Starting phenix.real_space_refine on Sat Oct 11 11:23:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utm_42542/10_2025/8utm_42542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utm_42542/10_2025/8utm_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 { model { file = "/net/cci-nas-00/data/ceres_data/8utm_42542/10_2025/8utm_42542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utm_42542/10_2025/8utm_42542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8utm_42542/10_2025/8utm_42542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utm_42542/10_2025/8utm_42542.map" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} 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: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 521 Time building chain proxies: 4.09, per 1000 atoms: 0.29 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: 1.54 Conformation dependent library (CDL) restraints added in 777.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.63 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: 3.09 Time building geometry restraints manager: 1.82 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: 0.01 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: 0.510 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.000 Find NCS groups from input model: 0.360 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- 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= 0.692 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (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 TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00905 (14168) covalent geometry : angle 1.54869 (19760) hydrogen bonds : bond 0.15768 ( 1774) hydrogen bonds : angle 7.45270 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.470 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0576 time to fit residues: 4.1495 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.131795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102712 restraints weight = 41062.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.104250 restraints weight = 37732.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104610 restraints weight = 32828.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104782 restraints weight = 32178.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105245 restraints weight = 30651.426| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14168 Z= 0.190 Angle : 0.417 6.725 19760 Z= 0.288 Chirality : 0.039 0.144 2752 Planarity : 0.003 0.021 2848 Dihedral : 4.533 24.820 2848 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.15), residues: 2840 helix: 1.78 (0.11), residues: 2039 sheet: -0.37 (0.25), residues: 332 loop : -0.16 (0.32), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00249 (14168) covalent geometry : angle 0.41693 (19760) hydrogen bonds : bond 0.04122 ( 1774) hydrogen bonds : angle 4.19260 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.529 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0629 time to fit residues: 4.5584 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 130 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.124607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093719 restraints weight = 39817.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094784 restraints weight = 36016.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095303 restraints weight = 32000.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095834 restraints weight = 30410.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096072 restraints weight = 29072.834| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 14168 Z= 0.426 Angle : 0.577 7.450 19760 Z= 0.425 Chirality : 0.039 0.163 2752 Planarity : 0.004 0.021 2848 Dihedral : 5.343 32.679 2848 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % 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 : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 2840 helix: 0.82 (0.11), residues: 2026 sheet: -0.92 (0.27), residues: 326 loop : -0.54 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00556 (14168) covalent geometry : angle 0.57703 (19760) hydrogen bonds : bond 0.06227 ( 1774) hydrogen bonds : angle 5.72297 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.557 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0622 time to fit residues: 4.5374 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 213 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 201 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095271 restraints weight = 39916.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096272 restraints weight = 37006.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096539 restraints weight = 33640.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096826 restraints weight = 32434.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097081 restraints weight = 31568.893| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 14168 Z= 0.305 Angle : 0.464 6.911 19760 Z= 0.336 Chirality : 0.039 0.155 2752 Planarity : 0.003 0.020 2848 Dihedral : 4.526 24.984 2848 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.16), residues: 2840 helix: 1.47 (0.11), residues: 2034 sheet: -1.05 (0.27), residues: 334 loop : -0.70 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00399 (14168) covalent geometry : angle 0.46387 (19760) hydrogen bonds : bond 0.04651 ( 1774) hydrogen bonds : angle 4.78090 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.657 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0624 time to fit residues: 4.6391 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097883 restraints weight = 40104.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098999 restraints weight = 37096.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099294 restraints weight = 33446.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099921 restraints weight = 31595.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100076 restraints weight = 30516.463| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 14168 Z= 0.177 Angle : 0.351 3.822 19760 Z= 0.246 Chirality : 0.038 0.136 2752 Planarity : 0.002 0.019 2848 Dihedral : 3.785 21.462 2848 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.16), residues: 2840 helix: 2.48 (0.11), residues: 2049 sheet: -1.03 (0.28), residues: 337 loop : -0.38 (0.33), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00231 (14168) covalent geometry : angle 0.35103 (19760) hydrogen bonds : bond 0.03379 ( 1774) hydrogen bonds : angle 3.87060 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0599 time to fit residues: 4.3444 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 271 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.129053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099528 restraints weight = 40903.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101646 restraints weight = 36205.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101871 restraints weight = 30798.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102715 restraints weight = 29423.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103134 restraints weight = 27597.413| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14168 Z= 0.137 Angle : 0.316 3.939 19760 Z= 0.218 Chirality : 0.038 0.136 2752 Planarity : 0.002 0.020 2848 Dihedral : 3.393 21.882 2848 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.16), residues: 2840 helix: 3.05 (0.11), residues: 2066 sheet: -0.93 (0.28), residues: 343 loop : -0.34 (0.34), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00180 (14168) covalent geometry : angle 0.31618 (19760) hydrogen bonds : bond 0.02907 ( 1774) hydrogen bonds : angle 3.43205 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.534 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0644 time to fit residues: 4.6240 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 132 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.122943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093937 restraints weight = 40691.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095345 restraints weight = 37467.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095914 restraints weight = 32074.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096359 restraints weight = 30158.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096547 restraints weight = 29156.816| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 14168 Z= 0.472 Angle : 0.604 6.637 19760 Z= 0.453 Chirality : 0.039 0.183 2752 Planarity : 0.004 0.019 2848 Dihedral : 5.034 26.139 2848 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2840 helix: 1.08 (0.11), residues: 2042 sheet: -1.66 (0.27), residues: 338 loop : -0.70 (0.33), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00616 (14168) covalent geometry : angle 0.60394 (19760) hydrogen bonds : bond 0.06193 ( 1774) hydrogen bonds : angle 5.79474 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0560 time to fit residues: 4.1121 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 132 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 276 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.125083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096144 restraints weight = 40556.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097316 restraints weight = 38338.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097870 restraints weight = 32733.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098187 restraints weight = 30973.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.098455 restraints weight = 30103.810| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 14168 Z= 0.304 Angle : 0.451 4.868 19760 Z= 0.330 Chirality : 0.039 0.153 2752 Planarity : 0.003 0.020 2848 Dihedral : 4.328 23.862 2848 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.16), residues: 2840 helix: 1.65 (0.11), residues: 2046 sheet: -1.71 (0.27), residues: 337 loop : -0.78 (0.33), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00397 (14168) covalent geometry : angle 0.45130 (19760) hydrogen bonds : bond 0.04579 ( 1774) hydrogen bonds : angle 4.82121 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.522 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0624 time to fit residues: 4.5453 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 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 = 0.3875 r_free = 0.3875 target = 0.122660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093329 restraints weight = 39668.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.093429 restraints weight = 38322.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093729 restraints weight = 36613.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094069 restraints weight = 35550.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094308 restraints weight = 33421.946| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14168 Z= 0.404 Angle : 0.542 5.483 19760 Z= 0.403 Chirality : 0.039 0.167 2752 Planarity : 0.003 0.019 2848 Dihedral : 4.909 25.800 2848 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2840 helix: 0.89 (0.11), residues: 2046 sheet: -1.87 (0.28), residues: 332 loop : -1.16 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00527 (14168) covalent geometry : angle 0.54208 (19760) hydrogen bonds : bond 0.05683 ( 1774) hydrogen bonds : angle 5.63656 ( 5235) *********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.559 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0621 time to fit residues: 4.5685 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.124297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094809 restraints weight = 40291.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095914 restraints weight = 37554.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096372 restraints weight = 33283.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096969 restraints weight = 31252.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097095 restraints weight = 29725.314| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5383 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= 0.314 Angle : 0.459 4.943 19760 Z= 0.336 Chirality : 0.038 0.158 2752 Planarity : 0.003 0.021 2848 Dihedral : 4.426 24.260 2848 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2840 helix: 1.37 (0.11), residues: 2054 sheet: -1.79 (0.28), residues: 321 loop : -1.33 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00410 (14168) covalent geometry : angle 0.45863 (19760) hydrogen bonds : bond 0.04717 ( 1774) hydrogen bonds : angle 5.01565 ( 5235) ********************** 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.508 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0616 time to fit residues: 4.4895 Evaluate side-chains 32 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 103 optimal weight: 0.0770 chunk 261 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.127804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100673 restraints weight = 41499.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103104 restraints weight = 35489.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103669 restraints weight = 29124.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104309 restraints weight = 26834.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104577 restraints weight = 25511.282| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 14168 Z= 0.183 Angle : 0.353 3.554 19760 Z= 0.250 Chirality : 0.038 0.139 2752 Planarity : 0.002 0.020 2848 Dihedral : 3.793 22.627 2848 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.16), residues: 2840 helix: 2.35 (0.11), residues: 2065 sheet: -1.61 (0.28), residues: 321 loop : -1.21 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00239 (14168) covalent geometry : angle 0.35292 (19760) hydrogen bonds : bond 0.03450 ( 1774) hydrogen bonds : angle 4.10523 ( 5235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1767.51 seconds wall clock time: 31 minutes 0.81 seconds (1860.81 seconds total)