Starting phenix.real_space_refine on Sun Aug 24 11:59:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxh_40852/08_2025/8sxh_40852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxh_40852/08_2025/8sxh_40852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sxh_40852/08_2025/8sxh_40852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxh_40852/08_2025/8sxh_40852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sxh_40852/08_2025/8sxh_40852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxh_40852/08_2025/8sxh_40852.map" } resolution = 3.94 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= 0.050 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12327 2.51 5 N 3468 2.21 5 O 3894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19719 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2706 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2988 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 844 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2706 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "F" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2988 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 844 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2706 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2988 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain: "K" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 844 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.06, per 1000 atoms: 0.26 Number of scatterers: 19719 At special positions: 0 Unit cell: (197.478, 192.51, 89.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3894 8.00 N 3468 7.00 C 12327 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: 1.76 Conformation dependent library (CDL) restraints added in 795.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 30 sheets defined 41.4% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.670A pdb=" N LEU A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.736A pdb=" N ASP A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 340 " --> pdb=" O ASN A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 417 through 434 removed outlier: 3.806A pdb=" N ARG A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.653A pdb=" N LEU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.794A pdb=" N GLU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 214 through 230 removed outlier: 5.309A pdb=" N VAL B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.697A pdb=" N ALA B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.591A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.944A pdb=" N SER B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 417' Processing helix chain 'B' and resid 417 through 435 Processing helix chain 'C' and resid 49 through 65 Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.559A pdb=" N ALA C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 135 through 148 Processing helix chain 'E' and resid 42 through 60 removed outlier: 3.646A pdb=" N ALA E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 80 Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 214 through 230 Processing helix chain 'E' and resid 248 through 260 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 336 through 340 removed outlier: 3.727A pdb=" N ASP E 339 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 340 " --> pdb=" O ASN E 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 336 through 340' Processing helix chain 'E' and resid 417 through 434 removed outlier: 3.833A pdb=" N ARG E 434 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 60 removed outlier: 3.807A pdb=" N LEU F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 82 Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.826A pdb=" N GLU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 152 through 161 Processing helix chain 'F' and resid 214 through 230 removed outlier: 5.228A pdb=" N VAL F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.718A pdb=" N ALA F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.732A pdb=" N ILE F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 417 removed outlier: 3.886A pdb=" N SER F 416 " --> pdb=" O ARG F 412 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP F 417 " --> pdb=" O PRO F 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 412 through 417' Processing helix chain 'F' and resid 417 through 435 Processing helix chain 'G' and resid 49 through 65 Processing helix chain 'G' and resid 67 through 83 removed outlier: 3.615A pdb=" N ALA G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 118 through 133 Processing helix chain 'G' and resid 135 through 148 Processing helix chain 'I' and resid 42 through 60 removed outlier: 3.544A pdb=" N LEU I 46 " --> pdb=" O PRO I 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 80 Processing helix chain 'I' and resid 91 through 101 Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 152 through 161 Processing helix chain 'I' and resid 214 through 230 Processing helix chain 'I' and resid 248 through 260 Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 302 through 314 removed outlier: 3.507A pdb=" N GLN I 314 " --> pdb=" O ALA I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 340 removed outlier: 3.744A pdb=" N ASP I 339 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG I 340 " --> pdb=" O ASN I 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 336 through 340' Processing helix chain 'I' and resid 417 through 434 removed outlier: 3.797A pdb=" N ARG I 434 " --> pdb=" O LEU I 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 60 removed outlier: 3.682A pdb=" N LEU J 46 " --> pdb=" O PRO J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 82 Processing helix chain 'J' and resid 89 through 98 Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 152 through 161 Processing helix chain 'J' and resid 214 through 230 removed outlier: 5.350A pdb=" N VAL J 220 " --> pdb=" O GLY J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 260 removed outlier: 3.665A pdb=" N ALA J 252 " --> pdb=" O VAL J 248 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 314 removed outlier: 3.628A pdb=" N ILE J 306 " --> pdb=" O ALA J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 417 removed outlier: 3.960A pdb=" N SER J 416 " --> pdb=" O ARG J 412 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP J 417 " --> pdb=" O PRO J 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 412 through 417' Processing helix chain 'J' and resid 417 through 435 Processing helix chain 'K' and resid 49 through 65 Processing helix chain 'K' and resid 67 through 83 removed outlier: 3.549A pdb=" N ALA K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 99 Processing helix chain 'K' and resid 101 through 115 Processing helix chain 'K' and resid 118 through 133 Processing helix chain 'K' and resid 135 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106 removed outlier: 3.684A pdb=" N PHE A 104 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 187 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 114 removed outlier: 7.991A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147 removed outlier: 5.361A pdb=" N ILE A 140 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 173 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.973A pdb=" N LEU A 292 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET A 320 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 294 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280 removed outlier: 3.572A pdb=" N LEU A 277 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS A 343 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU A 334 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR A 345 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 332 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 88 removed outlier: 5.645A pdb=" N LYS B 343 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU B 334 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR B 345 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 332 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.599A pdb=" N THR B 171 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE B 143 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 169 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 5.429A pdb=" N SER B 196 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ARG B 207 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL B 198 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 205 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 204 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP B 240 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 206 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 237 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU B 295 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU B 239 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 375 Processing sheet with id=AB3, first strand: chain 'E' and resid 104 through 106 removed outlier: 3.742A pdb=" N PHE E 104 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 187 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 114 removed outlier: 8.032A pdb=" N GLU E 110 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 121 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 147 removed outlier: 5.311A pdb=" N ILE E 140 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 173 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 194 through 196 removed outlier: 6.930A pdb=" N LEU E 292 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET E 320 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL E 294 " --> pdb=" O MET E 320 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 277 through 280 removed outlier: 3.509A pdb=" N LEU E 277 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 266 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR E 267 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS E 343 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU E 334 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR E 345 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR E 332 " --> pdb=" O THR E 345 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 86 through 88 removed outlier: 5.647A pdb=" N LYS F 343 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU F 334 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N THR F 345 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR F 332 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 109 through 111 Processing sheet with id=AC1, first strand: chain 'F' and resid 146 through 147 removed outlier: 6.597A pdb=" N THR F 171 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE F 143 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 169 " --> pdb=" O ILE F 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 194 through 200 removed outlier: 5.481A pdb=" N SER F 196 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG F 207 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL F 198 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR F 205 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA F 204 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP F 240 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU F 206 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU F 237 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU F 295 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU F 239 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 372 through 375 Processing sheet with id=AC4, first strand: chain 'I' and resid 104 through 106 removed outlier: 3.713A pdb=" N PHE I 104 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA I 187 " --> pdb=" O GLY I 106 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 109 through 114 removed outlier: 7.893A pdb=" N GLU I 110 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 146 through 147 removed outlier: 5.342A pdb=" N ILE I 140 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL I 173 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 194 through 196 Processing sheet with id=AC8, first strand: chain 'I' and resid 277 through 280 removed outlier: 3.502A pdb=" N LEU I 277 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 266 " --> pdb=" O PHE I 279 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR I 267 " --> pdb=" O TYR I 350 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR I 345 " --> pdb=" O THR I 332 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR I 332 " --> pdb=" O THR I 345 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 86 through 88 removed outlier: 5.588A pdb=" N LYS J 343 " --> pdb=" O LEU J 334 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU J 334 " --> pdb=" O LYS J 343 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR J 345 " --> pdb=" O THR J 332 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR J 332 " --> pdb=" O THR J 345 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 109 through 111 Processing sheet with id=AD2, first strand: chain 'J' and resid 146 through 147 removed outlier: 6.618A pdb=" N THR J 171 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE J 143 " --> pdb=" O THR J 169 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR J 169 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 194 through 200 removed outlier: 5.517A pdb=" N SER J 196 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG J 207 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL J 198 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR J 205 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA J 204 " --> pdb=" O VAL J 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP J 240 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU J 206 " --> pdb=" O ASP J 240 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU J 237 " --> pdb=" O VAL J 293 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU J 295 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU J 239 " --> pdb=" O LEU J 295 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6821 1.34 - 1.46: 3011 1.46 - 1.57: 10091 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 19983 Sorted by residual: bond pdb=" C GLU E 200 " pdb=" N PRO E 201 " ideal model delta sigma weight residual 1.330 1.340 -0.010 1.19e-02 7.06e+03 7.26e-01 bond pdb=" C VAL J 61 " pdb=" N GLU J 62 " ideal model delta sigma weight residual 1.339 1.293 0.046 5.57e-02 3.22e+02 6.97e-01 bond pdb=" N VAL I 333 " pdb=" CA VAL I 333 " ideal model delta sigma weight residual 1.474 1.463 0.011 1.57e-02 4.06e+03 5.11e-01 bond pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 1.474 1.463 0.011 1.57e-02 4.06e+03 5.04e-01 bond pdb=" CA THR A 345 " pdb=" C THR A 345 " ideal model delta sigma weight residual 1.526 1.519 0.008 1.15e-02 7.56e+03 4.63e-01 ... (remaining 19978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 25477 0.81 - 1.62: 1253 1.62 - 2.43: 142 2.43 - 3.24: 79 3.24 - 4.05: 85 Bond angle restraints: 27036 Sorted by residual: angle pdb=" N LEU E 292 " pdb=" CA LEU E 292 " pdb=" C LEU E 292 " ideal model delta sigma weight residual 108.26 110.87 -2.61 1.66e+00 3.63e-01 2.48e+00 angle pdb=" N VAL F 219 " pdb=" CA VAL F 219 " pdb=" C VAL F 219 " ideal model delta sigma weight residual 110.36 108.80 1.56 1.05e+00 9.07e-01 2.22e+00 angle pdb=" N VAL F 293 " pdb=" CA VAL F 293 " pdb=" C VAL F 293 " ideal model delta sigma weight residual 109.34 106.26 3.08 2.08e+00 2.31e-01 2.20e+00 angle pdb=" N ALA J 301 " pdb=" CA ALA J 301 " pdb=" C ALA J 301 " ideal model delta sigma weight residual 111.96 114.03 -2.07 1.41e+00 5.03e-01 2.16e+00 angle pdb=" C MET I 77 " pdb=" N LEU I 78 " pdb=" CA LEU I 78 " ideal model delta sigma weight residual 121.81 119.20 2.61 1.83e+00 2.99e-01 2.03e+00 ... (remaining 27031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 11146 17.37 - 34.74: 890 34.74 - 52.10: 203 52.10 - 69.47: 28 69.47 - 86.84: 24 Dihedral angle restraints: 12291 sinusoidal: 4863 harmonic: 7428 Sorted by residual: dihedral pdb=" CA ASP J 323 " pdb=" CB ASP J 323 " pdb=" CG ASP J 323 " pdb=" OD1 ASP J 323 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP F 323 " pdb=" CB ASP F 323 " pdb=" CG ASP F 323 " pdb=" OD1 ASP F 323 " ideal model delta sinusoidal sigma weight residual -30.00 -88.95 58.95 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 323 " pdb=" CB ASP B 323 " pdb=" CG ASP B 323 " pdb=" OD1 ASP B 323 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 12288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1917 0.027 - 0.053: 789 0.053 - 0.080: 167 0.080 - 0.106: 153 0.106 - 0.133: 94 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA VAL F 173 " pdb=" N VAL F 173 " pdb=" C VAL F 173 " pdb=" CB VAL F 173 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE J 366 " pdb=" N ILE J 366 " pdb=" C ILE J 366 " pdb=" CB ILE J 366 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL J 173 " pdb=" N VAL J 173 " pdb=" C VAL J 173 " pdb=" CB VAL J 173 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 3117 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 285 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO E 286 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 286 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 286 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 285 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO I 286 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 286 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 286 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 285 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 286 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.017 5.00e-02 4.00e+02 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 252 2.58 - 3.16: 18038 3.16 - 3.74: 30550 3.74 - 4.32: 39952 4.32 - 4.90: 66953 Nonbonded interactions: 155745 Sorted by model distance: nonbonded pdb=" OD2 ASP A 285 " pdb=" OG SER A 287 " model vdw 1.996 3.040 nonbonded pdb=" OG1 THR B 332 " pdb=" OG1 THR B 346 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR J 332 " pdb=" OG1 THR J 346 " model vdw 2.055 3.040 nonbonded pdb=" OG1 THR F 332 " pdb=" OG1 THR F 346 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR A 332 " pdb=" OG1 THR A 346 " model vdw 2.111 3.040 ... (remaining 155740 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 38 through 375 or resid 414 through 436)) selection = chain 'E' selection = (chain 'F' and (resid 38 through 375 or resid 414 through 436)) selection = chain 'I' selection = (chain 'J' and (resid 38 through 375 or resid 414 through 436)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.620 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.003 0.046 19983 Z= 0.117 Angle : 0.457 4.047 27036 Z= 0.235 Chirality : 0.039 0.133 3120 Planarity : 0.003 0.033 3597 Dihedral : 13.702 86.839 7539 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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 aren not related in a simple way. whole: 1.11 (0.17), residues: 2580 helix: 2.19 (0.17), residues: 978 sheet: -0.18 (0.25), residues: 438 loop : -0.09 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 55 TYR 0.010 0.001 TYR A 87 PHE 0.006 0.001 PHE B 211 TRP 0.002 0.001 TRP C 111 HIS 0.001 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00257 (19983) covalent geometry : angle 0.45747 (27036) hydrogen bonds : bond 0.16381 ( 903) hydrogen bonds : angle 5.52998 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8984 (tt) cc_final: 0.8584 (tt) REVERT: B 175 ASP cc_start: 0.6566 (t0) cc_final: 0.6299 (t0) REVERT: C 139 MET cc_start: 0.7643 (mtm) cc_final: 0.7361 (mtp) REVERT: F 175 ASP cc_start: 0.6899 (t0) cc_final: 0.6522 (t0) REVERT: F 391 HIS cc_start: 0.8563 (p-80) cc_final: 0.8272 (p-80) REVERT: G 66 ASN cc_start: 0.8090 (t0) cc_final: 0.7744 (t0) REVERT: G 93 ARG cc_start: 0.8561 (mmt90) cc_final: 0.8153 (mmt90) REVERT: J 153 MET cc_start: 0.7590 (tmm) cc_final: 0.7190 (tmm) REVERT: K 137 GLU cc_start: 0.8161 (pm20) cc_final: 0.7954 (pm20) REVERT: K 145 VAL cc_start: 0.8003 (t) cc_final: 0.7784 (t) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1665 time to fit residues: 68.4422 Evaluate side-chains 183 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 360 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN E 225 GLN E 230 ASN E 360 GLN ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 394 ASN I 360 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.148579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119052 restraints weight = 35721.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117012 restraints weight = 42924.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118155 restraints weight = 44116.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118577 restraints weight = 28504.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119032 restraints weight = 26249.117| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 19983 Z= 0.287 Angle : 0.705 8.310 27036 Z= 0.358 Chirality : 0.045 0.154 3120 Planarity : 0.005 0.038 3597 Dihedral : 4.567 24.073 2823 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.53 % Allowed : 11.32 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2580 helix: 1.48 (0.16), residues: 1005 sheet: -0.34 (0.25), residues: 435 loop : -0.09 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 123 TYR 0.021 0.003 TYR B 267 PHE 0.025 0.002 PHE B 180 TRP 0.023 0.004 TRP G 111 HIS 0.003 0.001 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00692 (19983) covalent geometry : angle 0.70495 (27036) hydrogen bonds : bond 0.04989 ( 903) hydrogen bonds : angle 4.69210 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8555 (mm) REVERT: B 175 ASP cc_start: 0.6792 (t0) cc_final: 0.6546 (t0) REVERT: F 175 ASP cc_start: 0.7062 (t0) cc_final: 0.6763 (t0) REVERT: F 391 HIS cc_start: 0.8761 (p-80) cc_final: 0.8385 (p-80) REVERT: J 153 MET cc_start: 0.7853 (tmm) cc_final: 0.7481 (tmm) REVERT: K 93 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8309 (tpp80) outliers start: 32 outliers final: 23 residues processed: 221 average time/residue: 0.1512 time to fit residues: 49.8697 Evaluate side-chains 186 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 349 TYR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 329 SER Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 94 optimal weight: 0.0060 chunk 103 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 59 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN I 360 GLN I 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.147450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112404 restraints weight = 37670.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111105 restraints weight = 32118.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113010 restraints weight = 32218.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113377 restraints weight = 21405.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114448 restraints weight = 20305.734| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19983 Z= 0.112 Angle : 0.544 8.107 27036 Z= 0.279 Chirality : 0.041 0.156 3120 Planarity : 0.004 0.042 3597 Dihedral : 4.009 17.295 2823 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.86 % Allowed : 15.04 % Favored : 84.10 % 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 aren not related in a simple way. whole: 0.90 (0.17), residues: 2580 helix: 1.70 (0.16), residues: 1011 sheet: -0.04 (0.26), residues: 384 loop : -0.06 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.024 0.001 TYR K 54 PHE 0.020 0.001 PHE B 180 TRP 0.009 0.002 TRP G 111 HIS 0.007 0.001 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00250 (19983) covalent geometry : angle 0.54369 (27036) hydrogen bonds : bond 0.03754 ( 903) hydrogen bonds : angle 4.06767 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7998 (ptmt) REVERT: A 358 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 43 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8510 (tt) REVERT: B 160 MET cc_start: 0.8873 (tpp) cc_final: 0.8598 (tpp) REVERT: B 175 ASP cc_start: 0.7186 (t0) cc_final: 0.6890 (t0) REVERT: B 391 HIS cc_start: 0.8682 (p-80) cc_final: 0.8097 (p-80) REVERT: C 83 ARG cc_start: 0.7988 (ptt180) cc_final: 0.7253 (tmm-80) REVERT: C 93 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8364 (tpp80) REVERT: F 175 ASP cc_start: 0.7435 (t0) cc_final: 0.7099 (t0) REVERT: F 391 HIS cc_start: 0.8682 (p-80) cc_final: 0.8285 (p-80) REVERT: J 153 MET cc_start: 0.7508 (tmm) cc_final: 0.6990 (tmm) REVERT: J 375 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7631 (tm-30) REVERT: K 137 GLU cc_start: 0.8230 (pm20) cc_final: 0.7837 (pm20) outliers start: 18 outliers final: 8 residues processed: 215 average time/residue: 0.1627 time to fit residues: 52.0699 Evaluate side-chains 189 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 207 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 422 GLN F 297 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111548 restraints weight = 37642.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110697 restraints weight = 32082.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112506 restraints weight = 32136.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112690 restraints weight = 21121.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114154 restraints weight = 20075.753| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19983 Z= 0.128 Angle : 0.554 9.084 27036 Z= 0.280 Chirality : 0.042 0.238 3120 Planarity : 0.004 0.113 3597 Dihedral : 3.982 19.124 2823 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.67 % Allowed : 16.81 % Favored : 81.52 % 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 aren not related in a simple way. whole: 0.90 (0.16), residues: 2580 helix: 1.77 (0.16), residues: 1002 sheet: -0.12 (0.26), residues: 384 loop : -0.08 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.024 0.001 TYR K 141 PHE 0.028 0.001 PHE G 92 TRP 0.009 0.002 TRP G 111 HIS 0.004 0.001 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00297 (19983) covalent geometry : angle 0.55390 (27036) hydrogen bonds : bond 0.03632 ( 903) hydrogen bonds : angle 4.00346 ( 2583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.8920 (tpp) cc_final: 0.8572 (tpp) REVERT: B 175 ASP cc_start: 0.7211 (t0) cc_final: 0.6913 (t0) REVERT: B 422 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8348 (tp40) REVERT: C 93 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8156 (tpp80) REVERT: C 134 ARG cc_start: 0.8318 (mpp-170) cc_final: 0.7836 (mpp-170) REVERT: F 153 MET cc_start: 0.7832 (tmm) cc_final: 0.7259 (tmm) REVERT: F 175 ASP cc_start: 0.7431 (t0) cc_final: 0.7185 (t0) REVERT: F 391 HIS cc_start: 0.8693 (p-80) cc_final: 0.8270 (p-80) REVERT: J 153 MET cc_start: 0.7653 (tmm) cc_final: 0.7137 (tmm) REVERT: J 375 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7553 (tm-30) REVERT: K 137 GLU cc_start: 0.8010 (pm20) cc_final: 0.7725 (pm20) outliers start: 35 outliers final: 23 residues processed: 226 average time/residue: 0.1460 time to fit residues: 49.9578 Evaluate side-chains 202 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 173 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 68 optimal weight: 0.0000 chunk 246 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111858 restraints weight = 37380.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110962 restraints weight = 31878.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112860 restraints weight = 31594.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113029 restraints weight = 20878.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114552 restraints weight = 19939.713| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19983 Z= 0.118 Angle : 0.553 9.343 27036 Z= 0.279 Chirality : 0.042 0.236 3120 Planarity : 0.004 0.105 3597 Dihedral : 3.935 18.643 2823 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.53 % Allowed : 18.24 % Favored : 80.23 % 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 aren not related in a simple way. whole: 0.90 (0.16), residues: 2580 helix: 1.77 (0.16), residues: 999 sheet: -0.09 (0.26), residues: 384 loop : -0.10 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 134 TYR 0.030 0.001 TYR K 141 PHE 0.027 0.001 PHE G 92 TRP 0.008 0.002 TRP G 111 HIS 0.002 0.000 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00272 (19983) covalent geometry : angle 0.55317 (27036) hydrogen bonds : bond 0.03430 ( 903) hydrogen bonds : angle 3.96884 ( 2583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ASP cc_start: 0.7292 (t0) cc_final: 0.7003 (t0) REVERT: F 43 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8620 (tt) REVERT: F 153 MET cc_start: 0.7824 (tmm) cc_final: 0.7241 (tmm) REVERT: F 175 ASP cc_start: 0.7443 (t0) cc_final: 0.7199 (t0) REVERT: F 391 HIS cc_start: 0.8735 (p-80) cc_final: 0.8362 (p-80) REVERT: J 153 MET cc_start: 0.7513 (tmm) cc_final: 0.7028 (tmm) REVERT: J 375 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7589 (tm-30) outliers start: 32 outliers final: 23 residues processed: 217 average time/residue: 0.1372 time to fit residues: 45.0273 Evaluate side-chains 207 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 167 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 179 optimal weight: 0.4980 chunk 187 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN ** G 64 GLN ** 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 = 0.3966 r_free = 0.3966 target = 0.145560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109996 restraints weight = 37435.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109604 restraints weight = 31036.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110680 restraints weight = 30850.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111885 restraints weight = 21130.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112015 restraints weight = 19318.894| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19983 Z= 0.136 Angle : 0.568 9.975 27036 Z= 0.286 Chirality : 0.042 0.253 3120 Planarity : 0.004 0.039 3597 Dihedral : 3.957 18.969 2823 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.15 % Allowed : 18.53 % Favored : 79.32 % 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 aren not related in a simple way. whole: 0.85 (0.17), residues: 2580 helix: 1.71 (0.16), residues: 1005 sheet: -0.12 (0.26), residues: 384 loop : -0.11 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 401 TYR 0.023 0.001 TYR K 54 PHE 0.031 0.001 PHE G 92 TRP 0.005 0.002 TRP G 111 HIS 0.002 0.001 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00321 (19983) covalent geometry : angle 0.56819 (27036) hydrogen bonds : bond 0.03523 ( 903) hydrogen bonds : angle 3.98253 ( 2583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (mm) REVERT: B 160 MET cc_start: 0.8934 (tpp) cc_final: 0.8640 (tpp) REVERT: B 175 ASP cc_start: 0.7319 (t0) cc_final: 0.7047 (t0) REVERT: C 83 ARG cc_start: 0.7990 (ptt180) cc_final: 0.7784 (ptt180) REVERT: F 43 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8664 (tt) REVERT: F 153 MET cc_start: 0.7828 (tmm) cc_final: 0.7262 (tmm) REVERT: F 175 ASP cc_start: 0.7444 (t0) cc_final: 0.7239 (t0) REVERT: F 391 HIS cc_start: 0.8683 (p-80) cc_final: 0.8301 (p-80) REVERT: J 153 MET cc_start: 0.7523 (tmm) cc_final: 0.7027 (tmm) REVERT: J 375 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7583 (tm-30) outliers start: 45 outliers final: 31 residues processed: 222 average time/residue: 0.1439 time to fit residues: 48.5443 Evaluate side-chains 206 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 240 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 119 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.146198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111091 restraints weight = 37130.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110041 restraints weight = 31090.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111704 restraints weight = 32593.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112263 restraints weight = 21946.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113863 restraints weight = 20382.549| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19983 Z= 0.124 Angle : 0.567 10.516 27036 Z= 0.288 Chirality : 0.042 0.269 3120 Planarity : 0.004 0.038 3597 Dihedral : 3.906 18.552 2823 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.96 % Allowed : 19.29 % Favored : 78.75 % 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 aren not related in a simple way. whole: 0.84 (0.16), residues: 2580 helix: 1.71 (0.16), residues: 1005 sheet: -0.11 (0.26), residues: 384 loop : -0.14 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 123 TYR 0.022 0.001 TYR K 54 PHE 0.024 0.001 PHE G 92 TRP 0.007 0.002 TRP G 111 HIS 0.002 0.000 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00291 (19983) covalent geometry : angle 0.56687 (27036) hydrogen bonds : bond 0.03425 ( 903) hydrogen bonds : angle 3.97129 ( 2583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 160 MET cc_start: 0.8875 (tpp) cc_final: 0.8595 (tpp) REVERT: B 175 ASP cc_start: 0.7264 (t0) cc_final: 0.7003 (t0) REVERT: F 43 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8650 (tt) REVERT: F 153 MET cc_start: 0.7824 (tmm) cc_final: 0.7258 (tmm) REVERT: F 391 HIS cc_start: 0.8680 (p-80) cc_final: 0.8266 (p-80) REVERT: G 89 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7620 (mm-30) REVERT: I 92 ASP cc_start: 0.7743 (m-30) cc_final: 0.7331 (t0) REVERT: I 98 GLU cc_start: 0.6804 (tp30) cc_final: 0.6491 (tp30) REVERT: J 153 MET cc_start: 0.7427 (tmm) cc_final: 0.6973 (tmm) REVERT: J 375 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7547 (tm-30) outliers start: 41 outliers final: 32 residues processed: 225 average time/residue: 0.1476 time to fit residues: 49.8697 Evaluate side-chains 212 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain I residue 259 PHE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 112 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 160 optimal weight: 0.0670 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 145 optimal weight: 0.0670 chunk 169 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.146495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111375 restraints weight = 37252.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110880 restraints weight = 31713.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112492 restraints weight = 31667.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112692 restraints weight = 20782.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114352 restraints weight = 19697.542| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19983 Z= 0.133 Angle : 0.588 11.118 27036 Z= 0.298 Chirality : 0.042 0.279 3120 Planarity : 0.004 0.066 3597 Dihedral : 3.977 20.670 2823 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.01 % Allowed : 19.96 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.16), residues: 2580 helix: 1.67 (0.16), residues: 1005 sheet: -0.11 (0.26), residues: 384 loop : -0.16 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 401 TYR 0.023 0.001 TYR K 54 PHE 0.032 0.001 PHE G 92 TRP 0.034 0.004 TRP K 111 HIS 0.002 0.000 HIS J 391 Details of bonding type rmsd covalent geometry : bond 0.00314 (19983) covalent geometry : angle 0.58774 (27036) hydrogen bonds : bond 0.03491 ( 903) hydrogen bonds : angle 4.03005 ( 2583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.7988 (p90) cc_final: 0.7788 (p90) REVERT: B 69 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8283 (mm) REVERT: B 160 MET cc_start: 0.8933 (tpp) cc_final: 0.8623 (tpp) REVERT: B 175 ASP cc_start: 0.7280 (t0) cc_final: 0.7031 (t0) REVERT: B 184 LEU cc_start: 0.9023 (mm) cc_final: 0.8792 (mt) REVERT: F 43 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8656 (tt) REVERT: F 153 MET cc_start: 0.7850 (tmm) cc_final: 0.7275 (tmm) REVERT: G 92 PHE cc_start: 0.7639 (t80) cc_final: 0.7320 (t80) REVERT: I 92 ASP cc_start: 0.7699 (m-30) cc_final: 0.7248 (t0) REVERT: I 95 GLU cc_start: 0.8665 (pp20) cc_final: 0.8225 (pp20) REVERT: J 153 MET cc_start: 0.7416 (tmm) cc_final: 0.6956 (tmm) REVERT: J 375 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7550 (tm-30) REVERT: K 123 ARG cc_start: 0.7917 (mmp-170) cc_final: 0.7664 (mmm160) outliers start: 42 outliers final: 33 residues processed: 215 average time/residue: 0.1434 time to fit residues: 46.4131 Evaluate side-chains 209 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain I residue 259 PHE Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 206 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 186 optimal weight: 0.0470 chunk 246 optimal weight: 0.5980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.148463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112676 restraints weight = 37415.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111638 restraints weight = 30598.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113167 restraints weight = 29835.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113934 restraints weight = 21141.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114259 restraints weight = 19580.012| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19983 Z= 0.109 Angle : 0.577 11.731 27036 Z= 0.293 Chirality : 0.042 0.293 3120 Planarity : 0.004 0.042 3597 Dihedral : 3.836 17.384 2823 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.53 % Allowed : 20.77 % Favored : 77.70 % 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 aren not related in a simple way. whole: 0.83 (0.17), residues: 2580 helix: 1.71 (0.16), residues: 1011 sheet: -0.03 (0.26), residues: 384 loop : -0.19 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 134 TYR 0.023 0.001 TYR K 54 PHE 0.040 0.001 PHE G 92 TRP 0.026 0.003 TRP K 111 HIS 0.006 0.001 HIS F 391 Details of bonding type rmsd covalent geometry : bond 0.00251 (19983) covalent geometry : angle 0.57722 (27036) hydrogen bonds : bond 0.03258 ( 903) hydrogen bonds : angle 3.96091 ( 2583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.8837 (tpp) cc_final: 0.8516 (tpp) REVERT: B 184 LEU cc_start: 0.8996 (mm) cc_final: 0.8792 (mt) REVERT: B 391 HIS cc_start: 0.8593 (p-80) cc_final: 0.7881 (p-80) REVERT: G 96 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: I 95 GLU cc_start: 0.8681 (pp20) cc_final: 0.8480 (pp20) REVERT: I 98 GLU cc_start: 0.6843 (tp30) cc_final: 0.6556 (tp30) REVERT: J 153 MET cc_start: 0.7467 (tmm) cc_final: 0.6839 (tmm) outliers start: 32 outliers final: 26 residues processed: 211 average time/residue: 0.1508 time to fit residues: 47.6920 Evaluate side-chains 202 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain I residue 259 PHE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 11 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 206 optimal weight: 0.1980 chunk 25 optimal weight: 0.0570 chunk 147 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** G 64 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.148772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113379 restraints weight = 37163.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112435 restraints weight = 30688.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114448 restraints weight = 30019.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114583 restraints weight = 20080.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115565 restraints weight = 19324.875| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19983 Z= 0.112 Angle : 0.593 12.276 27036 Z= 0.300 Chirality : 0.043 0.282 3120 Planarity : 0.004 0.048 3597 Dihedral : 3.802 19.061 2823 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.53 % Allowed : 20.77 % Favored : 77.70 % 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 aren not related in a simple way. whole: 0.86 (0.17), residues: 2580 helix: 1.78 (0.17), residues: 1005 sheet: -0.01 (0.26), residues: 384 loop : -0.21 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 123 TYR 0.032 0.001 TYR A 267 PHE 0.062 0.001 PHE G 92 TRP 0.042 0.005 TRP K 111 HIS 0.005 0.001 HIS F 391 Details of bonding type rmsd covalent geometry : bond 0.00257 (19983) covalent geometry : angle 0.59282 (27036) hydrogen bonds : bond 0.03296 ( 903) hydrogen bonds : angle 3.96963 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.8822 (tpp) cc_final: 0.8490 (tpp) REVERT: B 184 LEU cc_start: 0.8970 (mm) cc_final: 0.8739 (mt) REVERT: B 391 HIS cc_start: 0.8472 (p-80) cc_final: 0.7752 (p-80) REVERT: F 43 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8597 (tt) REVERT: G 96 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8853 (mt-10) REVERT: I 98 GLU cc_start: 0.6869 (tp30) cc_final: 0.6573 (tp30) REVERT: I 226 LEU cc_start: 0.8066 (mm) cc_final: 0.7811 (tt) REVERT: J 153 MET cc_start: 0.7464 (tmm) cc_final: 0.6848 (tmm) outliers start: 32 outliers final: 23 residues processed: 216 average time/residue: 0.1518 time to fit residues: 49.5041 Evaluate side-chains 202 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 146 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** 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 = 0.3988 r_free = 0.3988 target = 0.147640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111830 restraints weight = 37168.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110616 restraints weight = 31142.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112584 restraints weight = 31699.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112918 restraints weight = 21351.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114071 restraints weight = 20263.549| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19983 Z= 0.127 Angle : 0.598 13.264 27036 Z= 0.304 Chirality : 0.043 0.286 3120 Planarity : 0.004 0.048 3597 Dihedral : 3.844 19.497 2823 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.34 % Allowed : 21.16 % Favored : 77.51 % 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 aren not related in a simple way. whole: 0.87 (0.17), residues: 2580 helix: 1.80 (0.17), residues: 1002 sheet: -0.01 (0.26), residues: 384 loop : -0.22 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 123 TYR 0.026 0.001 TYR K 54 PHE 0.060 0.001 PHE G 92 TRP 0.032 0.004 TRP K 111 HIS 0.005 0.001 HIS F 391 Details of bonding type rmsd covalent geometry : bond 0.00297 (19983) covalent geometry : angle 0.59833 (27036) hydrogen bonds : bond 0.03403 ( 903) hydrogen bonds : angle 4.01218 ( 2583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2664.04 seconds wall clock time: 47 minutes 5.82 seconds (2825.82 seconds total)