Starting phenix.real_space_refine on Fri Sep 27 08:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/09_2024/6cno_7539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/09_2024/6cno_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/09_2024/6cno_7539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/09_2024/6cno_7539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/09_2024/6cno_7539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/09_2024/6cno_7539.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} 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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} 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: G, F, H, C, B, D Time building chain proxies: 7.47, per 1000 atoms: 0.48 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: 4.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.62 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: 4.60 Time building geometry restraints manager: 4.72 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: 0.00 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 34.590 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- 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= 0.402 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 : 5.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (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 TRP 0.035 0.002 TRP B 221 HIS 0.011 0.003 HIS A 80 PHE 0.017 0.003 PHE G 92 TYR 0.022 0.003 TYR D 307 ARG 0.007 0.001 ARG A 189 *********************** 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 fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.332 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: 0.8337 (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: 0.9168 (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: 0.8791 (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: 0.1949 time to fit residues: 32.9153 Evaluate side-chains 90 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.329 Evaluate side-chains 66 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.129 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: 0.9017 (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: 0.8782 (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: 0.1735 time to fit residues: 12.2245 Evaluate side-chains 54 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.0000 chunk 116 optimal weight: 0.0670 chunk 181 optimal weight: 0.1980 overall best weight: 0.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.880 15696 Z= 2.110 Angle : 0.796 21.844 21232 Z= 0.404 Chirality : 0.037 0.121 2480 Planarity : 0.004 0.044 2660 Dihedral : 5.424 25.401 2168 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2000 helix: 0.34 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.30 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 242 HIS 0.004 0.001 HIS D 328 PHE 0.026 0.002 PHE F 89 TYR 0.014 0.001 TYR G 138 ARG 0.007 0.001 ARG A 17 *********************** 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 125 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9580 (mt) cc_final: 0.9198 (pp) REVERT: A 19 LEU cc_start: 0.9529 (mt) cc_final: 0.9161 (mt) REVERT: A 30 LEU cc_start: 0.8833 (tt) cc_final: 0.8627 (tp) REVERT: A 82 LYS cc_start: 0.9381 (mmtt) cc_final: 0.9045 (mmmt) REVERT: A 111 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 115 CYS cc_start: 0.9332 (t) cc_final: 0.8699 (p) REVERT: A 198 LEU cc_start: 0.9244 (mt) cc_final: 0.8650 (mt) REVERT: A 200 MET cc_start: 0.9384 (ttm) cc_final: 0.8890 (tpp) REVERT: A 201 ASN cc_start: 0.9369 (m-40) cc_final: 0.9040 (p0) REVERT: A 207 LEU cc_start: 0.8934 (mt) cc_final: 0.8508 (pp) REVERT: A 261 MET cc_start: 0.8533 (tmm) cc_final: 0.8172 (mmt) REVERT: A 264 LYS cc_start: 0.7944 (mttt) cc_final: 0.7655 (tttp) REVERT: A 270 THR cc_start: 0.8680 (p) cc_final: 0.8333 (p) REVERT: A 273 MET cc_start: 0.9123 (mtm) cc_final: 0.8729 (ptp) REVERT: A 288 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8677 (tmtt) REVERT: A 292 ASN cc_start: 0.9441 (t0) cc_final: 0.9203 (t0) REVERT: A 303 MET cc_start: 0.8815 (mmm) cc_final: 0.8545 (mmp) REVERT: A 309 LYS cc_start: 0.9469 (ttpt) cc_final: 0.9062 (ttmm) REVERT: A 310 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9064 (mt-10) REVERT: A 321 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8427 (tp30) REVERT: A 324 MET cc_start: 0.9423 (tpt) cc_final: 0.9161 (tpp) REVERT: A 343 LYS cc_start: 0.9579 (mttt) cc_final: 0.9097 (mptt) REVERT: A 359 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8056 (ttp80) REVERT: A 373 LYS cc_start: 0.7587 (pttp) cc_final: 0.7238 (pttm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1828 time to fit residues: 26.0720 Evaluate side-chains 89 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.329 Evaluate side-chains 67 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.9591 (tppt) cc_final: 0.9256 (mmmm) REVERT: H 16 PHE cc_start: 0.9508 (t80) cc_final: 0.9074 (t80) REVERT: H 48 LEU cc_start: 0.9726 (mt) cc_final: 0.9373 (tt) REVERT: H 51 MET cc_start: 0.8758 (tpp) cc_final: 0.8295 (tpp) REVERT: H 52 ILE cc_start: 0.9749 (mt) cc_final: 0.9534 (mt) REVERT: H 54 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8335 (mt-10) REVERT: H 74 ARG cc_start: 0.8892 (mtm110) cc_final: 0.8567 (mtm-85) REVERT: H 75 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8611 (mttt) REVERT: H 84 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8061 (mm-30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1822 time to fit residues: 12.9977 Evaluate side-chains 55 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.907 > 50: distance: 1 - 2: 3.496 distance: 1 - 3: 3.329 distance: 4 - 5: 45.780 distance: 5 - 6: 50.050 distance: 5 - 8: 38.739 distance: 6 - 7: 33.174 distance: 6 - 12: 42.630 distance: 7 - 36: 33.509 distance: 8 - 9: 16.046 distance: 8 - 10: 34.620 distance: 9 - 11: 33.384 distance: 12 - 13: 37.044 distance: 13 - 14: 36.756 distance: 13 - 16: 33.748 distance: 14 - 15: 50.673 distance: 14 - 19: 19.366 distance: 15 - 44: 33.634 distance: 16 - 17: 32.609 distance: 16 - 18: 20.816 distance: 19 - 20: 38.689 distance: 20 - 21: 44.772 distance: 20 - 23: 26.946 distance: 21 - 22: 14.239 distance: 21 - 27: 30.369 distance: 22 - 51: 19.682 distance: 23 - 24: 24.786 distance: 24 - 25: 24.250 distance: 24 - 26: 23.557 distance: 27 - 28: 45.148 distance: 28 - 29: 57.760 distance: 28 - 31: 42.273 distance: 29 - 30: 20.468 distance: 29 - 36: 53.443 distance: 30 - 58: 27.587 distance: 31 - 32: 32.480 distance: 32 - 33: 18.577 distance: 33 - 34: 13.780 distance: 33 - 35: 45.707 distance: 36 - 37: 37.469 distance: 37 - 38: 32.852 distance: 37 - 40: 21.911 distance: 38 - 39: 41.926 distance: 38 - 44: 39.099 distance: 40 - 41: 23.305 distance: 41 - 42: 12.218 distance: 41 - 43: 6.173 distance: 44 - 45: 38.467 distance: 45 - 46: 16.834 distance: 45 - 48: 31.092 distance: 46 - 47: 34.849 distance: 46 - 51: 21.653 distance: 48 - 49: 36.164 distance: 48 - 50: 19.595 distance: 51 - 52: 30.903 distance: 52 - 53: 43.847 distance: 52 - 55: 13.859 distance: 53 - 54: 49.102 distance: 53 - 58: 41.853 distance: 55 - 56: 54.614 distance: 55 - 57: 22.416 distance: 58 - 59: 46.192 distance: 59 - 60: 38.884 distance: 59 - 62: 48.652 distance: 60 - 61: 38.375 distance: 60 - 64: 24.393 distance: 62 - 63: 25.572 distance: 64 - 65: 25.714 distance: 65 - 66: 24.835 distance: 66 - 67: 10.715 distance: 66 - 68: 15.270 distance: 68 - 69: 18.645