Starting phenix.real_space_refine on Thu Sep 26 21:58:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utm_42542/09_2024/8utm_42542.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utm_42542/09_2024/8utm_42542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utm_42542/09_2024/8utm_42542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utm_42542/09_2024/8utm_42542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utm_42542/09_2024/8utm_42542.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utm_42542/09_2024/8utm_42542.cif" } resolution = 4.32 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: 3 Type Number sf(0) Gaussians C 8464 2.51 5 N 2856 2.21 5 O 2856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "C" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "D" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "E" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "F" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "G" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Chain: "H" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Time building chain proxies: 9.61, per 1000 atoms: 0.68 Number of scatterers: 14176 At special positions: 0 Unit cell: (208.32, 115.92, 147.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2856 8.00 N 2856 7.00 C 8464 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: 4.54 Conformation dependent library (CDL) restraints added in 3.0 seconds 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5504 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 11 sheets defined 74.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.931A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 removed outlier: 6.883A pdb=" N THR A 30 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 32 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 66 Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.759A pdb=" N ILE A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 131 Processing helix chain 'A' and resid 134 through 158 removed outlier: 3.862A pdb=" N ALA A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 191 removed outlier: 4.186A pdb=" N ALA A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.254A pdb=" N ALA A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 255 removed outlier: 3.950A pdb=" N GLN A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 294 Processing helix chain 'A' and resid 315 through 334 Processing helix chain 'A' and resid 338 through 357 removed outlier: 3.821A pdb=" N GLU A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 12 No H-bonds generated for 'chain 'B' and resid 10 through 12' Processing helix chain 'B' and resid 13 through 24 removed outlier: 3.714A pdb=" N ILE B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.978A pdb=" N ARG B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 87 Processing helix chain 'B' and resid 91 through 106 removed outlier: 4.409A pdb=" N GLN B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.748A pdb=" N ALA B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 191 Processing helix chain 'B' and resid 193 through 227 removed outlier: 3.674A pdb=" N LYS B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 254 removed outlier: 3.938A pdb=" N LEU B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 294 removed outlier: 4.230A pdb=" N GLN B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 334 removed outlier: 3.983A pdb=" N GLN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'C' and resid 10 through 26 Processing helix chain 'C' and resid 49 through 64 Processing helix chain 'C' and resid 70 through 88 removed outlier: 4.049A pdb=" N THR C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 106 removed outlier: 4.538A pdb=" N GLU C 100 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 removed outlier: 5.056A pdb=" N LYS C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 159 removed outlier: 4.293A pdb=" N ALA C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 191 Processing helix chain 'C' and resid 194 through 227 removed outlier: 4.118A pdb=" N LYS C 207 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 254 removed outlier: 3.713A pdb=" N ILE C 242 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 294 removed outlier: 4.046A pdb=" N LEU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 Processing helix chain 'C' and resid 338 through 355 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.567A pdb=" N GLU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.840A pdb=" N ILE D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 88 removed outlier: 3.505A pdb=" N GLU D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 106 Processing helix chain 'D' and resid 110 through 131 removed outlier: 4.609A pdb=" N LYS D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.595A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 191 Processing helix chain 'D' and resid 194 through 227 removed outlier: 3.698A pdb=" N ALA D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE D 209 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 254 removed outlier: 3.933A pdb=" N LEU D 240 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA D 248 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 294 removed outlier: 4.408A pdb=" N GLU D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 removed outlier: 4.504A pdb=" N ARG D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.641A pdb=" N GLN D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TRP D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 23 removed outlier: 4.009A pdb=" N ILE E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP E 15 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 4.346A pdb=" N GLU E 31 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 67 removed outlier: 3.954A pdb=" N ILE E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 90 through 108 removed outlier: 3.947A pdb=" N ILE E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 131 removed outlier: 3.932A pdb=" N LEU E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 157 removed outlier: 4.322A pdb=" N ALA E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N MET E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 164 through 191 Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 204 through 227 removed outlier: 4.505A pdb=" N ALA E 208 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 254 removed outlier: 4.071A pdb=" N MET E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 294 removed outlier: 3.592A pdb=" N ARG E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 292 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 333 removed outlier: 3.780A pdb=" N LYS E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'F' and resid 13 through 26 removed outlier: 3.681A pdb=" N ILE F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 removed outlier: 4.448A pdb=" N ASP F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 88 Processing helix chain 'F' and resid 90 through 106 removed outlier: 4.379A pdb=" N ILE F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS F 99 " --> pdb=" O GLN F 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 132 removed outlier: 4.219A pdb=" N LEU F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 137 removed outlier: 3.710A pdb=" N ALA F 137 " --> pdb=" O ASP F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 134 through 137' Processing helix chain 'F' and resid 138 through 160 removed outlier: 3.793A pdb=" N MET F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N MET F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 189 Processing helix chain 'F' and resid 194 through 227 removed outlier: 3.814A pdb=" N GLU F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 255 Processing helix chain 'F' and resid 277 through 294 removed outlier: 3.953A pdb=" N GLN F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 334 Processing helix chain 'F' and resid 338 through 354 Processing helix chain 'G' and resid 10 through 26 removed outlier: 3.690A pdb=" N LYS G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 29 No H-bonds generated for 'chain 'G' and resid 27 through 29' Processing helix chain 'G' and resid 49 through 64 removed outlier: 4.096A pdb=" N LEU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 88 Processing helix chain 'G' and resid 90 through 108 removed outlier: 5.305A pdb=" N GLU G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU G 101 " --> pdb=" O ILE G 97 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 133 removed outlier: 5.107A pdb=" N LYS G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 161 removed outlier: 3.804A pdb=" N LEU G 139 " --> pdb=" O PRO G 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 191 removed outlier: 4.017A pdb=" N ALA G 170 " --> pdb=" O ILE G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 227 removed outlier: 4.904A pdb=" N ALA G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 210 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 215 " --> pdb=" O ALA G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 254 removed outlier: 4.526A pdb=" N ILE G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR G 244 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA G 248 " --> pdb=" O THR G 244 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN G 253 " --> pdb=" O TYR G 249 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET G 254 " --> pdb=" O LYS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 287 removed outlier: 4.225A pdb=" N PHE G 285 " --> pdb=" O GLN G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 315 through 334 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'H' and resid 10 through 29 removed outlier: 4.063A pdb=" N HIS H 27 " --> pdb=" O GLY H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 66 Processing helix chain 'H' and resid 70 through 88 Processing helix chain 'H' and resid 90 through 106 Processing helix chain 'H' and resid 110 through 130 removed outlier: 3.958A pdb=" N LYS H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 161 removed outlier: 4.785A pdb=" N LEU H 139 " --> pdb=" O PRO H 135 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 191 removed outlier: 4.052A pdb=" N ALA H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 225 removed outlier: 3.530A pdb=" N ALA H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 254 removed outlier: 3.733A pdb=" N HIS H 238 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU H 243 " --> pdb=" O LYS H 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA H 248 " --> pdb=" O THR H 244 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR H 249 " --> pdb=" O ILE H 245 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 291 removed outlier: 4.559A pdb=" N GLU H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN H 281 " --> pdb=" O GLN H 277 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS H 291 " --> pdb=" O HIS H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 334 removed outlier: 3.536A pdb=" N VAL H 322 " --> pdb=" O GLU H 318 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG H 323 " --> pdb=" O LYS H 319 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS H 324 " --> pdb=" O LYS H 320 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS H 327 " --> pdb=" O ARG H 323 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU H 333 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 334 " --> pdb=" O ALA H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'H' and resid 353 through 355 No H-bonds generated for 'chain 'H' and resid 353 through 355' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.702A pdb=" N GLN A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 257 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 263 removed outlier: 3.848A pdb=" N ILE D 43 " --> pdb=" O PHE D 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 7 removed outlier: 4.054A pdb=" N THR C 257 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 4 removed outlier: 3.740A pdb=" N THR D 311 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS D 261 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 270 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 4 removed outlier: 3.740A pdb=" N THR D 311 " --> pdb=" O THR D 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.698A pdb=" N PHE E 34 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 305 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR F 257 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 257 through 262 removed outlier: 4.116A pdb=" N VAL E 267 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 310 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 7 removed outlier: 3.849A pdb=" N LEU F 41 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL F 32 " --> pdb=" O PHE G 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'H' and resid 259 through 262 removed outlier: 3.645A pdb=" N VAL H 270 " --> pdb=" O LEU H 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 259 through 262 removed outlier: 3.645A pdb=" N VAL H 270 " --> pdb=" O LEU H 259 " (cutoff:3.500A) 1794 hydrogen bonds defined for protein. 5235 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: 6.45 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 2856 1.28 - 1.35: 2842 1.35 - 1.42: 6 1.42 - 1.49: 2854 1.49 - 1.56: 5610 Bond restraints: 14168 Sorted by residual: bond pdb=" CA HIS C 161 " pdb=" C HIS C 161 " ideal model delta sigma weight residual 1.517 1.546 -0.029 1.07e-02 8.73e+03 7.17e+00 bond pdb=" CA ASP B 70 " pdb=" C ASP B 70 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.26e-02 6.30e+03 6.02e+00 bond pdb=" CA ASP E 110 " pdb=" C ASP E 110 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.06e-02 8.90e+03 5.96e+00 bond pdb=" CA ASP A 110 " pdb=" C ASP A 110 " ideal model delta sigma weight residual 1.521 1.550 -0.029 1.19e-02 7.06e+03 5.90e+00 bond pdb=" CA GLN H 42 " pdb=" C GLN H 42 " ideal model delta sigma weight residual 1.521 1.549 -0.028 1.20e-02 6.94e+03 5.60e+00 ... (remaining 14163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14773 1.67 - 3.34: 4206 3.34 - 5.01: 694 5.01 - 6.69: 82 6.69 - 8.36: 5 Bond angle restraints: 19760 Sorted by residual: angle pdb=" C GLU A 44 " pdb=" CA GLU A 44 " pdb=" CB GLU A 44 " ideal model delta sigma weight residual 111.22 117.77 -6.55 1.23e+00 6.61e-01 2.84e+01 angle pdb=" N LEU G 297 " pdb=" CA LEU G 297 " pdb=" C LEU G 297 " ideal model delta sigma weight residual 108.96 116.45 -7.49 1.49e+00 4.50e-01 2.52e+01 angle pdb=" N PHE F 34 " pdb=" CA PHE F 34 " pdb=" CB PHE F 34 " ideal model delta sigma weight residual 110.57 102.21 8.36 1.69e+00 3.50e-01 2.44e+01 angle pdb=" C ILE H 271 " pdb=" CA ILE H 271 " pdb=" CB ILE H 271 " ideal model delta sigma weight residual 111.29 119.21 -7.92 1.64e+00 3.72e-01 2.33e+01 angle pdb=" N PHE B 34 " pdb=" CA PHE B 34 " pdb=" CB PHE B 34 " ideal model delta sigma weight residual 110.71 103.02 7.69 1.66e+00 3.63e-01 2.15e+01 ... (remaining 19755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.84: 6965 5.84 - 11.67: 1068 11.67 - 17.51: 230 17.51 - 23.35: 59 23.35 - 29.18: 30 Dihedral angle restraints: 8352 sinusoidal: 0 harmonic: 8352 Sorted by residual: dihedral pdb=" CA ILE D 299 " pdb=" C ILE D 299 " pdb=" N THR D 300 " pdb=" CA THR D 300 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA THR G 1 " pdb=" C THR G 1 " pdb=" N VAL G 2 " pdb=" CA VAL G 2 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU A 297 " pdb=" C LEU A 297 " pdb=" N SER A 298 " pdb=" CA SER A 298 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2153 0.095 - 0.191: 469 0.191 - 0.286: 110 0.286 - 0.381: 18 0.381 - 0.477: 2 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CA LYS C 200 " pdb=" N LYS C 200 " pdb=" C LYS C 200 " pdb=" CB LYS C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA LEU C 114 " pdb=" N LEU C 114 " pdb=" C LEU C 114 " pdb=" CB LEU C 114 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA ASN H 47 " pdb=" N ASN H 47 " pdb=" C ASN H 47 " pdb=" CB ASN H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 2749 not shown) Planarity restraints: 2848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 142 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C MET C 142 " 0.045 2.00e-02 2.50e+03 pdb=" O MET C 142 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL C 143 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 149 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C LEU A 149 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 149 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 150 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 299 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C ILE D 299 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE D 299 " 0.016 2.00e-02 2.50e+03 pdb=" N THR D 300 " 0.014 2.00e-02 2.50e+03 ... (remaining 2845 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 9812 3.06 - 3.52: 17466 3.52 - 3.98: 17278 3.98 - 4.44: 21137 4.44 - 4.90: 30427 Nonbonded interactions: 96120 Sorted by model distance: nonbonded pdb=" N HIS D 261 " pdb=" O HIS D 261 " model vdw 2.603 2.496 nonbonded pdb=" N GLU A 37 " pdb=" O GLU A 37 " model vdw 2.629 2.496 nonbonded pdb=" N VAL H 270 " pdb=" O VAL H 270 " model vdw 2.633 2.496 nonbonded pdb=" N HIS H 261 " pdb=" O HIS H 261 " model vdw 2.640 2.496 nonbonded pdb=" N LEU D 259 " pdb=" O LEU D 259 " model vdw 2.650 2.496 ... (remaining 96115 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 38.510 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.009 0.032 14168 Z= 0.657 Angle : 1.549 8.356 19760 Z= 1.106 Chirality : 0.087 0.477 2752 Planarity : 0.010 0.026 2848 Dihedral : 7.593 29.184 2848 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 0.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.33 % 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: -1.95 (0.13), residues: 2840 helix: -1.28 (0.09), residues: 2017 sheet: -0.66 (0.28), residues: 268 loop : -0.71 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.500 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1357 time to fit residues: 10.4218 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 0.0060 chunk 219 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14168 Z= 0.212 Angle : 0.439 7.946 19760 Z= 0.307 Chirality : 0.039 0.140 2752 Planarity : 0.003 0.021 2848 Dihedral : 4.606 24.988 2848 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.64 (0.15), residues: 2840 helix: 1.69 (0.11), residues: 2033 sheet: -0.46 (0.25), residues: 332 loop : -0.15 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.525 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1210 time to fit residues: 9.5256 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 14168 Z= 0.302 Angle : 0.485 6.461 19760 Z= 0.351 Chirality : 0.039 0.154 2752 Planarity : 0.003 0.021 2848 Dihedral : 4.771 28.786 2848 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.49 (0.16), residues: 2840 helix: 1.64 (0.11), residues: 2037 sheet: -0.58 (0.27), residues: 332 loop : -0.47 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.387 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1209 time to fit residues: 9.5155 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 14168 Z= 0.207 Angle : 0.387 5.728 19760 Z= 0.275 Chirality : 0.038 0.141 2752 Planarity : 0.002 0.020 2848 Dihedral : 3.981 23.320 2848 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 2.39 (0.16), residues: 2840 helix: 2.39 (0.11), residues: 2036 sheet: -0.63 (0.27), residues: 341 loop : -0.26 (0.33), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.659 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1266 time to fit residues: 10.3086 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 0.4980 chunk 153 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 230 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 14168 Z= 0.172 Angle : 0.350 3.984 19760 Z= 0.246 Chirality : 0.038 0.137 2752 Planarity : 0.002 0.019 2848 Dihedral : 3.667 21.285 2848 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 2.88 (0.16), residues: 2840 helix: 2.81 (0.11), residues: 2056 sheet: -0.75 (0.27), residues: 341 loop : -0.31 (0.34), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 2.373 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2125 time to fit residues: 15.1314 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 142 optimal weight: 0.0050 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 14168 Z= 0.278 Angle : 0.441 5.070 19760 Z= 0.321 Chirality : 0.038 0.154 2752 Planarity : 0.003 0.019 2848 Dihedral : 4.243 24.325 2848 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.95 (0.16), residues: 2840 helix: 2.12 (0.11), residues: 2051 sheet: -1.10 (0.28), residues: 335 loop : -0.53 (0.33), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1350 time to fit residues: 10.8350 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 197 optimal weight: 30.0000 chunk 153 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 14168 Z= 0.227 Angle : 0.390 4.229 19760 Z= 0.282 Chirality : 0.038 0.146 2752 Planarity : 0.002 0.019 2848 Dihedral : 3.882 22.394 2848 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 2.28 (0.16), residues: 2840 helix: 2.42 (0.11), residues: 2057 sheet: -1.25 (0.28), residues: 337 loop : -0.57 (0.33), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.566 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1211 time to fit residues: 9.7127 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 14168 Z= 0.362 Angle : 0.518 5.463 19760 Z= 0.384 Chirality : 0.039 0.168 2752 Planarity : 0.003 0.020 2848 Dihedral : 4.693 26.476 2848 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.98 (0.16), residues: 2840 helix: 1.43 (0.11), residues: 2047 sheet: -1.60 (0.28), residues: 339 loop : -0.81 (0.33), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.650 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1886 time to fit residues: 15.6018 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 7.9990 chunk 258 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 197 optimal weight: 40.0000 chunk 77 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 14168 Z= 0.250 Angle : 0.413 4.359 19760 Z= 0.300 Chirality : 0.038 0.151 2752 Planarity : 0.002 0.020 2848 Dihedral : 4.134 23.127 2848 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.56 (0.16), residues: 2840 helix: 1.94 (0.11), residues: 2057 sheet: -1.68 (0.27), residues: 337 loop : -0.91 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.498 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1213 time to fit residues: 9.5451 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.0000 chunk 265 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 278 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 171 optimal weight: 0.3980 chunk 136 optimal weight: 10.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 14168 Z= 0.195 Angle : 0.364 3.712 19760 Z= 0.261 Chirality : 0.038 0.143 2752 Planarity : 0.002 0.019 2848 Dihedral : 3.781 22.426 2848 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 2.21 (0.17), residues: 2840 helix: 2.48 (0.11), residues: 2067 sheet: -1.72 (0.28), residues: 323 loop : -0.92 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.528 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1296 time to fit residues: 9.9728 Evaluate side-chains 32 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.122752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095928 restraints weight = 39600.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095483 restraints weight = 36726.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096220 restraints weight = 36610.985| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 14168 Z= 0.383 Angle : 0.535 5.350 19760 Z= 0.400 Chirality : 0.039 0.168 2752 Planarity : 0.003 0.020 2848 Dihedral : 4.712 26.154 2848 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.72 (0.16), residues: 2840 helix: 1.30 (0.11), residues: 2050 sheet: -1.84 (0.28), residues: 333 loop : -1.15 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.44 seconds wall clock time: 34 minutes 39.79 seconds (2079.79 seconds total)