Starting phenix.real_space_refine on Sat Aug 23 23:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cno_7539/08_2025/6cno_7539.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cno_7539/08_2025/6cno_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6cno_7539/08_2025/6cno_7539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cno_7539/08_2025/6cno_7539.map" model { file = "/net/cci-nas-00/data/ceres_data/6cno_7539/08_2025/6cno_7539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cno_7539/08_2025/6cno_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.73, per 1000 atoms: 0.18 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: 0.96 Conformation dependent library (CDL) restraints added in 807.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.46 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: 2.61 Time building geometry restraints manager: 1.36 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: 0.05 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: 1.670 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 aren 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 covalent geometry : bond 0.00619 (15696) covalent geometry : angle 1.02937 (21232) hydrogen bonds : bond 0.13878 ( 1076) hydrogen bonds : angle 6.37617 ( 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 : 0.110 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: 0.9175 (pp) 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: 0.8949 (t80) REVERT: A 176 ASN cc_start: 0.9284 (t0) cc_final: 0.8684 (t0) REVERT: A 179 TYR cc_start: 0.9090 (m-80) cc_final: 0.8336 (m-10) REVERT: A 186 ASN cc_start: 0.9406 (t0) cc_final: 0.9182 (t0) REVERT: A 194 PHE cc_start: 0.8762 (t80) cc_final: 0.8097 (t80) REVERT: A 200 MET cc_start: 0.9434 (ttm) cc_final: 0.8810 (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: 0.7963 (mmt) REVERT: A 273 MET cc_start: 0.9087 (mtm) cc_final: 0.8837 (ptt) REVERT: A 278 THR cc_start: 0.9168 (m) cc_final: 0.8926 (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: 0.9184 (t0) REVERT: A 303 MET cc_start: 0.8791 (mmm) cc_final: 0.8501 (mmm) REVERT: A 309 LYS cc_start: 0.9557 (ttpt) cc_final: 0.9182 (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: 0.8503 (tp30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.0846 time to fit residues: 14.3418 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 : 0.081 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 : 0.047 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: 0.8537 (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: 0.0746 time to fit residues: 5.2537 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 : 0.039 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 192 HIS A 300 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.094004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069583 restraints weight = 12071.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071473 restraints weight = 7226.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072716 restraints weight = 5104.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.073545 restraints weight = 4035.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073898 restraints weight = 3461.955| |-----------------------------------------------------------------------------| r_work (final): 0.3324 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.040341 restraints weight = 5969.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.041912 restraints weight = 3604.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.043138 restraints weight = 2531.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043882 restraints weight = 1877.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.044635 restraints weight = 1530.552| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.858 15696 Z= 1.147 Angle : 0.815 22.859 21232 Z= 0.420 Chirality : 0.038 0.126 2480 Planarity : 0.005 0.042 2660 Dihedral : 5.476 26.427 2168 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.83 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 aren not related in a simple way. whole: -0.18 (0.18), residues: 2000 helix: 0.30 (0.12), residues: 1544 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 317 TYR 0.013 0.001 TYR G 138 PHE 0.024 0.002 PHE F 89 TRP 0.042 0.004 TRP B 242 HIS 0.005 0.001 HIS C 375 Details of bonding type rmsd covalent geometry : bond 0.03262 (15696) covalent geometry : angle 0.81461 (21232) hydrogen bonds : bond 0.04971 ( 1076) hydrogen bonds : angle 4.69596 ( 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 122 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.069 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: 0.9192 (mm) REVERT: A 82 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9173 (mmmt) REVERT: A 91 ASN cc_start: 0.9072 (m-40) cc_final: 0.8351 (m110) REVERT: A 111 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 115 CYS cc_start: 0.9320 (t) cc_final: 0.8737 (p) REVERT: A 156 MET cc_start: 0.8573 (tpt) cc_final: 0.8294 (tpp) REVERT: A 186 ASN cc_start: 0.9482 (t0) cc_final: 0.9277 (t0) REVERT: A 194 PHE cc_start: 0.9034 (t80) cc_final: 0.8779 (t80) REVERT: A 198 LEU cc_start: 0.9293 (mt) cc_final: 0.8922 (mt) REVERT: A 201 ASN cc_start: 0.9504 (m-40) cc_final: 0.9168 (p0) REVERT: A 207 LEU cc_start: 0.8936 (mt) cc_final: 0.8578 (pp) REVERT: A 261 MET cc_start: 0.8567 (tmm) cc_final: 0.8175 (mmt) REVERT: A 264 LYS cc_start: 0.7932 (mttt) cc_final: 0.7642 (tttp) REVERT: A 270 THR cc_start: 0.8795 (p) cc_final: 0.8466 (p) REVERT: A 273 MET cc_start: 0.9239 (mtm) cc_final: 0.8806 (ptp) REVERT: A 288 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8716 (tmtt) REVERT: A 292 ASN cc_start: 0.9651 (t0) cc_final: 0.9205 (t0) REVERT: A 295 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9249 (mm-30) REVERT: A 303 MET cc_start: 0.9290 (mmm) cc_final: 0.8842 (mmm) REVERT: A 309 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9358 (ttmm) REVERT: A 310 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9076 (mt-10) REVERT: A 321 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8368 (tp30) REVERT: A 324 MET cc_start: 0.9585 (tpt) cc_final: 0.8949 (tpp) REVERT: A 341 GLN cc_start: 0.9110 (pm20) cc_final: 0.8859 (pm20) REVERT: A 343 LYS cc_start: 0.9591 (mttt) cc_final: 0.9135 (mptt) REVERT: A 359 ARG cc_start: 0.8695 (ttt180) cc_final: 0.8025 (ttp80) REVERT: A 364 GLN cc_start: 0.9518 (tp-100) cc_final: 0.9315 (tp-100) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0800 time to fit residues: 11.2113 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 : 0.144 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 : 0.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 GLN cc_start: 0.9460 (mp10) cc_final: 0.9240 (mp10) REVERT: H 11 GLU cc_start: 0.8747 (pp20) cc_final: 0.8539 (pp20) REVERT: H 13 LYS cc_start: 0.9625 (tppt) cc_final: 0.9293 (mmmm) REVERT: H 16 PHE cc_start: 0.9651 (t80) cc_final: 0.9077 (t80) REVERT: H 36 MET cc_start: 0.9425 (tpt) cc_final: 0.9070 (mmm) REVERT: H 48 LEU cc_start: 0.9797 (mt) cc_final: 0.9500 (tt) REVERT: H 51 MET cc_start: 0.9023 (tpp) cc_final: 0.8631 (tpp) REVERT: H 53 ASN cc_start: 0.9618 (m110) cc_final: 0.9094 (m110) REVERT: H 54 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8302 (mt-10) REVERT: H 74 ARG cc_start: 0.9262 (mtm110) cc_final: 0.8816 (mtm-85) REVERT: H 75 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8395 (mttt) REVERT: H 84 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8481 (mm-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0851 time to fit residues: 5.8962 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 ------------------------------------------------------------------------------- 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: 0.6980 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 chunk 111 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.095442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070764 restraints weight = 12115.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072710 restraints weight = 7159.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073997 restraints weight = 5065.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074821 restraints weight = 4051.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075291 restraints weight = 3478.300| |-----------------------------------------------------------------------------| r_work (final): 0.3346 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.040485 restraints weight = 6011.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.042171 restraints weight = 3570.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.043488 restraints weight = 2450.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.044457 restraints weight = 1792.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.045179 restraints weight = 1378.803| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 1.940 15696 Z= 1.168 Angle : 0.859 19.894 21232 Z= 0.437 Chirality : 0.039 0.137 2480 Planarity : 0.007 0.086 2660 Dihedral : 5.642 24.821 2168 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % 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 aren not related in a simple way. whole: 0.18 (0.19), residues: 2000 helix: 0.53 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -0.98 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 17 TYR 0.017 0.002 TYR H 138 PHE 0.028 0.003 PHE A 144 TRP 0.073 0.005 TRP D 242 HIS 0.010 0.002 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.03351 (15696) covalent geometry : angle 0.85854 (21232) hydrogen bonds : bond 0.04774 ( 1076) hydrogen bonds : angle 4.61950 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 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 : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9629 (mt) cc_final: 0.9252 (mm) REVERT: A 22 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8950 (mt-10) REVERT: A 82 LYS cc_start: 0.9529 (mmtt) cc_final: 0.9150 (mmmt) REVERT: A 91 ASN cc_start: 0.8923 (m-40) cc_final: 0.8227 (m110) REVERT: A 111 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 115 CYS cc_start: 0.9364 (t) cc_final: 0.8795 (p) REVERT: A 156 MET cc_start: 0.8471 (tpt) cc_final: 0.8235 (tpp) REVERT: A 176 ASN cc_start: 0.9524 (t0) cc_final: 0.9056 (t0) REVERT: A 179 TYR cc_start: 0.8684 (m-80) cc_final: 0.8233 (m-80) REVERT: A 186 ASN cc_start: 0.9393 (t0) cc_final: 0.9163 (t0) REVERT: A 198 LEU cc_start: 0.9297 (mt) cc_final: 0.8835 (mt) REVERT: A 207 LEU cc_start: 0.8955 (mt) cc_final: 0.8517 (pp) REVERT: A 217 LEU cc_start: 0.8801 (mm) cc_final: 0.8593 (tt) REVERT: A 261 MET cc_start: 0.8560 (tmm) cc_final: 0.8127 (mmt) REVERT: A 270 THR cc_start: 0.8927 (p) cc_final: 0.8560 (p) REVERT: A 273 MET cc_start: 0.9252 (mtm) cc_final: 0.8850 (ptp) REVERT: A 292 ASN cc_start: 0.9559 (t0) cc_final: 0.9319 (t0) REVERT: A 303 MET cc_start: 0.9280 (mmm) cc_final: 0.8792 (mmm) REVERT: A 309 LYS cc_start: 0.9640 (ttpt) cc_final: 0.9298 (ttmm) REVERT: A 310 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9032 (mt-10) REVERT: A 320 GLN cc_start: 0.8678 (pp30) cc_final: 0.8272 (pp30) REVERT: A 359 ARG cc_start: 0.8459 (ttt180) cc_final: 0.7860 (ttp80) REVERT: A 364 GLN cc_start: 0.9490 (tp-100) cc_final: 0.9275 (tp-100) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0616 time to fit residues: 7.9412 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 : 0.108 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 : 0.042 Fit side-chains REVERT: E 13 LYS cc_start: 0.9621 (tppt) cc_final: 0.9285 (mmmm) REVERT: E 16 PHE cc_start: 0.9672 (t80) cc_final: 0.9044 (t80) REVERT: E 36 MET cc_start: 0.9494 (tpt) cc_final: 0.9019 (tpt) REVERT: E 48 LEU cc_start: 0.9782 (mt) cc_final: 0.9519 (tt) REVERT: E 51 MET cc_start: 0.9082 (tpp) cc_final: 0.8676 (tpp) REVERT: E 54 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8349 (mt-10) REVERT: E 74 ARG cc_start: 0.9127 (mtm110) cc_final: 0.8873 (mtm-85) REVERT: E 75 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8324 (mttt) REVERT: E 137 ASN cc_start: 0.8722 (m-40) cc_final: 0.8480 (m-40) REVERT: E 143 GLN cc_start: 0.9734 (mt0) cc_final: 0.9467 (pt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0875 time to fit residues: 6.0453 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 : 0.047 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3702 r_free = 0.3702 target = 0.095194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070501 restraints weight = 12360.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072555 restraints weight = 7115.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073868 restraints weight = 4948.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074603 restraints weight = 3898.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.075102 restraints weight = 3382.338| |-----------------------------------------------------------------------------| r_work (final): 0.3336 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.047818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.037968 restraints weight = 6317.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.039583 restraints weight = 3906.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.040772 restraints weight = 2710.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.041623 restraints weight = 2036.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.042387 restraints weight = 1626.826| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5889 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= 1.165 Angle : 0.850 20.473 21232 Z= 0.434 Chirality : 0.039 0.158 2480 Planarity : 0.007 0.096 2660 Dihedral : 5.573 32.178 2168 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.26 % Allowed : 3.17 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.19), residues: 2000 helix: 0.64 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.21 (0.34), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 17 TYR 0.022 0.003 TYR G 138 PHE 0.028 0.003 PHE B 291 TRP 0.045 0.004 TRP A 242 HIS 0.011 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.03332 (15696) covalent geometry : angle 0.85023 (21232) hydrogen bonds : bond 0.04345 ( 1076) hydrogen bonds : angle 4.59589 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 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: 1 poor density : 108 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9667 (mt) cc_final: 0.9464 (mt) REVERT: A 19 LEU cc_start: 0.9667 (mt) cc_final: 0.9302 (mm) REVERT: A 22 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8947 (mt-10) REVERT: A 82 LYS cc_start: 0.9494 (mmtt) cc_final: 0.9146 (mmmt) REVERT: A 91 ASN cc_start: 0.9013 (m-40) cc_final: 0.8442 (m-40) REVERT: A 156 MET cc_start: 0.8568 (tpt) cc_final: 0.8284 (tpp) REVERT: A 186 ASN cc_start: 0.9366 (t0) cc_final: 0.9142 (t0) REVERT: A 198 LEU cc_start: 0.9273 (mt) cc_final: 0.8791 (mt) REVERT: A 207 LEU cc_start: 0.8689 (mt) cc_final: 0.8272 (pp) REVERT: A 217 LEU cc_start: 0.8793 (mm) cc_final: 0.8584 (tt) REVERT: A 261 MET cc_start: 0.8531 (tmm) cc_final: 0.8142 (mmt) REVERT: A 270 THR cc_start: 0.9056 (p) cc_final: 0.8709 (p) REVERT: A 273 MET cc_start: 0.9338 (mtm) cc_final: 0.8953 (ptp) REVERT: A 295 GLU cc_start: 0.9491 (mp0) cc_final: 0.9128 (mp0) REVERT: A 303 MET cc_start: 0.9277 (mmm) cc_final: 0.8814 (mmp) REVERT: A 309 LYS cc_start: 0.9629 (ttpt) cc_final: 0.9314 (ttmm) REVERT: A 310 GLU cc_start: 0.9354 (mt-10) cc_final: 0.9050 (mt-10) REVERT: A 313 GLU cc_start: 0.9037 (pp20) cc_final: 0.8688 (pp20) REVERT: A 321 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8516 (tp30) REVERT: A 349 ASN cc_start: 0.9456 (m110) cc_final: 0.8957 (m110) REVERT: A 359 ARG cc_start: 0.8626 (ttt180) cc_final: 0.8024 (ttp80) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.0621 time to fit residues: 8.0907 Evaluate side-chains 86 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.107 Evaluate side-chains 58 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9029 (tp) cc_final: 0.8206 (tp) REVERT: H 8 GLN cc_start: 0.9516 (mp10) cc_final: 0.9144 (mp10) REVERT: H 12 PHE cc_start: 0.9748 (m-80) cc_final: 0.9160 (m-80) REVERT: H 13 LYS cc_start: 0.9620 (tppt) cc_final: 0.9270 (mmmm) REVERT: H 16 PHE cc_start: 0.9662 (t80) cc_final: 0.8978 (t80) REVERT: H 36 MET cc_start: 0.9532 (tpt) cc_final: 0.9226 (tpt) REVERT: H 48 LEU cc_start: 0.9788 (mt) cc_final: 0.9541 (tt) REVERT: H 74 ARG cc_start: 0.9199 (mtm110) cc_final: 0.8902 (mtm-85) REVERT: H 75 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8238 (mttt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0869 time to fit residues: 5.3565 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 : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.932 > 50: distance: 0 - 1: 41.284 distance: 1 - 2: 57.605 distance: 1 - 4: 38.957 distance: 2 - 3: 39.301 distance: 2 - 8: 40.580 distance: 4 - 5: 41.966 distance: 4 - 6: 40.150 distance: 5 - 7: 46.941 distance: 8 - 9: 45.136 distance: 9 - 10: 22.434 distance: 9 - 12: 35.673 distance: 10 - 11: 57.193 distance: 11 - 40: 38.702 distance: 12 - 13: 27.670 distance: 12 - 14: 34.727 distance: 15 - 16: 39.010 distance: 16 - 17: 55.834 distance: 16 - 19: 57.109 distance: 17 - 18: 57.290 distance: 17 - 23: 49.003 distance: 18 - 47: 42.674 distance: 20 - 21: 40.743 distance: 20 - 22: 55.271 distance: 23 - 24: 26.167 distance: 24 - 25: 59.208 distance: 24 - 27: 39.461 distance: 25 - 26: 11.900 distance: 25 - 32: 13.815 distance: 26 - 54: 47.523 distance: 27 - 28: 41.376 distance: 28 - 29: 56.329 distance: 29 - 30: 57.415 distance: 29 - 31: 39.504 distance: 32 - 33: 35.408 distance: 33 - 34: 41.555 distance: 33 - 36: 41.471 distance: 34 - 35: 18.236 distance: 34 - 40: 60.416 distance: 36 - 37: 38.848 distance: 37 - 38: 46.616 distance: 37 - 39: 23.909 distance: 40 - 41: 55.924 distance: 41 - 42: 46.707 distance: 41 - 44: 43.352 distance: 42 - 43: 24.254 distance: 42 - 47: 29.093 distance: 44 - 45: 49.584 distance: 44 - 46: 44.524 distance: 47 - 48: 13.391 distance: 48 - 49: 44.030 distance: 48 - 51: 69.077 distance: 49 - 50: 37.892 distance: 49 - 54: 34.977 distance: 51 - 52: 6.193 distance: 51 - 53: 32.135 distance: 54 - 55: 48.784 distance: 55 - 56: 38.106 distance: 55 - 58: 26.988 distance: 56 - 57: 47.978 distance: 56 - 60: 16.728 distance: 58 - 59: 40.753 distance: 60 - 61: 41.458 distance: 61 - 62: 58.094 distance: 62 - 63: 13.542 distance: 62 - 64: 62.900 distance: 64 - 65: 5.975 distance: 65 - 66: 40.204 distance: 65 - 68: 26.808 distance: 66 - 67: 38.496 distance: 68 - 69: 28.076 distance: 69 - 70: 14.962 distance: 69 - 71: 17.933