Starting phenix.real_space_refine on Sat Sep 12 11:11:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.map" model { file = "/net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cno_7539/09_2026/6cno_7539.cif" } resolution = 4.7 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 108 5.16 5 C 9884 2.51 5 N 2744 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15428 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 2.69, per 1000 atoms: 0.17 Number of scatterers: 15428 At special positions: 0 Unit cell: (116.39, 116.39, 106.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 108 16.00 O 2680 8.00 N 2744 7.00 C 9884 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: 1.01 Conformation dependent library (CDL) restraints added in 682.8 milliseconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 75.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.543A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.539A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 162 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.630A pdb=" N GLY A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 261 through 289 removed outlier: 3.507A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 removed outlier: 3.935A pdb=" N HIS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 367 removed outlier: 4.221A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 Processing helix chain 'B' and resid 9 through 49 removed outlier: 3.599A pdb=" N ARG B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.542A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.539A pdb=" N LEU B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 162 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 4.345A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 261 through 289 removed outlier: 3.506A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 367 removed outlier: 4.219A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 Processing helix chain 'C' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.542A pdb=" N LEU C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 147 through 155 removed outlier: 4.540A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 162 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 261 through 289 removed outlier: 3.506A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 4.219A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 Processing helix chain 'D' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.543A pdb=" N LEU D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 91 " --> pdb=" O PHE D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.540A pdb=" N LEU D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 162 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 261 through 289 removed outlier: 3.507A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 367 removed outlier: 4.220A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 386 Processing helix chain 'E' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 65 through 74 removed outlier: 3.531A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 92 Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 65 through 74 removed outlier: 3.530A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 65 through 74 removed outlier: 3.531A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 44 through 55 Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.530A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 92 Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.671A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 138 through 147 Processing sheet with id=A, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=B, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=D, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=E, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=F, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=G, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=H, first strand: chain 'H' and resid 99 through 101 1076 hydrogen bonds defined for protein. 3204 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: 2.11 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4963 1.34 - 1.46: 2695 1.46 - 1.57: 7850 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15696 Sorted by residual: bond pdb=" CG1 ILE C 244 " pdb=" CD1 ILE C 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE D 244 " pdb=" CD1 ILE D 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE B 244 " pdb=" CD1 ILE B 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CG1 ILE A 244 " pdb=" CD1 ILE A 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CA ALA D 220 " pdb=" CB ALA D 220 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.59e-02 3.96e+03 1.97e+00 ... (remaining 15691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 20070 1.94 - 3.89: 946 3.89 - 5.83: 152 5.83 - 7.77: 48 7.77 - 9.71: 16 Bond angle restraints: 21232 Sorted by residual: angle pdb=" C ASP F 64 " pdb=" N PHE F 65 " pdb=" CA PHE F 65 " ideal model delta sigma weight residual 120.58 127.19 -6.61 1.32e+00 5.74e-01 2.50e+01 angle pdb=" C ASP E 64 " pdb=" N PHE E 65 " pdb=" CA PHE E 65 " ideal model delta sigma weight residual 120.58 127.19 -6.61 1.32e+00 5.74e-01 2.50e+01 angle pdb=" C ASP G 64 " pdb=" N PHE G 65 " pdb=" CA PHE G 65 " ideal model delta sigma weight residual 120.58 127.16 -6.58 1.32e+00 5.74e-01 2.49e+01 angle pdb=" C ASP H 64 " pdb=" N PHE H 65 " pdb=" CA PHE H 65 " ideal model delta sigma weight residual 120.58 127.13 -6.55 1.32e+00 5.74e-01 2.46e+01 angle pdb=" C THR E 5 " pdb=" N GLU E 6 " pdb=" CA GLU E 6 " ideal model delta sigma weight residual 120.28 124.98 -4.70 1.34e+00 5.57e-01 1.23e+01 ... (remaining 21227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.69: 8093 9.69 - 19.37: 991 19.37 - 29.06: 124 29.06 - 38.74: 96 38.74 - 48.43: 16 Dihedral angle restraints: 9320 sinusoidal: 3512 harmonic: 5808 Sorted by residual: dihedral pdb=" CA GLU F 114 " pdb=" C GLU F 114 " pdb=" N LYS F 115 " pdb=" CA LYS F 115 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N LYS E 115 " pdb=" CA LYS E 115 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU G 114 " pdb=" C GLU G 114 " pdb=" N LYS G 115 " pdb=" CA LYS G 115 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 9317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1592 0.044 - 0.088: 694 0.088 - 0.131: 159 0.131 - 0.175: 27 0.175 - 0.219: 8 Chirality restraints: 2480 Sorted by residual: chirality pdb=" CB ILE D 377 " pdb=" CA ILE D 377 " pdb=" CG1 ILE D 377 " pdb=" CG2 ILE D 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 377 " pdb=" CA ILE B 377 " pdb=" CG1 ILE B 377 " pdb=" CG2 ILE B 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE C 377 " pdb=" CA ILE C 377 " pdb=" CG1 ILE C 377 " pdb=" CG2 ILE C 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2477 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 189 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.43e+00 pdb=" C ARG C 189 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG C 189 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 190 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 189 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C ARG A 189 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG A 189 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 190 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 369 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C VAL C 369 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL C 369 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP C 370 " 0.014 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 251 2.53 - 3.12: 11797 3.12 - 3.71: 24852 3.71 - 4.31: 32150 4.31 - 4.90: 51120 Nonbonded interactions: 120170 Sorted by model distance: nonbonded pdb=" OD1 ASP E 93 " pdb=" OD1 ASN E 97 " model vdw 1.936 3.040 nonbonded pdb=" OD1 ASP H 93 " pdb=" OD1 ASN H 97 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP G 93 " pdb=" OD1 ASN G 97 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP F 93 " pdb=" OD1 ASN F 97 " model vdw 1.937 3.040 nonbonded pdb=" OD2 ASP F 24 " pdb="CA CA F 201 " model vdw 1.939 2.510 ... (remaining 120165 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.006 0.066 15696 Z= 0.324 Angle : 1.029 9.714 21232 Z= 0.595 Chirality : 0.049 0.219 2480 Planarity : 0.006 0.054 2660 Dihedral : 9.243 48.428 5560 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.26 % Allowed : 0.53 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.15), residues: 2000 helix: -1.61 (0.10), residues: 1528 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 189 TYR 0.022 0.003 TYR D 307 PHE 0.017 0.003 PHE G 92 TRP 0.035 0.002 TRP B 221 HIS 0.011 0.003 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.32 (15696) covalent geometry : angle 1.02937 / 0.60 (21232) hydrogen bonds : bond 0.13878 / 9.22 ( 1076) hydrogen bonds : angle 6.37617 / 4.53 ( 3204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.104 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: A 18 LEU cc_start: 0.9531 (mt) cc_final: 0.9146 (pp) REVERT: A 22 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 82 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9067 (mmmm) REVERT: A 87 PHE cc_start: 0.9171 (t80) cc_final: 0.8950 (t80) REVERT: A 176 ASN cc_start: 0.9284 (t0) cc_final: 0.8677 (t0) REVERT: A 179 TYR cc_start: 0.9090 (m-80) cc_final: 0.8338 (m-10) REVERT: A 186 ASN cc_start: 0.9406 (t0) cc_final: 0.9183 (t0) REVERT: A 194 PHE cc_start: 0.8762 (t80) cc_final: 0.8096 (t80) REVERT: A 200 MET cc_start: 0.9434 (ttm) cc_final: 0.8812 (tpp) REVERT: A 201 ASN cc_start: 0.9348 (m-40) cc_final: 0.9076 (p0) REVERT: A 261 MET cc_start: 0.8292 (tmm) cc_final: 0.7964 (mmt) REVERT: A 273 MET cc_start: 0.9087 (mtm) cc_final: 0.8842 (ptt) REVERT: A 278 THR cc_start: 0.9167 (m) cc_final: 0.8927 (p) REVERT: A 288 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8381 (tmtt) REVERT: A 292 ASN cc_start: 0.9399 (t0) cc_final: 0.9183 (t0) REVERT: A 303 MET cc_start: 0.8792 (mmm) cc_final: 0.8500 (mmm) REVERT: A 309 LYS cc_start: 0.9557 (ttpt) cc_final: 0.9184 (ttmm) REVERT: A 312 LYS cc_start: 0.9498 (mttm) cc_final: 0.9137 (tmtt) REVERT: A 321 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8504 (tp30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.0755 time to fit residues: 12.9193 Evaluate side-chains 90 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.112 Evaluate side-chains 66 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9065 (tp) cc_final: 0.8852 (tp) REVERT: E 9 ILE cc_start: 0.9586 (mt) cc_final: 0.9346 (mt) REVERT: E 16 PHE cc_start: 0.9531 (t80) cc_final: 0.9146 (t80) REVERT: E 48 LEU cc_start: 0.9689 (mt) cc_final: 0.9402 (tt) REVERT: E 54 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8136 (mt-10) REVERT: E 68 PHE cc_start: 0.9296 (t80) cc_final: 0.9018 (t80) REVERT: E 74 ARG cc_start: 0.8871 (mtm110) cc_final: 0.8536 (mtm-85) REVERT: E 75 LYS cc_start: 0.9330 (mmtt) cc_final: 0.8783 (mmmt) REVERT: E 90 ARG cc_start: 0.9351 (ttm110) cc_final: 0.9100 (ttm110) REVERT: E 92 PHE cc_start: 0.8926 (m-10) cc_final: 0.8331 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0727 time to fit residues: 5.1391 Evaluate side-chains 54 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.094276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070115 restraints weight = 12065.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072107 restraints weight = 7125.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073413 restraints weight = 4969.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074149 restraints weight = 3899.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074672 restraints weight = 3373.532| |-----------------------------------------------------------------------------| r_work (final): 0.3339 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.040861 restraints weight = 6224.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.042559 restraints weight = 3729.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.043778 restraints weight = 2546.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.044702 restraints weight = 1890.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.045331 restraints weight = 1474.952| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.887 15696 Z= 1.153 Angle : 0.802 22.606 21232 Z= 0.411 Chirality : 0.038 0.124 2480 Planarity : 0.005 0.041 2660 Dihedral : 5.426 25.991 2168 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2000 helix: 0.38 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.22 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.013 0.001 TYR H 138 PHE 0.025 0.002 PHE G 89 TRP 0.048 0.004 TRP B 242 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03293 / 1.15 (15696) covalent geometry : angle 0.80151 / 0.41 (21232) hydrogen bonds : bond 0.04843 / 3.24 ( 1076) hydrogen bonds : angle 4.59925 / 3.31 ( 3204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9634 (mt) cc_final: 0.9167 (mm) REVERT: A 82 LYS cc_start: 0.9421 (mmtt) cc_final: 0.9101 (mmmt) REVERT: A 91 ASN cc_start: 0.8960 (m-40) cc_final: 0.8322 (m110) REVERT: A 111 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 115 CYS cc_start: 0.9317 (t) cc_final: 0.8692 (p) REVERT: A 186 ASN cc_start: 0.9470 (t0) cc_final: 0.9259 (t0) REVERT: A 194 PHE cc_start: 0.9029 (t80) cc_final: 0.8779 (t80) REVERT: A 198 LEU cc_start: 0.9293 (mt) cc_final: 0.8911 (mt) REVERT: A 200 MET cc_start: 0.9509 (ttm) cc_final: 0.9080 (tpp) REVERT: A 201 ASN cc_start: 0.9501 (m-40) cc_final: 0.9192 (p0) REVERT: A 207 LEU cc_start: 0.8970 (mt) cc_final: 0.8482 (pp) REVERT: A 261 MET cc_start: 0.8566 (tmm) cc_final: 0.8172 (mmt) REVERT: A 264 LYS cc_start: 0.7948 (mttt) cc_final: 0.7662 (tttp) REVERT: A 270 THR cc_start: 0.8786 (p) cc_final: 0.8463 (p) REVERT: A 273 MET cc_start: 0.9237 (mtm) cc_final: 0.8804 (ptp) REVERT: A 288 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8678 (tmtt) REVERT: A 292 ASN cc_start: 0.9652 (t0) cc_final: 0.9225 (t0) REVERT: A 303 MET cc_start: 0.9296 (mmm) cc_final: 0.8848 (mmm) REVERT: A 309 LYS cc_start: 0.9680 (ttpt) cc_final: 0.9350 (ttmm) REVERT: A 310 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9068 (mt-10) REVERT: A 321 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8366 (tp30) REVERT: A 324 MET cc_start: 0.9580 (tpt) cc_final: 0.9206 (tpp) REVERT: A 343 LYS cc_start: 0.9606 (mttt) cc_final: 0.9133 (mptt) REVERT: A 359 ARG cc_start: 0.8542 (ttt180) cc_final: 0.7928 (ttp80) REVERT: A 364 GLN cc_start: 0.9506 (tp-100) cc_final: 0.9297 (tp-100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0733 time to fit residues: 10.4552 Evaluate side-chains 91 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.102 Evaluate side-chains 65 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.9625 (tppt) cc_final: 0.9275 (mmmm) REVERT: H 16 PHE cc_start: 0.9641 (t80) cc_final: 0.9026 (t80) REVERT: H 36 MET cc_start: 0.9361 (tpt) cc_final: 0.8987 (mmm) REVERT: H 37 ARG cc_start: 0.9410 (ptp-110) cc_final: 0.9206 (ptp-110) REVERT: H 48 LEU cc_start: 0.9792 (mt) cc_final: 0.9488 (tt) REVERT: H 51 MET cc_start: 0.8991 (tpp) cc_final: 0.8565 (tpp) REVERT: H 52 ILE cc_start: 0.9828 (mt) cc_final: 0.9626 (mt) REVERT: H 54 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8276 (mt-10) REVERT: H 74 ARG cc_start: 0.9237 (mtm110) cc_final: 0.8864 (mtm-85) REVERT: H 75 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8459 (mttt) REVERT: H 84 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8349 (mm-30) REVERT: H 92 PHE cc_start: 0.8778 (m-10) cc_final: 0.8465 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0767 time to fit residues: 5.3076 Evaluate side-chains 55 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 149 optimal weight: 0.0030 chunk 27 optimal weight: 0.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070489 restraints weight = 11851.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072535 restraints weight = 7009.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073803 restraints weight = 4913.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.074639 restraints weight = 3901.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075159 restraints weight = 3334.101| |-----------------------------------------------------------------------------| r_work (final): 0.3352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.039867 restraints weight = 5994.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.041619 restraints weight = 3642.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.042906 restraints weight = 2460.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.043804 restraints weight = 1800.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.044492 restraints weight = 1384.504| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.918 15696 Z= 1.164 Angle : 0.794 19.220 21232 Z= 0.415 Chirality : 0.039 0.221 2480 Planarity : 0.005 0.046 2660 Dihedral : 5.351 24.998 2168 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.79 % Allowed : 3.17 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 2000 helix: 0.94 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.21 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 15 TYR 0.022 0.002 TYR A 253 PHE 0.009 0.001 PHE H 89 TRP 0.079 0.005 TRP B 242 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03333 / 1.16 (15696) covalent geometry : angle 0.79364 / 0.42 (21232) hydrogen bonds : bond 0.04414 / 2.91 ( 1076) hydrogen bonds : angle 4.50323 / 3.25 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LEU cc_start: 0.9610 (mt) cc_final: 0.9090 (mm) REVERT: B 82 LYS cc_start: 0.9541 (mmtt) cc_final: 0.9139 (mmmt) REVERT: B 91 ASN cc_start: 0.8904 (m-40) cc_final: 0.8356 (m-40) REVERT: B 111 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 115 CYS cc_start: 0.9487 (t) cc_final: 0.8899 (p) REVERT: B 117 LEU cc_start: 0.9187 (mt) cc_final: 0.8970 (mt) REVERT: B 186 ASN cc_start: 0.9343 (t0) cc_final: 0.9127 (t0) REVERT: B 194 PHE cc_start: 0.9043 (t80) cc_final: 0.8816 (t80) REVERT: B 198 LEU cc_start: 0.9285 (mt) cc_final: 0.8800 (mt) REVERT: B 200 MET cc_start: 0.9528 (ttm) cc_final: 0.9304 (tmm) REVERT: B 201 ASN cc_start: 0.9473 (m-40) cc_final: 0.9095 (p0) REVERT: B 207 LEU cc_start: 0.8875 (mt) cc_final: 0.8450 (pp) REVERT: B 261 MET cc_start: 0.8547 (tmm) cc_final: 0.8153 (mmt) REVERT: B 270 THR cc_start: 0.9018 (p) cc_final: 0.8612 (p) REVERT: B 273 MET cc_start: 0.9298 (mtm) cc_final: 0.8939 (ptp) REVERT: B 295 GLU cc_start: 0.9425 (mp0) cc_final: 0.9204 (mp0) REVERT: B 303 MET cc_start: 0.9316 (mmm) cc_final: 0.8790 (mmm) REVERT: B 309 LYS cc_start: 0.9650 (ttpt) cc_final: 0.9353 (ttmm) REVERT: B 310 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9077 (mt-10) REVERT: B 313 GLU cc_start: 0.8994 (pp20) cc_final: 0.8604 (pp20) REVERT: B 320 GLN cc_start: 0.8656 (pp30) cc_final: 0.8221 (pp30) REVERT: B 359 ARG cc_start: 0.8621 (ttt180) cc_final: 0.8018 (ttp80) REVERT: B 364 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9279 (tp-100) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.0623 time to fit residues: 8.2623 Evaluate side-chains 91 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.103 Evaluate side-chains 65 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8998 (tp) cc_final: 0.8218 (tp) REVERT: H 8 GLN cc_start: 0.9421 (mp10) cc_final: 0.9183 (mp10) REVERT: H 12 PHE cc_start: 0.9677 (m-80) cc_final: 0.9231 (m-80) REVERT: H 13 LYS cc_start: 0.9627 (tppt) cc_final: 0.9337 (mmmm) REVERT: H 14 GLU cc_start: 0.9638 (OUTLIER) cc_final: 0.9312 (pm20) REVERT: H 16 PHE cc_start: 0.9680 (t80) cc_final: 0.9001 (t80) REVERT: H 36 MET cc_start: 0.9419 (tpt) cc_final: 0.8906 (tpt) REVERT: H 37 ARG cc_start: 0.9355 (ptp-110) cc_final: 0.9150 (ptp-110) REVERT: H 48 LEU cc_start: 0.9762 (mt) cc_final: 0.9474 (tt) REVERT: H 51 MET cc_start: 0.9024 (tpp) cc_final: 0.8542 (tpp) REVERT: H 52 ILE cc_start: 0.9806 (mt) cc_final: 0.9593 (mt) REVERT: H 54 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8223 (mt-10) REVERT: H 75 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8242 (mttt) REVERT: H 82 GLU cc_start: 0.8937 (pp20) cc_final: 0.8659 (pp20) REVERT: H 86 ARG cc_start: 0.9430 (ttm170) cc_final: 0.9120 (ttm170) REVERT: H 92 PHE cc_start: 0.8677 (m-10) cc_final: 0.8147 (m-80) REVERT: H 143 GLN cc_start: 0.9679 (mt0) cc_final: 0.9377 (pt0) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0716 time to fit residues: 4.9038 Evaluate side-chains 53 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 144 optimal weight: 0.0670 chunk 156 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 82 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 300 ASN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.096736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071931 restraints weight = 12227.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074042 restraints weight = 7098.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.075342 restraints weight = 4941.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.076210 restraints weight = 3924.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076542 restraints weight = 3351.872| |-----------------------------------------------------------------------------| r_work (final): 0.3384 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.049584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.039780 restraints weight = 5934.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.041429 restraints weight = 3705.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.042634 restraints weight = 2576.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043602 restraints weight = 1907.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.044212 restraints weight = 1478.319| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.921 15696 Z= 1.159 Angle : 0.769 19.232 21232 Z= 0.392 Chirality : 0.038 0.129 2480 Planarity : 0.004 0.039 2660 Dihedral : 5.128 21.368 2168 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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 are not related in a simple way. whole: 1.01 (0.19), residues: 2000 helix: 1.24 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -1.08 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 159 TYR 0.039 0.003 TYR B 253 PHE 0.021 0.001 PHE C 351 TRP 0.045 0.003 TRP B 242 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03323 / 1.16 (15696) covalent geometry : angle 0.76891 / 0.39 (21232) hydrogen bonds : bond 0.04003 / 2.65 ( 1076) hydrogen bonds : angle 4.22731 / 3.05 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9645 (mt) cc_final: 0.9122 (mm) REVERT: A 82 LYS cc_start: 0.9485 (mmtt) cc_final: 0.9068 (mmmt) REVERT: A 91 ASN cc_start: 0.8775 (m-40) cc_final: 0.8360 (m110) REVERT: A 117 LEU cc_start: 0.9076 (mt) cc_final: 0.8492 (mt) REVERT: A 176 ASN cc_start: 0.9372 (t0) cc_final: 0.7995 (t0) REVERT: A 179 TYR cc_start: 0.8266 (m-80) cc_final: 0.7764 (m-80) REVERT: A 198 LEU cc_start: 0.9307 (mt) cc_final: 0.8924 (mt) REVERT: A 201 ASN cc_start: 0.9476 (m-40) cc_final: 0.8990 (p0) REVERT: A 261 MET cc_start: 0.8500 (tmm) cc_final: 0.8122 (mmt) REVERT: A 270 THR cc_start: 0.8931 (p) cc_final: 0.8496 (p) REVERT: A 273 MET cc_start: 0.9325 (mtm) cc_final: 0.8924 (ptp) REVERT: A 292 ASN cc_start: 0.9492 (t0) cc_final: 0.9241 (t0) REVERT: A 295 GLU cc_start: 0.9404 (mp0) cc_final: 0.9166 (mp0) REVERT: A 303 MET cc_start: 0.9321 (mmm) cc_final: 0.8824 (mmm) REVERT: A 309 LYS cc_start: 0.9639 (ttpt) cc_final: 0.9319 (ttmm) REVERT: A 310 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9001 (mt-10) REVERT: A 313 GLU cc_start: 0.8989 (pp20) cc_final: 0.8638 (pp20) REVERT: A 321 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8451 (tp30) REVERT: A 359 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8462 (ttp80) REVERT: A 360 LYS cc_start: 0.9621 (pptt) cc_final: 0.9404 (tmmt) REVERT: A 364 GLN cc_start: 0.9477 (tp-100) cc_final: 0.9246 (tp-100) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0555 time to fit residues: 7.2822 Evaluate side-chains 91 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.104 Evaluate side-chains 62 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9025 (tp) cc_final: 0.8206 (tp) REVERT: E 8 GLN cc_start: 0.9513 (mp10) cc_final: 0.9261 (mp10) REVERT: E 12 PHE cc_start: 0.9681 (m-80) cc_final: 0.9243 (m-80) REVERT: E 16 PHE cc_start: 0.9656 (t80) cc_final: 0.9028 (t80) REVERT: E 36 MET cc_start: 0.9484 (tpt) cc_final: 0.9234 (tpt) REVERT: E 37 ARG cc_start: 0.9405 (ptp-110) cc_final: 0.9155 (ptp-110) REVERT: E 48 LEU cc_start: 0.9772 (mt) cc_final: 0.9494 (tt) REVERT: E 51 MET cc_start: 0.9145 (tpp) cc_final: 0.8728 (tpp) REVERT: E 54 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8377 (mt-10) REVERT: E 75 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8200 (mttt) REVERT: E 83 GLU cc_start: 0.9005 (pp20) cc_final: 0.8650 (pp20) REVERT: E 92 PHE cc_start: 0.8710 (m-10) cc_final: 0.8251 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0626 time to fit residues: 4.1913 Evaluate side-chains 52 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 177 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 182 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 34 optimal weight: 0.0470 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 300 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.097543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072715 restraints weight = 11933.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074833 restraints weight = 6993.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.076072 restraints weight = 4878.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076913 restraints weight = 3869.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.077336 restraints weight = 3312.010| |-----------------------------------------------------------------------------| r_work (final): 0.3394 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.041002 restraints weight = 5940.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.042505 restraints weight = 3713.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.043658 restraints weight = 2588.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.044514 restraints weight = 1933.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.045164 restraints weight = 1511.155| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.915 15696 Z= 1.158 Angle : 0.766 19.302 21232 Z= 0.400 Chirality : 0.041 0.411 2480 Planarity : 0.004 0.038 2660 Dihedral : 4.919 20.088 2168 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.53 % Allowed : 2.90 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 2000 helix: 1.34 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.92 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 74 TYR 0.032 0.002 TYR E 138 PHE 0.016 0.001 PHE F 141 TRP 0.038 0.003 TRP C 242 HIS 0.008 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.03318 / 1.16 (15696) covalent geometry : angle 0.76594 / 0.40 (21232) hydrogen bonds : bond 0.03899 / 2.56 ( 1076) hydrogen bonds : angle 4.15535 / 3.02 ( 3204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LEU cc_start: 0.9635 (mt) cc_final: 0.9344 (mt) REVERT: B 82 LYS cc_start: 0.9491 (mmtt) cc_final: 0.9072 (mmmt) REVERT: B 91 ASN cc_start: 0.8768 (m-40) cc_final: 0.8135 (m-40) REVERT: B 111 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: B 161 TYR cc_start: 0.8564 (p90) cc_final: 0.7751 (p90) REVERT: B 175 LEU cc_start: 0.9592 (mt) cc_final: 0.9355 (pp) REVERT: B 176 ASN cc_start: 0.9383 (t0) cc_final: 0.8386 (t0) REVERT: B 179 TYR cc_start: 0.8131 (m-80) cc_final: 0.7846 (m-80) REVERT: B 198 LEU cc_start: 0.9329 (mt) cc_final: 0.8923 (mt) REVERT: B 261 MET cc_start: 0.8569 (tmm) cc_final: 0.8100 (mmt) REVERT: B 270 THR cc_start: 0.8910 (p) cc_final: 0.8658 (p) REVERT: B 273 MET cc_start: 0.9381 (mtm) cc_final: 0.9013 (ptp) REVERT: B 292 ASN cc_start: 0.9493 (t0) cc_final: 0.9273 (t0) REVERT: B 295 GLU cc_start: 0.9364 (mp0) cc_final: 0.9076 (mp0) REVERT: B 303 MET cc_start: 0.9271 (mmm) cc_final: 0.8851 (mmm) REVERT: B 309 LYS cc_start: 0.9619 (ttpt) cc_final: 0.9287 (ttmm) REVERT: B 310 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8902 (mt-10) REVERT: B 313 GLU cc_start: 0.8968 (pp20) cc_final: 0.8616 (pp20) REVERT: B 314 SER cc_start: 0.9638 (t) cc_final: 0.9185 (p) REVERT: B 321 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8417 (tp30) REVERT: B 344 LEU cc_start: 0.9668 (tt) cc_final: 0.9425 (tt) REVERT: B 349 ASN cc_start: 0.9472 (m110) cc_final: 0.8968 (m110) REVERT: B 364 GLN cc_start: 0.9486 (tp-100) cc_final: 0.9271 (tp-100) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0553 time to fit residues: 7.5299 Evaluate side-chains 93 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.114 Evaluate side-chains 64 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9006 (tp) cc_final: 0.8160 (tp) REVERT: H 12 PHE cc_start: 0.9625 (m-80) cc_final: 0.9192 (m-10) REVERT: H 13 LYS cc_start: 0.9592 (mmmm) cc_final: 0.8937 (mmmm) REVERT: H 16 PHE cc_start: 0.9586 (t80) cc_final: 0.8977 (t80) REVERT: H 36 MET cc_start: 0.9362 (tpp) cc_final: 0.9148 (tpt) REVERT: H 37 ARG cc_start: 0.9349 (ptp-110) cc_final: 0.9125 (ptp-110) REVERT: H 48 LEU cc_start: 0.9757 (mt) cc_final: 0.9476 (tt) REVERT: H 51 MET cc_start: 0.9153 (tpp) cc_final: 0.8728 (tpp) REVERT: H 54 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8475 (mt-10) REVERT: H 75 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8139 (mttt) REVERT: H 92 PHE cc_start: 0.8646 (m-10) cc_final: 0.8228 (m-80) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0691 time to fit residues: 4.6747 Evaluate side-chains 49 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 19 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 195 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 300 ASN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072366 restraints weight = 11754.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074280 restraints weight = 7066.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075541 restraints weight = 4987.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.076326 restraints weight = 3948.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076758 restraints weight = 3383.765| |-----------------------------------------------------------------------------| r_work (final): 0.3385 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.050429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.041636 restraints weight = 6411.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043261 restraints weight = 3750.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.044416 restraints weight = 2498.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045303 restraints weight = 1801.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.045960 restraints weight = 1368.227| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.912 15696 Z= 1.157 Angle : 0.788 19.244 21232 Z= 0.408 Chirality : 0.038 0.136 2480 Planarity : 0.003 0.037 2660 Dihedral : 4.913 29.044 2168 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2000 helix: 1.47 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 74 TYR 0.026 0.002 TYR E 138 PHE 0.016 0.001 PHE F 141 TRP 0.032 0.002 TRP A 242 HIS 0.006 0.001 HIS D 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03315 / 1.16 (15696) covalent geometry : angle 0.78825 / 0.41 (21232) hydrogen bonds : bond 0.03645 / 2.38 ( 1076) hydrogen bonds : angle 4.21960 / 3.04 ( 3204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.9674 (mt) cc_final: 0.9395 (mt) REVERT: D 82 LYS cc_start: 0.9532 (mmtt) cc_final: 0.9093 (mmmt) REVERT: D 91 ASN cc_start: 0.8612 (m-40) cc_final: 0.8273 (m-40) REVERT: D 111 GLU cc_start: 0.8997 (mp0) cc_final: 0.8783 (pm20) REVERT: D 175 LEU cc_start: 0.9600 (mt) cc_final: 0.9382 (pp) REVERT: D 176 ASN cc_start: 0.9406 (t0) cc_final: 0.8593 (t0) REVERT: D 261 MET cc_start: 0.8552 (tmm) cc_final: 0.8100 (mmt) REVERT: D 270 THR cc_start: 0.8859 (p) cc_final: 0.8528 (p) REVERT: D 273 MET cc_start: 0.9400 (mtm) cc_final: 0.9092 (ptp) REVERT: D 303 MET cc_start: 0.9284 (mmm) cc_final: 0.8875 (mmm) REVERT: D 310 GLU cc_start: 0.9372 (mt-10) cc_final: 0.8963 (mt-10) REVERT: D 313 GLU cc_start: 0.9039 (pp20) cc_final: 0.8652 (pp20) REVERT: D 314 SER cc_start: 0.9699 (t) cc_final: 0.9457 (p) REVERT: D 321 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8396 (tp30) REVERT: D 344 LEU cc_start: 0.9659 (tt) cc_final: 0.9408 (tt) REVERT: D 377 ILE cc_start: 0.9378 (tp) cc_final: 0.9039 (pt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0474 time to fit residues: 6.3783 Evaluate side-chains 89 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.103 Evaluate side-chains 59 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9064 (tp) cc_final: 0.8292 (tp) REVERT: H 8 GLN cc_start: 0.9614 (mp10) cc_final: 0.9229 (mp10) REVERT: H 12 PHE cc_start: 0.9589 (m-80) cc_final: 0.9086 (m-80) REVERT: H 13 LYS cc_start: 0.9643 (mmmm) cc_final: 0.8941 (mmmm) REVERT: H 16 PHE cc_start: 0.9584 (t80) cc_final: 0.8949 (t80) REVERT: H 36 MET cc_start: 0.9375 (tpp) cc_final: 0.9055 (tpp) REVERT: H 37 ARG cc_start: 0.9344 (ptp-110) cc_final: 0.9126 (ptp-110) REVERT: H 48 LEU cc_start: 0.9751 (mt) cc_final: 0.9459 (tt) REVERT: H 84 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8525 (mm-30) REVERT: H 87 GLU cc_start: 0.9264 (tt0) cc_final: 0.8919 (pp20) REVERT: H 89 PHE cc_start: 0.9434 (t80) cc_final: 0.9048 (t80) REVERT: H 137 ASN cc_start: 0.8409 (m-40) cc_final: 0.7995 (m-40) REVERT: H 141 PHE cc_start: 0.9071 (t80) cc_final: 0.8849 (t80) REVERT: H 143 GLN cc_start: 0.9570 (pm20) cc_final: 0.9291 (pm20) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0632 time to fit residues: 4.0224 Evaluate side-chains 52 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 109 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 185 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 300 ASN ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.097546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.071899 restraints weight = 12226.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073907 restraints weight = 7434.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075205 restraints weight = 5276.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076002 restraints weight = 4188.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076505 restraints weight = 3622.818| |-----------------------------------------------------------------------------| r_work (final): 0.3383 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.039069 restraints weight = 6288.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.040785 restraints weight = 3983.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.042063 restraints weight = 2779.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.042982 restraints weight = 2083.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.043737 restraints weight = 1647.362| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.911 15696 Z= 1.156 Angle : 0.796 19.206 21232 Z= 0.406 Chirality : 0.039 0.195 2480 Planarity : 0.004 0.037 2660 Dihedral : 4.749 23.585 2168 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2000 helix: 1.48 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 74 TYR 0.027 0.002 TYR H 138 PHE 0.022 0.001 PHE F 92 TRP 0.028 0.002 TRP A 242 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03313 / 1.16 (15696) covalent geometry : angle 0.79637 / 0.41 (21232) hydrogen bonds : bond 0.03590 / 2.36 ( 1076) hydrogen bonds : angle 4.08333 / 2.92 ( 3204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9062 (mt-10) REVERT: D 40 MET cc_start: 0.7594 (tmm) cc_final: 0.7390 (tmm) REVERT: D 82 LYS cc_start: 0.9529 (mmtt) cc_final: 0.9076 (mmmt) REVERT: D 91 ASN cc_start: 0.8617 (m-40) cc_final: 0.8303 (m-40) REVERT: D 175 LEU cc_start: 0.9551 (mt) cc_final: 0.9335 (pp) REVERT: D 176 ASN cc_start: 0.9153 (t0) cc_final: 0.8674 (t0) REVERT: D 179 TYR cc_start: 0.8221 (m-80) cc_final: 0.7819 (m-80) REVERT: D 261 MET cc_start: 0.8578 (tmm) cc_final: 0.8121 (mmt) REVERT: D 270 THR cc_start: 0.8862 (p) cc_final: 0.8561 (p) REVERT: D 273 MET cc_start: 0.9499 (mtm) cc_final: 0.9086 (ptp) REVERT: D 295 GLU cc_start: 0.9289 (pt0) cc_final: 0.8982 (pt0) REVERT: D 303 MET cc_start: 0.9308 (mmm) cc_final: 0.8891 (mmm) REVERT: D 310 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8940 (mt-10) REVERT: D 313 GLU cc_start: 0.9012 (pp20) cc_final: 0.8622 (pp20) REVERT: D 314 SER cc_start: 0.9705 (t) cc_final: 0.9438 (p) REVERT: D 321 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8224 (tp30) REVERT: D 344 LEU cc_start: 0.9623 (tt) cc_final: 0.9318 (tt) REVERT: D 349 ASN cc_start: 0.9410 (m110) cc_final: 0.9145 (m110) REVERT: D 353 GLN cc_start: 0.8979 (mp10) cc_final: 0.8765 (mp10) REVERT: D 364 GLN cc_start: 0.9488 (tp-100) cc_final: 0.9264 (tp-100) REVERT: D 377 ILE cc_start: 0.9421 (tp) cc_final: 0.9095 (pt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0476 time to fit residues: 6.4569 Evaluate side-chains 88 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.104 Evaluate side-chains 55 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9132 (tp) cc_final: 0.8348 (tp) REVERT: H 8 GLN cc_start: 0.9607 (mp10) cc_final: 0.9208 (mp10) REVERT: H 12 PHE cc_start: 0.9594 (m-80) cc_final: 0.8985 (m-80) REVERT: H 36 MET cc_start: 0.9400 (tpp) cc_final: 0.9066 (tpp) REVERT: H 37 ARG cc_start: 0.9332 (ptp-110) cc_final: 0.9127 (ptp-110) REVERT: H 48 LEU cc_start: 0.9773 (mt) cc_final: 0.9513 (tt) REVERT: H 77 LYS cc_start: 0.8794 (tppt) cc_final: 0.8304 (tptt) REVERT: H 83 GLU cc_start: 0.9419 (pm20) cc_final: 0.9096 (pm20) REVERT: H 84 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8528 (mm-30) REVERT: H 87 GLU cc_start: 0.9238 (tt0) cc_final: 0.8941 (pp20) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0603 time to fit residues: 3.5837 Evaluate side-chains 48 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 176 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071898 restraints weight = 12356.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073775 restraints weight = 7334.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074954 restraints weight = 5185.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.075692 restraints weight = 4164.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.076104 restraints weight = 3596.705| |-----------------------------------------------------------------------------| r_work (final): 0.3358 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.042020 restraints weight = 6825.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.043781 restraints weight = 4090.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.045069 restraints weight = 2786.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.046094 restraints weight = 2066.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046912 restraints weight = 1577.481| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.910 15696 Z= 1.157 Angle : 0.815 18.970 21232 Z= 0.420 Chirality : 0.038 0.169 2480 Planarity : 0.004 0.038 2660 Dihedral : 4.743 25.167 2168 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.19), residues: 2000 helix: 1.58 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.66 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 90 TYR 0.027 0.002 TYR E 138 PHE 0.018 0.001 PHE F 92 TRP 0.026 0.002 TRP B 242 HIS 0.003 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.03314 / 1.16 (15696) covalent geometry : angle 0.81469 / 0.42 (21232) hydrogen bonds : bond 0.03547 / 2.34 ( 1076) hydrogen bonds : angle 4.20053 / 3.01 ( 3204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9667 (mt) cc_final: 0.9439 (mt) REVERT: A 82 LYS cc_start: 0.9506 (mmtt) cc_final: 0.9018 (mmmt) REVERT: A 91 ASN cc_start: 0.8639 (m-40) cc_final: 0.8355 (m-40) REVERT: A 111 GLU cc_start: 0.9055 (mp0) cc_final: 0.8068 (tm-30) REVERT: A 161 TYR cc_start: 0.8385 (p90) cc_final: 0.8037 (p90) REVERT: A 175 LEU cc_start: 0.9521 (mt) cc_final: 0.9280 (pp) REVERT: A 176 ASN cc_start: 0.9227 (t0) cc_final: 0.8767 (t0) REVERT: A 179 TYR cc_start: 0.8236 (m-80) cc_final: 0.7802 (m-80) REVERT: A 198 LEU cc_start: 0.9366 (mt) cc_final: 0.9104 (mt) REVERT: A 261 MET cc_start: 0.8665 (tmm) cc_final: 0.8212 (mmt) REVERT: A 284 VAL cc_start: 0.9388 (t) cc_final: 0.9172 (t) REVERT: A 295 GLU cc_start: 0.9273 (pt0) cc_final: 0.8980 (pt0) REVERT: A 303 MET cc_start: 0.9223 (mmm) cc_final: 0.8882 (mmp) REVERT: A 310 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8943 (mt-10) REVERT: A 313 GLU cc_start: 0.8980 (pp20) cc_final: 0.8578 (pp20) REVERT: A 314 SER cc_start: 0.9724 (t) cc_final: 0.9440 (p) REVERT: A 321 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8277 (tp30) REVERT: A 344 LEU cc_start: 0.9652 (tt) cc_final: 0.9382 (tt) REVERT: A 349 ASN cc_start: 0.9410 (m110) cc_final: 0.9108 (m110) REVERT: A 355 ARG cc_start: 0.9139 (ptm-80) cc_final: 0.8898 (ttp80) REVERT: A 364 GLN cc_start: 0.9482 (tp-100) cc_final: 0.9263 (tp-100) REVERT: A 377 ILE cc_start: 0.9436 (tp) cc_final: 0.9103 (pt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0557 time to fit residues: 7.5702 Evaluate side-chains 91 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.106 Evaluate side-chains 54 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9053 (tp) cc_final: 0.8328 (tp) REVERT: E 8 GLN cc_start: 0.9552 (mp10) cc_final: 0.9188 (mp10) REVERT: E 12 PHE cc_start: 0.9577 (m-80) cc_final: 0.8940 (m-80) REVERT: E 36 MET cc_start: 0.9330 (tpp) cc_final: 0.9035 (tpp) REVERT: E 48 LEU cc_start: 0.9777 (mt) cc_final: 0.9507 (tt) REVERT: E 68 PHE cc_start: 0.9606 (t80) cc_final: 0.9307 (t80) REVERT: E 77 LYS cc_start: 0.8920 (tppt) cc_final: 0.8441 (tptt) REVERT: E 83 GLU cc_start: 0.9304 (pm20) cc_final: 0.9101 (pm20) REVERT: E 84 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8440 (mm-30) REVERT: E 87 GLU cc_start: 0.9238 (tt0) cc_final: 0.8883 (pp20) REVERT: E 141 PHE cc_start: 0.9226 (t80) cc_final: 0.8969 (t80) REVERT: E 143 GLN cc_start: 0.9580 (pm20) cc_final: 0.9366 (pm20) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0630 time to fit residues: 3.6947 Evaluate side-chains 50 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.0040 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 82 optimal weight: 0.0170 chunk 17 optimal weight: 10.0000 overall best weight: 0.6832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.098121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073563 restraints weight = 12193.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.075552 restraints weight = 7279.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.076773 restraints weight = 5142.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077519 restraints weight = 4064.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078006 restraints weight = 3519.117| |-----------------------------------------------------------------------------| r_work (final): 0.3388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.049761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.040855 restraints weight = 6213.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.042361 restraints weight = 3929.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.043481 restraints weight = 2745.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.044291 restraints weight = 2050.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.044932 restraints weight = 1605.978| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.909 15696 Z= 1.156 Angle : 0.853 19.113 21232 Z= 0.433 Chirality : 0.040 0.153 2480 Planarity : 0.003 0.037 2660 Dihedral : 4.666 23.564 2168 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.19), residues: 2000 helix: 1.57 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.67 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 90 TYR 0.024 0.001 TYR F 138 PHE 0.013 0.001 PHE G 92 TRP 0.023 0.002 TRP C 242 HIS 0.004 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03311 / 1.16 (15696) covalent geometry : angle 0.85263 / 0.43 (21232) hydrogen bonds : bond 0.03504 / 2.33 ( 1076) hydrogen bonds : angle 4.24916 / 3.05 ( 3204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9627 (mt) cc_final: 0.9424 (mt) REVERT: A 22 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9037 (mt-10) REVERT: A 82 LYS cc_start: 0.9462 (mmtt) cc_final: 0.9033 (mmmt) REVERT: A 91 ASN cc_start: 0.8670 (m-40) cc_final: 0.8383 (m-40) REVERT: A 175 LEU cc_start: 0.9506 (mt) cc_final: 0.9251 (pp) REVERT: A 176 ASN cc_start: 0.9187 (t0) cc_final: 0.8752 (t0) REVERT: A 179 TYR cc_start: 0.8212 (m-80) cc_final: 0.7854 (m-80) REVERT: A 198 LEU cc_start: 0.9334 (mt) cc_final: 0.9063 (mt) REVERT: A 207 LEU cc_start: 0.8743 (mt) cc_final: 0.8290 (pp) REVERT: A 261 MET cc_start: 0.8639 (tmm) cc_final: 0.8241 (mmt) REVERT: A 303 MET cc_start: 0.9250 (mmm) cc_final: 0.8837 (mmm) REVERT: A 310 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8915 (mt-10) REVERT: A 313 GLU cc_start: 0.8988 (pp20) cc_final: 0.8570 (pp20) REVERT: A 314 SER cc_start: 0.9729 (t) cc_final: 0.9456 (p) REVERT: A 321 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8266 (tp30) REVERT: A 344 LEU cc_start: 0.9634 (tt) cc_final: 0.9346 (tt) REVERT: A 349 ASN cc_start: 0.9423 (m110) cc_final: 0.9197 (m110) REVERT: A 364 GLN cc_start: 0.9485 (tp-100) cc_final: 0.9278 (tp-100) REVERT: A 377 ILE cc_start: 0.9453 (tp) cc_final: 0.9125 (pt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0522 time to fit residues: 6.8292 Evaluate side-chains 89 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.106 Evaluate side-chains 54 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4 LEU cc_start: 0.9002 (tp) cc_final: 0.7949 (tp) REVERT: G 8 GLN cc_start: 0.9590 (mp10) cc_final: 0.9207 (mp10) REVERT: G 12 PHE cc_start: 0.9576 (m-80) cc_final: 0.8997 (m-80) REVERT: G 16 PHE cc_start: 0.9493 (t80) cc_final: 0.9264 (t80) REVERT: G 21 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8338 (mmtm) REVERT: G 30 LYS cc_start: 0.9611 (mmpt) cc_final: 0.9320 (tptp) REVERT: G 36 MET cc_start: 0.9390 (tpp) cc_final: 0.9038 (tpp) REVERT: G 48 LEU cc_start: 0.9777 (mt) cc_final: 0.9494 (tt) REVERT: G 68 PHE cc_start: 0.9581 (t80) cc_final: 0.9270 (t80) REVERT: G 74 ARG cc_start: 0.9143 (mtm-85) cc_final: 0.8738 (mtm-85) REVERT: G 77 LYS cc_start: 0.8940 (tppt) cc_final: 0.8482 (tptt) REVERT: G 84 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8319 (mm-30) REVERT: G 87 GLU cc_start: 0.9123 (tt0) cc_final: 0.8776 (pp20) REVERT: G 143 GLN cc_start: 0.9535 (pm20) cc_final: 0.9212 (pm20) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0749 time to fit residues: 4.3538 Evaluate side-chains 48 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 8 optimal weight: 0.0970 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 119 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 174 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074105 restraints weight = 11979.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075997 restraints weight = 7262.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077228 restraints weight = 5169.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.078005 restraints weight = 4120.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078402 restraints weight = 3537.724| |-----------------------------------------------------------------------------| r_work (final): 0.3400 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.050606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.040925 restraints weight = 6358.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.042616 restraints weight = 3978.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.043909 restraints weight = 2741.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.044811 restraints weight = 2023.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.045569 restraints weight = 1575.067| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.908 15696 Z= 1.156 Angle : 0.869 19.069 21232 Z= 0.441 Chirality : 0.040 0.163 2480 Planarity : 0.003 0.037 2660 Dihedral : 4.587 23.833 2168 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 2000 helix: 1.63 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.61 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.027 0.002 TYR G 138 PHE 0.014 0.001 PHE G 92 TRP 0.022 0.002 TRP C 242 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.03311 / 1.16 (15696) covalent geometry : angle 0.86912 / 0.44 (21232) hydrogen bonds : bond 0.03572 / 2.39 ( 1076) hydrogen bonds : angle 4.19278 / 3.03 ( 3204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 LEU cc_start: 0.9645 (mt) cc_final: 0.9429 (mt) REVERT: D 22 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9042 (mt-10) REVERT: D 82 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9028 (mmmt) REVERT: D 91 ASN cc_start: 0.8654 (m-40) cc_final: 0.8353 (m-40) REVERT: D 175 LEU cc_start: 0.9511 (mt) cc_final: 0.9269 (pp) REVERT: D 176 ASN cc_start: 0.9220 (t0) cc_final: 0.8774 (t0) REVERT: D 179 TYR cc_start: 0.8097 (m-80) cc_final: 0.7734 (m-80) REVERT: D 198 LEU cc_start: 0.9341 (mt) cc_final: 0.9041 (mt) REVERT: D 207 LEU cc_start: 0.8655 (mt) cc_final: 0.8191 (pp) REVERT: D 261 MET cc_start: 0.8643 (tmm) cc_final: 0.8245 (mmt) REVERT: D 303 MET cc_start: 0.9253 (mmm) cc_final: 0.8819 (mmm) REVERT: D 310 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8907 (mt-10) REVERT: D 313 GLU cc_start: 0.8995 (pp20) cc_final: 0.8566 (pp20) REVERT: D 314 SER cc_start: 0.9723 (t) cc_final: 0.9453 (p) REVERT: D 321 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8213 (tp30) REVERT: D 344 LEU cc_start: 0.9636 (tt) cc_final: 0.9334 (tt) REVERT: D 349 ASN cc_start: 0.9386 (m110) cc_final: 0.9181 (m110) REVERT: D 355 ARG cc_start: 0.9091 (ptm-80) cc_final: 0.8793 (ttp80) REVERT: D 364 GLN cc_start: 0.9502 (tp-100) cc_final: 0.9301 (tp-100) REVERT: D 377 ILE cc_start: 0.9458 (tp) cc_final: 0.9132 (pt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0535 time to fit residues: 7.1351 Evaluate side-chains 89 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.096 Evaluate side-chains 55 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8844 (tp) cc_final: 0.7840 (tt) REVERT: H 8 GLN cc_start: 0.9596 (mp10) cc_final: 0.9310 (mp10) REVERT: H 12 PHE cc_start: 0.9556 (m-80) cc_final: 0.8936 (m-80) REVERT: H 16 PHE cc_start: 0.9481 (t80) cc_final: 0.9239 (t80) REVERT: H 30 LYS cc_start: 0.9622 (mmpt) cc_final: 0.9323 (tptp) REVERT: H 36 MET cc_start: 0.9376 (tpp) cc_final: 0.9044 (tpp) REVERT: H 48 LEU cc_start: 0.9762 (mt) cc_final: 0.9506 (tt) REVERT: H 68 PHE cc_start: 0.9559 (t80) cc_final: 0.9229 (t80) REVERT: H 74 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8727 (mtm-85) REVERT: H 77 LYS cc_start: 0.9009 (tppt) cc_final: 0.8559 (tptt) REVERT: H 84 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8278 (mm-30) REVERT: H 87 GLU cc_start: 0.9103 (tt0) cc_final: 0.8659 (pp20) REVERT: H 90 ARG cc_start: 0.9136 (ptm-80) cc_final: 0.8339 (ptp90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0758 time to fit residues: 4.4766 Evaluate side-chains 47 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 125 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 127 optimal weight: 0.3980 chunk 180 optimal weight: 0.9990 chunk 144 optimal weight: 0.0770 chunk 157 optimal weight: 0.2980 chunk 22 optimal weight: 0.0870 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS D 203 HIS ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.099705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074104 restraints weight = 11994.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075999 restraints weight = 7320.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.077209 restraints weight = 5261.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.077976 restraints weight = 4225.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078430 restraints weight = 3651.326| |-----------------------------------------------------------------------------| r_work (final): 0.3401 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.051164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.041321 restraints weight = 6279.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.042904 restraints weight = 3992.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.044073 restraints weight = 2823.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.044932 restraints weight = 2127.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.045647 restraints weight = 1682.663| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.908 15696 Z= 1.156 Angle : 0.857 19.075 21232 Z= 0.434 Chirality : 0.039 0.168 2480 Planarity : 0.003 0.036 2660 Dihedral : 4.610 21.287 2168 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 2000 helix: 1.75 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 90 TYR 0.024 0.002 TYR G 138 PHE 0.026 0.002 PHE B 325 TRP 0.021 0.002 TRP C 242 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.03311 / 1.16 (15696) covalent geometry : angle 0.85655 / 0.43 (21232) hydrogen bonds : bond 0.03604 / 2.40 ( 1076) hydrogen bonds : angle 4.11360 / 2.99 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.59 seconds wall clock time: 26 minutes 48.56 seconds (1608.56 seconds total)