.8314 (p) REVERT: C 157 GLU cc_start: 0.9169 (pp20) cc_final: 0.8902 (pp20) REVERT: C 183 ASN cc_start: 0.9096 (m110) cc_final: 0.8724 (m110) REVERT: D 18 ASP cc_start: 0.8499 (t0) cc_final: 0.8265 (t70) REVERT: D 58 MET cc_start: 0.7835 (ppp) cc_final: 0.7039 (ppp) REVERT: D 60 PHE cc_start: 0.8522 (p90) cc_final: 0.8221 (p90) REVERT: D 71 LEU cc_start: 0.8944 (mp) cc_final: 0.8496 (mp) REVERT: E 194 TYR cc_start: 0.8634 (m-80) cc_final: 0.8262 (m-80) REVERT: F 125 MET cc_start: 0.9284 (mmp) cc_final: 0.8995 (mmp) REVERT: F 155 TYR cc_start: 0.7874 (m-80) cc_final: 0.7621 (m-80) REVERT: F 190 HIS cc_start: 0.8199 (m170) cc_final: 0.7846 (m90) REVERT: F 265 ASP cc_start: 0.7388 (m-30) cc_final: 0.6890 (t0) outliers start: 19 outliers final: 11 residues processed: 246 average time/residue: 0.1014 time to fit residues: 38.0723 Evaluate side-chains 212 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 174 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.129800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088898 restraints weight = 41693.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091763 restraints weight = 21218.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093583 restraints weight = 14331.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094680 restraints weight = 11456.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095090 restraints weight = 10100.067| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14191 Z= 0.148 Angle : 0.641 7.818 19874 Z= 0.357 Chirality : 0.044 0.250 2233 Planarity : 0.004 0.050 2009 Dihedral : 25.496 177.790 3174 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.13 % Allowed : 18.13 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1311 helix: 0.86 (0.21), residues: 624 sheet: -0.42 (0.39), residues: 181 loop : -0.98 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.019 0.002 TYR E 194 PHE 0.029 0.001 PHE F 239 TRP 0.008 0.001 TRP C 166 HIS 0.011 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (14191) covalent geometry : angle 0.64079 / 0.36 (19874) hydrogen bonds : bond 0.04993 / 5.56 ( 670) hydrogen bonds : angle 4.38384 / 5.79 ( 1781) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8808 (mmt) cc_final: 0.8126 (mmt) REVERT: A 35 PHE cc_start: 0.8568 (m-10) cc_final: 0.8036 (m-10) REVERT: B 91 TYR cc_start: 0.7940 (t80) cc_final: 0.7235 (t80) REVERT: B 94 SER cc_start: 0.8410 (p) cc_final: 0.8046 (p) REVERT: B 163 ASN cc_start: 0.8816 (p0) cc_final: 0.8605 (p0) REVERT: C 54 MET cc_start: 0.9418 (mmt) cc_final: 0.9038 (mmt) REVERT: C 67 SER cc_start: 0.8894 (t) cc_final: 0.8254 (p) REVERT: C 128 MET cc_start: 0.8554 (mmm) cc_final: 0.8189 (mmm) REVERT: C 157 GLU cc_start: 0.9177 (pp20) cc_final: 0.8894 (pp20) REVERT: C 183 ASN cc_start: 0.9079 (m110) cc_final: 0.8716 (m110) REVERT: D 60 PHE cc_start: 0.8553 (p90) cc_final: 0.8157 (p90) REVERT: E 107 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8548 (mmtm) REVERT: F 119 LEU cc_start: 0.8865 (mm) cc_final: 0.8651 (mm) REVERT: F 155 TYR cc_start: 0.7925 (m-80) cc_final: 0.7694 (m-10) REVERT: F 190 HIS cc_start: 0.8116 (m170) cc_final: 0.7842 (m90) REVERT: F 265 ASP cc_start: 0.7358 (m-30) cc_final: 0.6871 (t0) outliers start: 23 outliers final: 17 residues processed: 225 average time/residue: 0.1062 time to fit residues: 36.6259 Evaluate side-chains 217 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 96 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089444 restraints weight = 41174.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.092270 restraints weight = 21193.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094081 restraints weight = 14463.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095207 restraints weight = 11583.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095860 restraints weight = 10204.737| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14191 Z= 0.142 Angle : 0.635 9.445 19874 Z= 0.352 Chirality : 0.044 0.253 2233 Planarity : 0.004 0.049 2009 Dihedral : 25.459 177.636 3174 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.94 % Allowed : 19.89 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1311 helix: 0.90 (0.20), residues: 628 sheet: -0.44 (0.38), residues: 186 loop : -0.99 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.017 0.002 TYR E 194 PHE 0.033 0.002 PHE F 239 TRP 0.009 0.001 TRP C 166 HIS 0.011 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (14191) covalent geometry : angle 0.63457 / 0.35 (19874) hydrogen bonds : bond 0.04626 / 5.16 ( 670) hydrogen bonds : angle 4.23932 / 5.60 ( 1781) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7419 (tmm) cc_final: 0.7139 (tmm) REVERT: A 23 MET cc_start: 0.8755 (mmt) cc_final: 0.8010 (mmt) REVERT: A 35 PHE cc_start: 0.8530 (m-10) cc_final: 0.8111 (m-10) REVERT: B 91 TYR cc_start: 0.7932 (t80) cc_final: 0.7213 (t80) REVERT: B 94 SER cc_start: 0.8428 (p) cc_final: 0.8029 (p) REVERT: B 125 MET cc_start: 0.9095 (mtt) cc_final: 0.8604 (tmm) REVERT: C 54 MET cc_start: 0.9391 (mmt) cc_final: 0.9052 (mmt) REVERT: C 67 SER cc_start: 0.8761 (t) cc_final: 0.8192 (p) REVERT: C 157 GLU cc_start: 0.9180 (pp20) cc_final: 0.8891 (pp20) REVERT: C 183 ASN cc_start: 0.9056 (m110) cc_final: 0.8819 (m110) REVERT: C 184 GLN cc_start: 0.8947 (pm20) cc_final: 0.8697 (pm20) REVERT: D 18 ASP cc_start: 0.8437 (t0) cc_final: 0.8049 (t70) REVERT: D 60 PHE cc_start: 0.8449 (p90) cc_final: 0.8162 (p90) REVERT: E 49 ARG cc_start: 0.8748 (ttt90) cc_final: 0.8531 (tpp80) REVERT: E 107 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8486 (mmtm) REVERT: F 54 MET cc_start: 0.9101 (mpp) cc_final: 0.8873 (mtm) REVERT: F 119 LEU cc_start: 0.8879 (mm) cc_final: 0.8663 (mm) REVERT: F 155 TYR cc_start: 0.7811 (m-80) cc_final: 0.7604 (m-80) REVERT: F 265 ASP cc_start: 0.7319 (m-30) cc_final: 0.6879 (t0) outliers start: 21 outliers final: 16 residues processed: 238 average time/residue: 0.1036 time to fit residues: 38.0292 Evaluate side-chains 228 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 272 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.130960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090229 restraints weight = 36887.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092900 restraints weight = 19947.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094626 restraints weight = 13965.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095650 restraints weight = 11380.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096252 restraints weight = 10153.018| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14191 Z= 0.139 Angle : 0.639 9.425 19874 Z= 0.355 Chirality : 0.044 0.253 2233 Planarity : 0.004 0.047 2009 Dihedral : 25.430 177.520 3174 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.22 % Allowed : 21.46 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1311 helix: 0.88 (0.21), residues: 626 sheet: -0.42 (0.38), residues: 186 loop : -0.97 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.018 0.001 TYR F 171 PHE 0.017 0.001 PHE F 176 TRP 0.008 0.001 TRP E 296 HIS 0.011 0.001 HIS F 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (14191) covalent geometry : angle 0.63895 / 0.36 (19874) hydrogen bonds : bond 0.04421 / 4.96 ( 670) hydrogen bonds : angle 4.17025 / 5.45 ( 1781) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7333 (tmm) cc_final: 0.7050 (tmm) REVERT: A 23 MET cc_start: 0.8742 (mmt) cc_final: 0.8022 (mmt) REVERT: A 35 PHE cc_start: 0.8550 (m-10) cc_final: 0.8207 (m-10) REVERT: A 42 TYR cc_start: 0.8217 (m-10) cc_final: 0.8004 (m-10) REVERT: A 46 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8251 (ttm-80) REVERT: B 91 TYR cc_start: 0.7930 (t80) cc_final: 0.7092 (t80) REVERT: B 94 SER cc_start: 0.8626 (p) cc_final: 0.8172 (p) REVERT: B 125 MET cc_start: 0.9085 (mtt) cc_final: 0.8614 (tmm) REVERT: C 54 MET cc_start: 0.9363 (mmt) cc_final: 0.9029 (mmt) REVERT: C 67 SER cc_start: 0.8726 (t) cc_final: 0.8157 (p) REVERT: C 128 MET cc_start: 0.8612 (mmm) cc_final: 0.8140 (mmm) REVERT: C 157 GLU cc_start: 0.9186 (pp20) cc_final: 0.8896 (pp20) REVERT: C 183 ASN cc_start: 0.9040 (m110) cc_final: 0.8767 (m-40) REVERT: C 184 GLN cc_start: 0.8915 (pm20) cc_final: 0.8680 (pm20) REVERT: D 18 ASP cc_start: 0.8395 (t0) cc_final: 0.8051 (t70) REVERT: E 107 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8481 (mmtm) REVERT: E 218 ASP cc_start: 0.8511 (p0) cc_final: 0.8291 (p0) REVERT: F 119 LEU cc_start: 0.8896 (mm) cc_final: 0.8664 (mm) REVERT: F 155 TYR cc_start: 0.7878 (m-80) cc_final: 0.7565 (m-80) REVERT: F 265 ASP cc_start: 0.7336 (m-30) cc_final: 0.6907 (t0) outliers start: 24 outliers final: 17 residues processed: 243 average time/residue: 0.1022 time to fit residues: 38.4250 Evaluate side-chains 228 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 272 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 82 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.129862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088787 restraints weight = 41242.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091494 restraints weight = 21821.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093210 restraints weight = 15096.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094263 restraints weight = 12227.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094869 restraints weight = 10853.229| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14191 Z= 0.159 Angle : 0.667 9.013 19874 Z= 0.366 Chirality : 0.044 0.247 2233 Planarity : 0.004 0.049 2009 Dihedral : 25.436 177.717 3174 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.22 % Allowed : 23.03 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1311 helix: 0.89 (0.20), residues: 628 sheet: -0.47 (0.38), residues: 186 loop : -1.00 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 124 TYR 0.021 0.002 TYR B 223 PHE 0.010 0.001 PHE F 239 TRP 0.007 0.001 TRP E 296 HIS 0.010 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (14191) covalent geometry : angle 0.66726 / 0.37 (19874) hydrogen bonds : bond 0.04418 / 4.95 ( 670) hydrogen bonds : angle 4.20116 / 5.51 ( 1781) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.398 Fit side-chains REVERT: A 1 MET cc_start: 0.7280 (tmm) cc_final: 0.6918 (tmm) REVERT: A 35 PHE cc_start: 0.8650 (m-10) cc_final: 0.8261 (m-10) REVERT: A 42 TYR cc_start: 0.8311 (m-10) cc_final: 0.8085 (m-10) REVERT: A 46 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8275 (ttm-80) REVERT: B 91 TYR cc_start: 0.7915 (t80) cc_final: 0.7058 (t80) REVERT: B 94 SER cc_start: 0.8649 (p) cc_final: 0.8155 (p) REVERT: B 125 MET cc_start: 0.9084 (mtt) cc_final: 0.8623 (tmm) REVERT: B 272 MET cc_start: 0.8560 (mpp) cc_final: 0.8298 (mpp) REVERT: C 54 MET cc_start: 0.9384 (mmt) cc_final: 0.9048 (mmt) REVERT: C 67 SER cc_start: 0.8763 (t) cc_final: 0.8189 (p) REVERT: C 128 MET cc_start: 0.8583 (mmm) cc_final: 0.8104 (mmm) REVERT: C 157 GLU cc_start: 0.9213 (pp20) cc_final: 0.8921 (pp20) REVERT: C 184 GLN cc_start: 0.8932 (pm20) cc_final: 0.8726 (pm20) REVERT: D 18 ASP cc_start: 0.8439 (t0) cc_final: 0.8177 (t70) REVERT: D 58 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7467 (ptt) REVERT: D 60 PHE cc_start: 0.8443 (p90) cc_final: 0.8033 (p90) REVERT: E 218 ASP cc_start: 0.8540 (p0) cc_final: 0.8306 (p0) REVERT: F 19 GLU cc_start: 0.8643 (mp0) cc_final: 0.8332 (mp0) REVERT: F 119 LEU cc_start: 0.8855 (mm) cc_final: 0.8610 (mm) REVERT: F 265 ASP cc_start: 0.7402 (m-30) cc_final: 0.6960 (t0) outliers start: 24 outliers final: 19 residues processed: 226 average time/residue: 0.1033 time to fit residues: 35.8802 Evaluate side-chains 225 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 272 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 HIS C 183 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.130499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089799 restraints weight = 37418.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092394 restraints weight = 20629.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094040 restraints weight = 14612.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095046 restraints weight = 11976.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095552 restraints weight = 10689.019| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14191 Z= 0.147 Angle : 0.671 14.066 19874 Z= 0.367 Chirality : 0.044 0.252 2233 Planarity : 0.004 0.049 2009 Dihedral : 25.414 177.616 3174 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.31 % Allowed : 23.40 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.23), residues: 1311 helix: 0.94 (0.21), residues: 629 sheet: -0.45 (0.39), residues: 186 loop : -0.97 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.020 0.001 TYR B 223 PHE 0.014 0.001 PHE A 35 TRP 0.010 0.001 TRP A 22 HIS 0.009 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14191) covalent geometry : angle 0.67087 / 0.37 (19874) hydrogen bonds : bond 0.04259 / 4.80 ( 670) hydrogen bonds : angle 4.15782 / 5.42 ( 1781) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.456 Fit side-chains REVERT: A 23 MET cc_start: 0.8649 (mmt) cc_final: 0.8217 (mmt) REVERT: A 35 PHE cc_start: 0.8653 (m-10) cc_final: 0.8422 (m-10) REVERT: A 42 TYR cc_start: 0.8272 (m-10) cc_final: 0.8037 (m-10) REVERT: A 46 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8232 (ttm-80) REVERT: B 91 TYR cc_start: 0.7920 (t80) cc_final: 0.6989 (t80) REVERT: B 94 SER cc_start: 0.8656 (p) cc_final: 0.8164 (p) REVERT: B 125 MET cc_start: 0.9091 (mtt) cc_final: 0.8602 (tmm) REVERT: B 163 ASN cc_start: 0.8960 (p0) cc_final: 0.8755 (p0) REVERT: B 272 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8284 (mpp) REVERT: C 54 MET cc_start: 0.9360 (mmt) cc_final: 0.9037 (mmt) REVERT: C 67 SER cc_start: 0.8747 (t) cc_final: 0.8161 (p) REVERT: C 157 GLU cc_start: 0.9221 (pp20) cc_final: 0.8924 (pp20) REVERT: C 184 GLN cc_start: 0.8973 (pm20) cc_final: 0.8715 (pm20) REVERT: D 18 ASP cc_start: 0.8433 (t0) cc_final: 0.8106 (t70) REVERT: D 58 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7378 (ptt) REVERT: D 60 PHE cc_start: 0.8479 (p90) cc_final: 0.8144 (p90) REVERT: E 49 ARG cc_start: 0.8830 (tpp80) cc_final: 0.8351 (tpp80) REVERT: E 107 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8592 (mmtm) REVERT: E 218 ASP cc_start: 0.8530 (p0) cc_final: 0.8297 (p0) REVERT: F 19 GLU cc_start: 0.8634 (mp0) cc_final: 0.8377 (mp0) REVERT: F 119 LEU cc_start: 0.8874 (mm) cc_final: 0.8624 (mm) REVERT: F 128 MET cc_start: 0.8112 (pmm) cc_final: 0.7908 (pmm) REVERT: F 265 ASP cc_start: 0.7406 (m-30) cc_final: 0.6959 (t0) outliers start: 25 outliers final: 20 residues processed: 239 average time/residue: 0.1057 time to fit residues: 38.4093 Evaluate side-chains 231 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 272 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 129 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 139 optimal weight: 30.0000 chunk 126 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.130936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088914 restraints weight = 52765.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092018 restraints weight = 25114.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094008 restraints weight = 16319.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095272 restraints weight = 12758.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095994 restraints weight = 11041.164| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14191 Z= 0.145 Angle : 0.687 12.809 19874 Z= 0.373 Chirality : 0.045 0.253 2233 Planarity : 0.004 0.046 2009 Dihedral : 25.395 177.501 3174 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.59 % Allowed : 23.68 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1311 helix: 0.84 (0.20), residues: 630 sheet: -0.44 (0.38), residues: 191 loop : -0.93 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.021 0.001 TYR B 223 PHE 0.054 0.002 PHE B 239 TRP 0.009 0.001 TRP A 22 HIS 0.009 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (14191) covalent geometry : angle 0.68746 / 0.37 (19874) hydrogen bonds : bond 0.04220 / 4.75 ( 670) hydrogen bonds : angle 4.14884 / 5.41 ( 1781) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8634 (mmt) cc_final: 0.8208 (mmt) REVERT: A 42 TYR cc_start: 0.8258 (m-10) cc_final: 0.8017 (m-10) REVERT: A 46 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8163 (ttm-80) REVERT: B 91 TYR cc_start: 0.7913 (t80) cc_final: 0.6989 (t80) REVERT: B 94 SER cc_start: 0.8642 (p) cc_final: 0.8120 (p) REVERT: B 125 MET cc_start: 0.9085 (mtt) cc_final: 0.8606 (tmm) REVERT: B 272 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8286 (mpp) REVERT: C 54 MET cc_start: 0.9349 (mmt) cc_final: 0.9041 (mmt) REVERT: C 67 SER cc_start: 0.8717 (t) cc_final: 0.8149 (p) REVERT: C 157 GLU cc_start: 0.9224 (pp20) cc_final: 0.8923 (pp20) REVERT: C 184 GLN cc_start: 0.8934 (pm20) cc_final: 0.8649 (pm20) REVERT: D 18 ASP cc_start: 0.8426 (t0) cc_final: 0.8088 (t70) REVERT: D 58 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7404 (ptt) REVERT: D 60 PHE cc_start: 0.8482 (p90) cc_final: 0.8228 (p90) REVERT: E 49 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8361 (tpp80) REVERT: E 107 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8596 (mmtm) REVERT: E 218 ASP cc_start: 0.8516 (p0) cc_final: 0.8283 (p0) REVERT: F 19 GLU cc_start: 0.8670 (mp0) cc_final: 0.8430 (mp0) REVERT: F 119 LEU cc_start: 0.8819 (mm) cc_final: 0.8565 (mm) REVERT: F 128 MET cc_start: 0.8050 (pmm) cc_final: 0.7770 (pmm) REVERT: F 155 TYR cc_start: 0.8012 (m-80) cc_final: 0.7706 (m-80) REVERT: F 265 ASP cc_start: 0.7385 (m-30) cc_final: 0.6939 (t0) outliers start: 28 outliers final: 20 residues processed: 236 average time/residue: 0.1097 time to fit residues: 39.0493 Evaluate side-chains 234 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.131364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089438 restraints weight = 53444.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092587 restraints weight = 25259.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094652 restraints weight = 16334.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095901 restraints weight = 12669.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.096659 restraints weight = 10963.092| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14191 Z= 0.145 Angle : 0.709 12.544 19874 Z= 0.380 Chirality : 0.045 0.253 2233 Planarity : 0.004 0.052 2009 Dihedral : 25.368 177.313 3174 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.59 % Allowed : 23.96 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1311 helix: 0.79 (0.20), residues: 629 sheet: -0.41 (0.39), residues: 186 loop : -0.95 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.026 0.002 TYR B 223 PHE 0.042 0.002 PHE A 35 TRP 0.012 0.001 TRP A 22 HIS 0.009 0.001 HIS F 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (14191) covalent geometry : angle 0.70865 / 0.38 (19874) hydrogen bonds : bond 0.04135 / 4.68 ( 670) hydrogen bonds : angle 4.16609 / 5.43 ( 1781) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8666 (mmt) cc_final: 0.8349 (mmt) REVERT: A 42 TYR cc_start: 0.8244 (m-10) cc_final: 0.7980 (m-10) REVERT: A 46 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8112 (ttm-80) REVERT: B 91 TYR cc_start: 0.7903 (t80) cc_final: 0.6961 (t80) REVERT: B 94 SER cc_start: 0.8653 (p) cc_final: 0.8136 (p) REVERT: B 125 MET cc_start: 0.9078 (mtt) cc_final: 0.8586 (tmm) REVERT: B 272 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8296 (mpp) REVERT: C 67 SER cc_start: 0.8746 (t) cc_final: 0.8191 (p) REVERT: C 128 MET cc_start: 0.8603 (mmm) cc_final: 0.8193 (mmm) REVERT: C 147 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8456 (mp0) REVERT: C 157 GLU cc_start: 0.9220 (pp20) cc_final: 0.8922 (pp20) REVERT: C 184 GLN cc_start: 0.8924 (pm20) cc_final: 0.8630 (pm20) REVERT: D 18 ASP cc_start: 0.8429 (t0) cc_final: 0.8087 (t70) REVERT: D 58 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7400 (ptt) REVERT: E 49 ARG cc_start: 0.8853 (tpp80) cc_final: 0.8372 (tpp80) REVERT: E 107 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8605 (mmtm) REVERT: E 218 ASP cc_start: 0.8505 (p0) cc_final: 0.8278 (p0) REVERT: F 119 LEU cc_start: 0.8805 (mm) cc_final: 0.8555 (mm) REVERT: F 128 MET cc_start: 0.8095 (pmm) cc_final: 0.7745 (pmm) REVERT: F 239 PHE cc_start: 0.8519 (t80) cc_final: 0.8310 (t80) REVERT: F 265 ASP cc_start: 0.7416 (m-30) cc_final: 0.6938 (t0) outliers start: 28 outliers final: 22 residues processed: 237 average time/residue: 0.1090 time to fit residues: 39.2006 Evaluate side-chains 236 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 0.0470 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.131042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.091082 restraints weight = 37175.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093790 restraints weight = 19677.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095547 restraints weight = 13628.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096589 restraints weight = 10971.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097213 restraints weight = 9729.315| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 14191 Z= 0.195 Angle : 0.902 59.200 19874 Z= 0.517 Chirality : 0.047 0.643 2233 Planarity : 0.004 0.052 2009 Dihedral : 25.366 177.311 3174 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.59 % Allowed : 24.05 % Favored : 73.36 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1311 helix: 0.78 (0.20), residues: 629 sheet: -0.41 (0.39), residues: 186 loop : -0.95 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 40 TYR 0.019 0.001 TYR B 223 PHE 0.031 0.002 PHE B 239 TRP 0.011 0.001 TRP A 22 HIS 0.010 0.001 HIS F 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (14191) covalent geometry : angle 0.90197 / 0.52 (19874) hydrogen bonds : bond 0.04134 / 4.68 ( 670) hydrogen bonds : angle 4.16516 / 5.43 ( 1781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.94 seconds wall clock time: 48 minutes 50.59 seconds (2930.59 seconds total)