Starting phenix.real_space_refine on Wed May 21 08:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej2_31149/05_2025/7ej2_31149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej2_31149/05_2025/7ej2_31149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ej2_31149/05_2025/7ej2_31149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej2_31149/05_2025/7ej2_31149.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej2_31149/05_2025/7ej2_31149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej2_31149/05_2025/7ej2_31149.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 13488 2.51 5 N 3548 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20968 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "E" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "F" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "G" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "H" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 179 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.87, per 1000 atoms: 0.57 Number of scatterers: 20968 At special positions: 0 Unit cell: (128.778, 128.778, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3824 8.00 N 3548 7.00 C 13488 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: 5.20 Conformation dependent library (CDL) restraints added in 2.9 seconds 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 57.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 107 removed outlier: 4.012A pdb=" N ILE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.754A pdb=" N MET A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.662A pdb=" N LYS A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.146A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 140 " --> pdb=" O MET B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.653A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.138A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.733A pdb=" N GLU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 255 removed outlier: 3.501A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.869A pdb=" N ILE B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 344' Processing helix chain 'B' and resid 360 through 370 removed outlier: 3.501A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.682A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 4.320A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.749A pdb=" N LEU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 removed outlier: 4.011A pdb=" N ILE C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.755A pdb=" N MET C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.662A pdb=" N LYS C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 4.146A pdb=" N GLU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER C 353 " --> pdb=" O HIS C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG D 138 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 140 " --> pdb=" O MET D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.653A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 4.138A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.733A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 255 removed outlier: 3.501A pdb=" N ILE D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.869A pdb=" N ILE D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 Processing helix chain 'D' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 339 through 344' Processing helix chain 'D' and resid 360 through 370 removed outlier: 4.159A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.682A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 removed outlier: 4.320A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 419 removed outlier: 3.749A pdb=" N LEU D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 500 " --> pdb=" O GLN D 496 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 removed outlier: 4.012A pdb=" N ILE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.754A pdb=" N MET E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 278 removed outlier: 3.662A pdb=" N LYS E 276 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA E 309 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 removed outlier: 4.146A pdb=" N GLU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 335 " --> pdb=" O MET E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 343 Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG F 138 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 140 " --> pdb=" O MET F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 166 removed outlier: 3.653A pdb=" N ILE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 187 removed outlier: 4.138A pdb=" N GLU F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.733A pdb=" N GLU F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 255 removed outlier: 3.500A pdb=" N ILE F 236 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 Processing helix chain 'F' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS F 302 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.869A pdb=" N ILE F 331 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 336 Processing helix chain 'F' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY F 344 " --> pdb=" O PHE F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 360 through 370 removed outlier: 3.501A pdb=" N ILE F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.683A pdb=" N ARG F 379 " --> pdb=" O LYS F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 removed outlier: 4.321A pdb=" N GLN F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 419 removed outlier: 3.749A pdb=" N LEU F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE F 406 " --> pdb=" O ILE F 402 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 472 " --> pdb=" O GLY F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE F 479 " --> pdb=" O PRO F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR F 499 " --> pdb=" O GLU F 495 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET F 500 " --> pdb=" O GLN F 496 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 107 removed outlier: 4.012A pdb=" N ILE G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR G 169 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.754A pdb=" N MET G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'G' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 278 removed outlier: 3.661A pdb=" N LYS G 276 " --> pdb=" O TRP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 4.145A pdb=" N GLU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER G 353 " --> pdb=" O HIS G 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 123 Processing helix chain 'H' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG H 138 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE H 140 " --> pdb=" O MET H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 166 removed outlier: 3.652A pdb=" N ILE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 187 removed outlier: 4.137A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 199 removed outlier: 3.734A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 255 removed outlier: 3.501A pdb=" N ILE H 236 " --> pdb=" O PRO H 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR H 255 " --> pdb=" O PHE H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 261 Processing helix chain 'H' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.868A pdb=" N ILE H 331 " --> pdb=" O ILE H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 336 Processing helix chain 'H' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU H 343 " --> pdb=" O TYR H 339 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY H 344 " --> pdb=" O PHE H 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 339 through 344' Processing helix chain 'H' and resid 360 through 370 removed outlier: 3.500A pdb=" N ILE H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 379 removed outlier: 3.682A pdb=" N ARG H 379 " --> pdb=" O LYS H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 removed outlier: 4.320A pdb=" N GLN H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE H 386 " --> pdb=" O LYS H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 419 removed outlier: 3.750A pdb=" N LEU H 400 " --> pdb=" O ARG H 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU H 405 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE H 406 " --> pdb=" O ILE H 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE H 466 " --> pdb=" O SER H 462 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 472 " --> pdb=" O GLY H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE H 479 " --> pdb=" O PRO H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET H 500 " --> pdb=" O GLN H 496 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.805A pdb=" N GLY A 53 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 242 " --> pdb=" O LEU A 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.669A pdb=" N ILE A 115 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE A 156 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 117 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN A 214 " --> pdb=" O TRP A 185 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR A 187 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.805A pdb=" N GLY C 53 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 242 " --> pdb=" O LEU C 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.669A pdb=" N ILE C 115 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR C 117 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN C 214 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C 187 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 118 Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.806A pdb=" N GLY E 53 " --> pdb=" O LEU E 322 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 242 " --> pdb=" O LEU E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.668A pdb=" N ILE E 115 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE E 156 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR E 117 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN E 214 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR E 187 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 113 through 118 Processing sheet with id=AB4, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'G' and resid 52 through 54 removed outlier: 6.805A pdb=" N GLY G 53 " --> pdb=" O LEU G 322 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR G 242 " --> pdb=" O LEU G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.668A pdb=" N ILE G 115 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE G 156 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR G 117 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN G 214 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR G 187 " --> pdb=" O GLN G 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 113 through 118 821 hydrogen bonds defined for protein. 2271 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: 5.59 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3392 1.31 - 1.43: 5730 1.43 - 1.56: 12134 1.56 - 1.68: 20 1.68 - 1.80: 160 Bond restraints: 21436 Sorted by residual: bond pdb=" C1B NAP C 401 " pdb=" C2B NAP C 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1B NAP E 401 " pdb=" C2B NAP E 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.312 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1B NAP A 401 " pdb=" C2B NAP A 401 " ideal model delta sigma weight residual 1.528 1.312 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4D NAP C 401 " pdb=" O4D NAP C 401 " ideal model delta sigma weight residual 1.447 1.307 0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 21431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 28569 2.77 - 5.54: 467 5.54 - 8.31: 68 8.31 - 11.08: 16 11.08 - 13.85: 16 Bond angle restraints: 29136 Sorted by residual: angle pdb=" N LEU F 330 " pdb=" CA LEU F 330 " pdb=" C LEU F 330 " ideal model delta sigma weight residual 112.54 120.93 -8.39 1.22e+00 6.72e-01 4.73e+01 angle pdb=" N LEU H 330 " pdb=" CA LEU H 330 " pdb=" C LEU H 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LEU D 330 " pdb=" CA LEU D 330 " pdb=" C LEU D 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LEU B 330 " pdb=" CA LEU B 330 " pdb=" C LEU B 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N1A NAP A 401 " pdb=" C6A NAP A 401 " pdb=" N6A NAP A 401 " ideal model delta sigma weight residual 119.30 105.45 13.85 3.00e+00 1.11e-01 2.13e+01 ... (remaining 29131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 11183 16.93 - 33.85: 1257 33.85 - 50.78: 272 50.78 - 67.71: 104 67.71 - 84.63: 52 Dihedral angle restraints: 12868 sinusoidal: 5020 harmonic: 7848 Sorted by residual: dihedral pdb=" N PHE E 120 " pdb=" C PHE E 120 " pdb=" CA PHE E 120 " pdb=" CB PHE E 120 " ideal model delta harmonic sigma weight residual 122.80 132.04 -9.24 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N PHE A 120 " pdb=" C PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual 122.80 132.03 -9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" N PHE C 120 " pdb=" C PHE C 120 " pdb=" CA PHE C 120 " pdb=" CB PHE C 120 " ideal model delta harmonic sigma weight residual 122.80 132.03 -9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 12865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3065 0.091 - 0.182: 211 0.182 - 0.273: 12 0.273 - 0.364: 8 0.364 - 0.455: 8 Chirality restraints: 3304 Sorted by residual: chirality pdb=" C2B NAP C 401 " pdb=" C1B NAP C 401 " pdb=" C3B NAP C 401 " pdb=" O2B NAP C 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C2B NAP E 401 " pdb=" C1B NAP E 401 " pdb=" C3B NAP E 401 " pdb=" O2B NAP E 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C2B NAP A 401 " pdb=" C1B NAP A 401 " pdb=" C3B NAP A 401 " pdb=" O2B NAP A 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3301 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 337 " 0.051 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO D 338 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 338 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 338 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO B 338 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 337 " -0.051 5.00e-02 4.00e+02 7.78e-02 9.67e+00 pdb=" N PRO H 338 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 338 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 338 " -0.042 5.00e-02 4.00e+02 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6930 2.81 - 3.33: 18292 3.33 - 3.86: 33805 3.86 - 4.38: 40026 4.38 - 4.90: 67707 Nonbonded interactions: 166760 Sorted by model distance: nonbonded pdb=" OH TYR A 184 " pdb=" OE2 GLU G 168 " model vdw 2.290 3.040 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR C 184 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR E 184 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR G 187 " pdb=" OE1 GLU G 213 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR E 187 " pdb=" OE1 GLU E 213 " model vdw 2.302 3.040 ... (remaining 166755 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: 0.15 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 43.890 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 0.217 21436 Z= 0.418 Angle : 0.938 13.854 29136 Z= 0.498 Chirality : 0.058 0.455 3304 Planarity : 0.006 0.086 3700 Dihedral : 16.550 84.632 7820 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.07 % Rotamer: Outliers : 0.19 % Allowed : 18.23 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.99 (0.11), residues: 2696 helix: -4.61 (0.05), residues: 1508 sheet: -2.47 (0.38), residues: 180 loop : -2.81 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 185 HIS 0.004 0.001 HIS E 218 PHE 0.010 0.001 PHE E 120 TYR 0.015 0.002 TYR E 270 ARG 0.003 0.000 ARG C 283 Details of bonding type rmsd hydrogen bonds : bond 0.31943 ( 821) hydrogen bonds : angle 9.75420 ( 2271) covalent geometry : bond 0.00895 (21436) covalent geometry : angle 0.93790 (29136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 551 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7769 (mtm180) REVERT: A 204 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: B 137 MET cc_start: 0.7836 (ttp) cc_final: 0.7584 (tmm) REVERT: B 194 MET cc_start: 0.8597 (tpp) cc_final: 0.8291 (tpt) REVERT: B 375 PHE cc_start: 0.8643 (m-80) cc_final: 0.8371 (m-80) REVERT: B 403 PHE cc_start: 0.8772 (t80) cc_final: 0.8548 (t80) REVERT: B 412 PHE cc_start: 0.9053 (m-80) cc_final: 0.8752 (m-80) REVERT: B 458 LYS cc_start: 0.8456 (mttt) cc_final: 0.7978 (mttm) REVERT: B 484 ASN cc_start: 0.8380 (t0) cc_final: 0.8091 (t0) REVERT: B 489 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7174 (tpt90) REVERT: C 109 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7777 (mtm180) REVERT: C 204 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: D 137 MET cc_start: 0.7836 (ttp) cc_final: 0.7575 (tmm) REVERT: D 141 ASP cc_start: 0.8777 (t0) cc_final: 0.8570 (t70) REVERT: D 194 MET cc_start: 0.8597 (tpp) cc_final: 0.8287 (tpt) REVERT: D 375 PHE cc_start: 0.8639 (m-80) cc_final: 0.8361 (m-80) REVERT: D 403 PHE cc_start: 0.8770 (t80) cc_final: 0.8521 (t80) REVERT: D 412 PHE cc_start: 0.9056 (m-80) cc_final: 0.8746 (m-80) REVERT: D 458 LYS cc_start: 0.8453 (mttt) cc_final: 0.7923 (mttm) REVERT: D 484 ASN cc_start: 0.8377 (t0) cc_final: 0.8088 (t0) REVERT: D 489 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7173 (tpt90) REVERT: E 109 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7785 (mtm180) REVERT: E 204 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: F 137 MET cc_start: 0.7831 (ttp) cc_final: 0.7582 (tmm) REVERT: F 141 ASP cc_start: 0.8771 (t0) cc_final: 0.8563 (t70) REVERT: F 151 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8411 (mtt-85) REVERT: F 194 MET cc_start: 0.8587 (tpp) cc_final: 0.8341 (tpt) REVERT: F 375 PHE cc_start: 0.8637 (m-80) cc_final: 0.8358 (m-80) REVERT: F 412 PHE cc_start: 0.9067 (m-80) cc_final: 0.8739 (m-80) REVERT: F 458 LYS cc_start: 0.8510 (mttt) cc_final: 0.8020 (mttm) REVERT: F 485 TYR cc_start: 0.7975 (t80) cc_final: 0.7743 (t80) REVERT: F 489 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7600 (mtp-110) REVERT: G 109 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7770 (mtm180) REVERT: G 204 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: H 137 MET cc_start: 0.7829 (ttp) cc_final: 0.7570 (tmm) REVERT: H 141 ASP cc_start: 0.8773 (t0) cc_final: 0.8564 (t70) REVERT: H 194 MET cc_start: 0.8589 (tpp) cc_final: 0.8318 (tpt) REVERT: H 375 PHE cc_start: 0.8665 (m-80) cc_final: 0.8390 (m-80) REVERT: H 412 PHE cc_start: 0.9055 (m-80) cc_final: 0.8838 (m-80) REVERT: H 458 LYS cc_start: 0.8528 (mttt) cc_final: 0.8024 (mttm) REVERT: H 489 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7177 (tpt90) outliers start: 4 outliers final: 0 residues processed: 555 average time/residue: 0.3852 time to fit residues: 305.3899 Evaluate side-chains 447 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 443 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain G residue 204 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 152 ASN C 314 ASN D 152 ASN E 314 ASN F 152 ASN G 314 ASN H 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.151988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102466 restraints weight = 30962.773| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.03 r_work: 0.3071 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21436 Z= 0.145 Angle : 0.591 6.146 29136 Z= 0.310 Chirality : 0.042 0.144 3304 Planarity : 0.005 0.051 3700 Dihedral : 10.354 59.075 3220 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.63 % Rotamer: Outliers : 3.34 % Allowed : 17.65 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.13), residues: 2696 helix: -3.05 (0.09), residues: 1496 sheet: -2.13 (0.38), residues: 180 loop : -2.06 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 221 HIS 0.004 0.001 HIS G 135 PHE 0.017 0.001 PHE F 403 TYR 0.016 0.001 TYR E 270 ARG 0.007 0.001 ARG F 214 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 821) hydrogen bonds : angle 5.38904 ( 2271) covalent geometry : bond 0.00319 (21436) covalent geometry : angle 0.59112 (29136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 508 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9105 (m-30) cc_final: 0.8853 (m-30) REVERT: B 137 MET cc_start: 0.8794 (ttp) cc_final: 0.8471 (tmm) REVERT: B 256 LEU cc_start: 0.7844 (tt) cc_final: 0.7613 (tt) REVERT: B 375 PHE cc_start: 0.8797 (m-80) cc_final: 0.8295 (m-80) REVERT: B 391 LEU cc_start: 0.9044 (mt) cc_final: 0.8842 (mp) REVERT: B 398 LEU cc_start: 0.9079 (mp) cc_final: 0.8814 (mp) REVERT: B 403 PHE cc_start: 0.8880 (t80) cc_final: 0.8580 (t80) REVERT: B 407 ILE cc_start: 0.8589 (mm) cc_final: 0.8211 (mm) REVERT: B 412 PHE cc_start: 0.9062 (m-80) cc_final: 0.8797 (m-80) REVERT: B 489 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7294 (tpt90) REVERT: C 78 ASP cc_start: 0.9092 (m-30) cc_final: 0.8838 (m-30) REVERT: D 118 GLN cc_start: 0.9044 (mt0) cc_final: 0.8843 (mm-40) REVERT: D 137 MET cc_start: 0.8784 (ttp) cc_final: 0.8455 (tmm) REVERT: D 375 PHE cc_start: 0.8804 (m-80) cc_final: 0.8271 (m-80) REVERT: D 391 LEU cc_start: 0.9037 (mt) cc_final: 0.8833 (mp) REVERT: D 398 LEU cc_start: 0.9080 (mp) cc_final: 0.8816 (mp) REVERT: D 403 PHE cc_start: 0.8843 (t80) cc_final: 0.8581 (t80) REVERT: D 407 ILE cc_start: 0.8599 (mm) cc_final: 0.8224 (mm) REVERT: D 412 PHE cc_start: 0.9058 (m-80) cc_final: 0.8787 (m-80) REVERT: D 489 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7291 (tpt90) REVERT: E 78 ASP cc_start: 0.9089 (m-30) cc_final: 0.8829 (m-30) REVERT: F 137 MET cc_start: 0.8776 (ttp) cc_final: 0.8453 (tmm) REVERT: F 375 PHE cc_start: 0.8823 (m-80) cc_final: 0.8371 (m-80) REVERT: F 391 LEU cc_start: 0.8981 (mt) cc_final: 0.8766 (mp) REVERT: F 403 PHE cc_start: 0.8824 (t80) cc_final: 0.8609 (t80) REVERT: F 405 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8556 (tp) REVERT: F 407 ILE cc_start: 0.8667 (mm) cc_final: 0.8326 (mm) REVERT: F 412 PHE cc_start: 0.9070 (m-80) cc_final: 0.8843 (m-80) REVERT: F 484 ASN cc_start: 0.8579 (m-40) cc_final: 0.8318 (t0) REVERT: F 489 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7268 (tpt90) REVERT: G 78 ASP cc_start: 0.9081 (m-30) cc_final: 0.8822 (m-30) REVERT: H 118 GLN cc_start: 0.9033 (mt0) cc_final: 0.8826 (mm-40) REVERT: H 137 MET cc_start: 0.8778 (ttp) cc_final: 0.8456 (tmm) REVERT: H 375 PHE cc_start: 0.8793 (m-80) cc_final: 0.8274 (m-80) REVERT: H 398 LEU cc_start: 0.9092 (mp) cc_final: 0.8831 (mp) REVERT: H 403 PHE cc_start: 0.8914 (t80) cc_final: 0.8630 (t80) REVERT: H 407 ILE cc_start: 0.8667 (mm) cc_final: 0.8337 (mm) REVERT: H 412 PHE cc_start: 0.9066 (m-80) cc_final: 0.8793 (m-80) REVERT: H 484 ASN cc_start: 0.8601 (m-40) cc_final: 0.8327 (t0) REVERT: H 489 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7284 (tpt90) outliers start: 70 outliers final: 39 residues processed: 554 average time/residue: 0.3123 time to fit residues: 265.6013 Evaluate side-chains 490 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 450 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 49 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.151090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102732 restraints weight = 30200.658| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.11 r_work: 0.3011 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 21436 Z= 0.218 Angle : 0.621 8.314 29136 Z= 0.314 Chirality : 0.044 0.152 3304 Planarity : 0.004 0.043 3700 Dihedral : 8.517 56.290 3208 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.86 % Favored : 97.00 % Rotamer: Outliers : 3.34 % Allowed : 18.08 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.15), residues: 2696 helix: -1.87 (0.12), residues: 1492 sheet: -1.95 (0.38), residues: 180 loop : -1.82 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 221 HIS 0.005 0.001 HIS F 380 PHE 0.014 0.002 PHE D 259 TYR 0.016 0.002 TYR B 339 ARG 0.004 0.001 ARG H 144 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 821) hydrogen bonds : angle 4.76813 ( 2271) covalent geometry : bond 0.00509 (21436) covalent geometry : angle 0.62073 (29136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 466 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 MET cc_start: 0.8858 (ttp) cc_final: 0.8514 (tmm) REVERT: B 375 PHE cc_start: 0.8789 (m-80) cc_final: 0.8329 (m-80) REVERT: B 403 PHE cc_start: 0.8921 (t80) cc_final: 0.8488 (t80) REVERT: B 407 ILE cc_start: 0.8651 (mm) cc_final: 0.8241 (mm) REVERT: B 489 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7346 (tpt90) REVERT: D 137 MET cc_start: 0.8847 (ttp) cc_final: 0.8497 (tmm) REVERT: D 375 PHE cc_start: 0.8794 (m-80) cc_final: 0.8343 (m-80) REVERT: D 403 PHE cc_start: 0.8861 (t80) cc_final: 0.8428 (t80) REVERT: D 407 ILE cc_start: 0.8627 (mm) cc_final: 0.8217 (mm) REVERT: D 489 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7352 (tpt90) REVERT: F 118 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8845 (mt0) REVERT: F 137 MET cc_start: 0.8839 (ttp) cc_final: 0.8497 (tmm) REVERT: F 375 PHE cc_start: 0.8794 (m-80) cc_final: 0.8403 (m-80) REVERT: F 405 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8627 (tp) REVERT: F 484 ASN cc_start: 0.8649 (m-40) cc_final: 0.8440 (t0) REVERT: F 489 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7320 (tpt90) REVERT: H 137 MET cc_start: 0.8852 (ttp) cc_final: 0.8503 (tmm) REVERT: H 375 PHE cc_start: 0.8779 (m-80) cc_final: 0.8340 (m-80) REVERT: H 470 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8019 (tp) REVERT: H 484 ASN cc_start: 0.8645 (m-40) cc_final: 0.8383 (t0) REVERT: H 489 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7304 (tpt90) outliers start: 70 outliers final: 55 residues processed: 515 average time/residue: 0.3128 time to fit residues: 248.4235 Evaluate side-chains 496 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 439 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 116 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 242 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS C 175 HIS E 175 HIS G 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.153275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104386 restraints weight = 30246.105| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.17 r_work: 0.3081 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21436 Z= 0.125 Angle : 0.560 8.658 29136 Z= 0.281 Chirality : 0.041 0.131 3304 Planarity : 0.004 0.041 3700 Dihedral : 7.235 59.781 3208 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.11 % Favored : 97.74 % Rotamer: Outliers : 4.20 % Allowed : 19.08 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.16), residues: 2696 helix: -1.35 (0.13), residues: 1504 sheet: -1.87 (0.38), residues: 176 loop : -1.50 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 221 HIS 0.005 0.001 HIS D 380 PHE 0.019 0.001 PHE B 216 TYR 0.015 0.001 TYR H 339 ARG 0.013 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 821) hydrogen bonds : angle 4.43774 ( 2271) covalent geometry : bond 0.00285 (21436) covalent geometry : angle 0.56031 (29136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 452 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 MET cc_start: 0.8881 (ttp) cc_final: 0.8500 (tmm) REVERT: B 258 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6634 (tm-30) REVERT: B 296 PHE cc_start: 0.7320 (t80) cc_final: 0.7046 (m-10) REVERT: B 339 TYR cc_start: 0.6158 (t80) cc_final: 0.5748 (t80) REVERT: B 375 PHE cc_start: 0.8847 (m-80) cc_final: 0.8480 (m-80) REVERT: B 403 PHE cc_start: 0.8889 (t80) cc_final: 0.8651 (t80) REVERT: B 405 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8614 (tp) REVERT: B 407 ILE cc_start: 0.8586 (mm) cc_final: 0.8228 (pt) REVERT: B 412 PHE cc_start: 0.9152 (m-80) cc_final: 0.8716 (m-80) REVERT: B 489 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7370 (tpt90) REVERT: D 118 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8766 (mt0) REVERT: D 137 MET cc_start: 0.8857 (ttp) cc_final: 0.8475 (tmm) REVERT: D 339 TYR cc_start: 0.6153 (t80) cc_final: 0.5771 (t80) REVERT: D 375 PHE cc_start: 0.8812 (m-80) cc_final: 0.8458 (m-80) REVERT: D 403 PHE cc_start: 0.8875 (t80) cc_final: 0.8439 (t80) REVERT: D 405 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8622 (tp) REVERT: D 407 ILE cc_start: 0.8570 (mm) cc_final: 0.8115 (mm) REVERT: D 412 PHE cc_start: 0.9167 (m-80) cc_final: 0.8733 (m-80) REVERT: D 489 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7375 (tpt90) REVERT: E 128 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8006 (mt-10) REVERT: F 137 MET cc_start: 0.8853 (ttp) cc_final: 0.8472 (tmm) REVERT: F 339 TYR cc_start: 0.6158 (t80) cc_final: 0.5743 (t80) REVERT: F 375 PHE cc_start: 0.8811 (m-80) cc_final: 0.8455 (m-80) REVERT: F 405 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8627 (tp) REVERT: F 412 PHE cc_start: 0.9197 (m-80) cc_final: 0.8808 (m-80) REVERT: F 489 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7316 (tpt90) REVERT: G 109 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8079 (mtm180) REVERT: H 118 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8754 (mt0) REVERT: H 137 MET cc_start: 0.8845 (ttp) cc_final: 0.8457 (tmm) REVERT: H 339 TYR cc_start: 0.6138 (t80) cc_final: 0.5765 (t80) REVERT: H 375 PHE cc_start: 0.8823 (m-80) cc_final: 0.8457 (m-80) REVERT: H 405 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8607 (tp) REVERT: H 412 PHE cc_start: 0.9166 (m-80) cc_final: 0.8737 (m-80) REVERT: H 484 ASN cc_start: 0.8591 (m-40) cc_final: 0.8386 (t0) REVERT: H 489 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7366 (tpt90) outliers start: 88 outliers final: 43 residues processed: 514 average time/residue: 0.3284 time to fit residues: 263.3270 Evaluate side-chains 475 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 428 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 72 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 249 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN C 285 GLN E 285 GLN G 285 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102774 restraints weight = 30301.862| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.96 r_work: 0.3085 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21436 Z= 0.159 Angle : 0.579 8.620 29136 Z= 0.291 Chirality : 0.043 0.221 3304 Planarity : 0.004 0.039 3700 Dihedral : 6.887 54.792 3208 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.52 % Favored : 97.33 % Rotamer: Outliers : 3.53 % Allowed : 19.37 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2696 helix: -1.02 (0.13), residues: 1504 sheet: -1.86 (0.38), residues: 176 loop : -1.36 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 221 HIS 0.004 0.001 HIS H 380 PHE 0.019 0.001 PHE H 403 TYR 0.011 0.001 TYR E 270 ARG 0.014 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 821) hydrogen bonds : angle 4.30766 ( 2271) covalent geometry : bond 0.00377 (21436) covalent geometry : angle 0.57945 (29136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 453 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 137 MET cc_start: 0.8816 (ttp) cc_final: 0.8459 (tmm) REVERT: B 241 VAL cc_start: 0.7951 (t) cc_final: 0.7729 (p) REVERT: B 245 LEU cc_start: 0.8752 (mt) cc_final: 0.8550 (mt) REVERT: B 296 PHE cc_start: 0.7220 (t80) cc_final: 0.7011 (m-10) REVERT: B 339 TYR cc_start: 0.6254 (t80) cc_final: 0.5827 (t80) REVERT: B 375 PHE cc_start: 0.8791 (m-80) cc_final: 0.8541 (m-80) REVERT: B 403 PHE cc_start: 0.8904 (t80) cc_final: 0.8666 (t80) REVERT: B 412 PHE cc_start: 0.9149 (m-80) cc_final: 0.8716 (m-80) REVERT: B 489 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7381 (tpt90) REVERT: D 137 MET cc_start: 0.8811 (ttp) cc_final: 0.8450 (tmm) REVERT: D 339 TYR cc_start: 0.6229 (t80) cc_final: 0.5794 (t80) REVERT: D 375 PHE cc_start: 0.8770 (m-80) cc_final: 0.8560 (m-80) REVERT: D 403 PHE cc_start: 0.8886 (t80) cc_final: 0.8647 (t80) REVERT: D 412 PHE cc_start: 0.9164 (m-80) cc_final: 0.8731 (m-80) REVERT: D 489 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7371 (tpt90) REVERT: F 137 MET cc_start: 0.8813 (ttp) cc_final: 0.8461 (tmm) REVERT: F 339 TYR cc_start: 0.6272 (t80) cc_final: 0.5842 (t80) REVERT: F 375 PHE cc_start: 0.8777 (m-80) cc_final: 0.8538 (m-80) REVERT: F 412 PHE cc_start: 0.9171 (m-80) cc_final: 0.8793 (m-80) REVERT: F 489 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7342 (tpt90) REVERT: G 128 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8303 (mt-10) REVERT: H 137 MET cc_start: 0.8796 (ttp) cc_final: 0.8437 (tmm) REVERT: H 241 VAL cc_start: 0.7952 (t) cc_final: 0.7736 (p) REVERT: H 339 TYR cc_start: 0.6167 (t80) cc_final: 0.5742 (t80) REVERT: H 375 PHE cc_start: 0.8774 (m-80) cc_final: 0.8523 (m-80) REVERT: H 412 PHE cc_start: 0.9167 (m-80) cc_final: 0.8734 (m-80) REVERT: H 484 ASN cc_start: 0.8613 (m-40) cc_final: 0.8404 (t0) REVERT: H 489 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7370 (tpt90) outliers start: 74 outliers final: 58 residues processed: 505 average time/residue: 0.3248 time to fit residues: 251.4968 Evaluate side-chains 493 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 435 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 20 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 154 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 135 HIS E 135 HIS E 285 GLN G 135 HIS G 285 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101629 restraints weight = 30561.610| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.43 r_work: 0.2979 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21436 Z= 0.243 Angle : 0.639 9.638 29136 Z= 0.321 Chirality : 0.045 0.181 3304 Planarity : 0.004 0.044 3700 Dihedral : 7.083 51.858 3208 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.67 % Allowed : 19.94 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2696 helix: -0.90 (0.13), residues: 1480 sheet: -2.10 (0.37), residues: 180 loop : -1.40 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 185 HIS 0.004 0.001 HIS B 380 PHE 0.020 0.002 PHE H 216 TYR 0.014 0.002 TYR A 184 ARG 0.007 0.001 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 821) hydrogen bonds : angle 4.36993 ( 2271) covalent geometry : bond 0.00574 (21436) covalent geometry : angle 0.63884 (29136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 440 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8402 (mtp-110) REVERT: B 137 MET cc_start: 0.8970 (ttp) cc_final: 0.8511 (tmm) REVERT: B 241 VAL cc_start: 0.7932 (t) cc_final: 0.7726 (p) REVERT: B 339 TYR cc_start: 0.6365 (t80) cc_final: 0.6016 (t80) REVERT: B 403 PHE cc_start: 0.9000 (t80) cc_final: 0.8758 (t80) REVERT: B 412 PHE cc_start: 0.9172 (m-80) cc_final: 0.8823 (m-80) REVERT: B 489 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7467 (tpt170) REVERT: C 128 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8452 (mt-10) REVERT: D 137 MET cc_start: 0.8982 (ttp) cc_final: 0.8523 (tmm) REVERT: D 339 TYR cc_start: 0.6286 (t80) cc_final: 0.5920 (t80) REVERT: D 375 PHE cc_start: 0.8781 (m-80) cc_final: 0.8421 (m-80) REVERT: D 403 PHE cc_start: 0.8933 (t80) cc_final: 0.8712 (t80) REVERT: D 412 PHE cc_start: 0.9179 (m-80) cc_final: 0.8826 (m-80) REVERT: D 489 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7463 (tpt170) REVERT: E 128 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8213 (mt-10) REVERT: F 137 MET cc_start: 0.9001 (ttp) cc_final: 0.8531 (tmm) REVERT: F 339 TYR cc_start: 0.6343 (t80) cc_final: 0.5940 (t80) REVERT: F 412 PHE cc_start: 0.9188 (m-80) cc_final: 0.8853 (m-80) REVERT: F 489 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7459 (tpt170) REVERT: H 137 MET cc_start: 0.8974 (ttp) cc_final: 0.8510 (tmm) REVERT: H 339 TYR cc_start: 0.6249 (t80) cc_final: 0.5891 (t80) REVERT: H 375 PHE cc_start: 0.8771 (m-80) cc_final: 0.8450 (m-80) REVERT: H 412 PHE cc_start: 0.9166 (m-80) cc_final: 0.8804 (m-80) REVERT: H 489 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7452 (tpt170) outliers start: 77 outliers final: 64 residues processed: 494 average time/residue: 0.3107 time to fit residues: 235.7907 Evaluate side-chains 504 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 440 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 227 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN E 285 GLN G 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106132 restraints weight = 30200.261| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.08 r_work: 0.3106 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21436 Z= 0.124 Angle : 0.574 9.369 29136 Z= 0.286 Chirality : 0.042 0.152 3304 Planarity : 0.004 0.040 3700 Dihedral : 6.860 59.667 3208 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.01 % Allowed : 20.47 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2696 helix: -0.64 (0.14), residues: 1484 sheet: -1.98 (0.46), residues: 136 loop : -1.41 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 185 HIS 0.003 0.001 HIS B 380 PHE 0.022 0.001 PHE H 403 TYR 0.011 0.001 TYR C 270 ARG 0.004 0.000 ARG F 144 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 821) hydrogen bonds : angle 4.14674 ( 2271) covalent geometry : bond 0.00289 (21436) covalent geometry : angle 0.57370 (29136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 469 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 137 MET cc_start: 0.8887 (ttp) cc_final: 0.8488 (tmm) REVERT: B 217 GLN cc_start: 0.5853 (tp-100) cc_final: 0.5458 (mm-40) REVERT: B 339 TYR cc_start: 0.6422 (t80) cc_final: 0.6068 (t80) REVERT: B 375 PHE cc_start: 0.8785 (m-80) cc_final: 0.8501 (m-80) REVERT: B 412 PHE cc_start: 0.9159 (m-80) cc_final: 0.8821 (m-80) REVERT: B 489 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7414 (tpt170) REVERT: C 109 ARG cc_start: 0.8532 (mtm180) cc_final: 0.8170 (mtm180) REVERT: C 128 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 285 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7874 (mm-40) REVERT: D 137 MET cc_start: 0.8872 (ttp) cc_final: 0.8465 (tmm) REVERT: D 339 TYR cc_start: 0.6373 (t80) cc_final: 0.6008 (t80) REVERT: D 375 PHE cc_start: 0.8820 (m-80) cc_final: 0.8559 (m-80) REVERT: D 412 PHE cc_start: 0.9185 (m-80) cc_final: 0.8863 (m-80) REVERT: D 489 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7407 (tpt170) REVERT: E 128 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 137 MET cc_start: 0.8855 (ttp) cc_final: 0.8451 (tmm) REVERT: F 217 GLN cc_start: 0.5881 (tp-100) cc_final: 0.5535 (mm-40) REVERT: F 339 TYR cc_start: 0.6296 (t80) cc_final: 0.5880 (t80) REVERT: F 375 PHE cc_start: 0.8783 (m-80) cc_final: 0.8490 (m-80) REVERT: F 412 PHE cc_start: 0.9189 (m-80) cc_final: 0.8863 (m-80) REVERT: F 489 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7354 (tpt170) REVERT: H 137 MET cc_start: 0.8851 (ttp) cc_final: 0.8450 (tmm) REVERT: H 339 TYR cc_start: 0.6372 (t80) cc_final: 0.6016 (t80) REVERT: H 375 PHE cc_start: 0.8804 (m-80) cc_final: 0.8503 (m-80) REVERT: H 412 PHE cc_start: 0.9163 (m-80) cc_final: 0.8811 (m-80) REVERT: H 489 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7381 (tpt170) outliers start: 63 outliers final: 59 residues processed: 519 average time/residue: 0.3094 time to fit residues: 247.4374 Evaluate side-chains 494 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 434 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 73 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 236 optimal weight: 0.0030 chunk 29 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 218 optimal weight: 0.0370 chunk 195 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.9270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105890 restraints weight = 30479.085| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.32 r_work: 0.3090 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21436 Z= 0.139 Angle : 0.594 10.144 29136 Z= 0.296 Chirality : 0.042 0.151 3304 Planarity : 0.004 0.040 3700 Dihedral : 6.711 56.585 3208 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.01 % Allowed : 21.76 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2696 helix: -0.49 (0.14), residues: 1480 sheet: -1.91 (0.46), residues: 136 loop : -1.37 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 185 HIS 0.002 0.000 HIS C 218 PHE 0.031 0.001 PHE D 403 TYR 0.011 0.001 TYR C 270 ARG 0.006 0.000 ARG F 144 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 821) hydrogen bonds : angle 4.12845 ( 2271) covalent geometry : bond 0.00336 (21436) covalent geometry : angle 0.59368 (29136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 454 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 137 MET cc_start: 0.8898 (ttp) cc_final: 0.8483 (tmm) REVERT: B 217 GLN cc_start: 0.5867 (tp-100) cc_final: 0.5449 (mm-40) REVERT: B 339 TYR cc_start: 0.6484 (t80) cc_final: 0.6134 (t80) REVERT: B 375 PHE cc_start: 0.8774 (m-80) cc_final: 0.8484 (m-80) REVERT: B 412 PHE cc_start: 0.9175 (m-80) cc_final: 0.8754 (m-80) REVERT: B 442 MET cc_start: 0.8849 (mtm) cc_final: 0.7864 (mmt) REVERT: B 489 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7400 (tpt170) REVERT: C 109 ARG cc_start: 0.8545 (mtm180) cc_final: 0.8148 (mtm180) REVERT: D 137 MET cc_start: 0.8896 (ttp) cc_final: 0.8460 (tmm) REVERT: D 339 TYR cc_start: 0.6466 (t80) cc_final: 0.6077 (t80) REVERT: D 375 PHE cc_start: 0.8806 (m-80) cc_final: 0.8503 (m-80) REVERT: D 412 PHE cc_start: 0.9198 (m-80) cc_final: 0.8780 (m-80) REVERT: D 442 MET cc_start: 0.8851 (mtm) cc_final: 0.7869 (mmt) REVERT: D 489 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7396 (tpt170) REVERT: E 128 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8300 (mt-10) REVERT: F 137 MET cc_start: 0.8875 (ttp) cc_final: 0.8458 (tmm) REVERT: F 217 GLN cc_start: 0.5862 (tp-100) cc_final: 0.5523 (mm-40) REVERT: F 339 TYR cc_start: 0.6391 (t80) cc_final: 0.5960 (t80) REVERT: F 375 PHE cc_start: 0.8772 (m-80) cc_final: 0.8427 (m-80) REVERT: F 412 PHE cc_start: 0.9195 (m-80) cc_final: 0.8771 (m-80) REVERT: F 442 MET cc_start: 0.8899 (mtm) cc_final: 0.7947 (mmt) REVERT: F 489 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7325 (tpt170) REVERT: H 137 MET cc_start: 0.8886 (ttp) cc_final: 0.8454 (tmm) REVERT: H 339 TYR cc_start: 0.6463 (t80) cc_final: 0.6083 (t80) REVERT: H 375 PHE cc_start: 0.8816 (m-80) cc_final: 0.8433 (m-80) REVERT: H 412 PHE cc_start: 0.9158 (m-80) cc_final: 0.8832 (m-80) REVERT: H 489 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7340 (tpt170) outliers start: 63 outliers final: 57 residues processed: 501 average time/residue: 0.3145 time to fit residues: 242.7195 Evaluate side-chains 500 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 443 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 134 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN C 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104444 restraints weight = 30325.921| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.3132 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21436 Z= 0.126 Angle : 0.593 11.737 29136 Z= 0.295 Chirality : 0.042 0.146 3304 Planarity : 0.004 0.038 3700 Dihedral : 6.464 47.661 3208 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.91 % Allowed : 22.33 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2696 helix: -0.34 (0.14), residues: 1484 sheet: -1.99 (0.45), residues: 140 loop : -1.32 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 185 HIS 0.005 0.001 HIS D 380 PHE 0.026 0.001 PHE H 403 TYR 0.011 0.001 TYR A 270 ARG 0.009 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 821) hydrogen bonds : angle 4.05206 ( 2271) covalent geometry : bond 0.00296 (21436) covalent geometry : angle 0.59277 (29136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 466 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 137 MET cc_start: 0.8802 (ttp) cc_final: 0.8412 (tmm) REVERT: B 217 GLN cc_start: 0.5930 (tp-100) cc_final: 0.5519 (mm-40) REVERT: B 339 TYR cc_start: 0.6514 (t80) cc_final: 0.6144 (t80) REVERT: B 375 PHE cc_start: 0.8730 (m-80) cc_final: 0.8320 (m-80) REVERT: B 412 PHE cc_start: 0.9125 (m-80) cc_final: 0.8707 (m-80) REVERT: B 442 MET cc_start: 0.8782 (mtm) cc_final: 0.7867 (mmt) REVERT: B 489 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7380 (tpt170) REVERT: C 109 ARG cc_start: 0.8451 (mtm180) cc_final: 0.8050 (mtm180) REVERT: D 137 MET cc_start: 0.8771 (ttp) cc_final: 0.8378 (tmm) REVERT: D 339 TYR cc_start: 0.6469 (t80) cc_final: 0.6084 (t80) REVERT: D 375 PHE cc_start: 0.8790 (m-80) cc_final: 0.8426 (m-10) REVERT: D 412 PHE cc_start: 0.9146 (m-80) cc_final: 0.8746 (m-80) REVERT: D 442 MET cc_start: 0.8802 (mtm) cc_final: 0.7871 (mmt) REVERT: D 489 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7311 (tpt170) REVERT: E 128 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8104 (mt-10) REVERT: F 137 MET cc_start: 0.8762 (ttp) cc_final: 0.8374 (tmm) REVERT: F 217 GLN cc_start: 0.5902 (tp-100) cc_final: 0.5474 (mm-40) REVERT: F 339 TYR cc_start: 0.6455 (t80) cc_final: 0.6028 (t80) REVERT: F 412 PHE cc_start: 0.9146 (m-80) cc_final: 0.8838 (m-80) REVERT: F 489 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7318 (tpt170) REVERT: H 137 MET cc_start: 0.8758 (ttp) cc_final: 0.8373 (tmm) REVERT: H 339 TYR cc_start: 0.6464 (t80) cc_final: 0.6084 (t80) REVERT: H 375 PHE cc_start: 0.8773 (m-80) cc_final: 0.8336 (m-80) REVERT: H 412 PHE cc_start: 0.9129 (m-80) cc_final: 0.8709 (m-80) REVERT: H 442 MET cc_start: 0.8822 (mtm) cc_final: 0.7900 (mmt) REVERT: H 489 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7308 (tpt170) outliers start: 61 outliers final: 52 residues processed: 513 average time/residue: 0.3283 time to fit residues: 259.5793 Evaluate side-chains 501 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 449 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 252 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 134 optimal weight: 0.0010 chunk 29 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.154262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106898 restraints weight = 30431.060| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.16 r_work: 0.3131 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21436 Z= 0.121 Angle : 0.594 11.740 29136 Z= 0.295 Chirality : 0.042 0.146 3304 Planarity : 0.003 0.037 3700 Dihedral : 6.311 47.074 3208 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.53 % Allowed : 23.66 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2696 helix: -0.14 (0.14), residues: 1456 sheet: -1.98 (0.45), residues: 140 loop : -1.23 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.005 0.001 HIS D 380 PHE 0.035 0.001 PHE B 403 TYR 0.010 0.001 TYR C 270 ARG 0.007 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 821) hydrogen bonds : angle 4.02092 ( 2271) covalent geometry : bond 0.00287 (21436) covalent geometry : angle 0.59369 (29136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 453 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 137 MET cc_start: 0.8855 (ttp) cc_final: 0.8447 (tmm) REVERT: B 217 GLN cc_start: 0.5845 (tp-100) cc_final: 0.5460 (mm-40) REVERT: B 339 TYR cc_start: 0.6535 (t80) cc_final: 0.6161 (t80) REVERT: B 412 PHE cc_start: 0.9121 (m-80) cc_final: 0.8705 (m-80) REVERT: B 442 MET cc_start: 0.8818 (mtm) cc_final: 0.7958 (mmt) REVERT: B 489 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7306 (tpt170) REVERT: C 109 ARG cc_start: 0.8495 (mtm180) cc_final: 0.8085 (mtm180) REVERT: D 137 MET cc_start: 0.8880 (ttp) cc_final: 0.8464 (tmm) REVERT: D 217 GLN cc_start: 0.5827 (tp-100) cc_final: 0.5467 (mm-40) REVERT: D 339 TYR cc_start: 0.6484 (t80) cc_final: 0.6091 (t80) REVERT: D 375 PHE cc_start: 0.8776 (m-80) cc_final: 0.8452 (m-10) REVERT: D 412 PHE cc_start: 0.9136 (m-80) cc_final: 0.8725 (m-80) REVERT: D 442 MET cc_start: 0.8814 (mtm) cc_final: 0.8031 (mmt) REVERT: D 489 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7303 (tpt170) REVERT: F 137 MET cc_start: 0.8879 (ttp) cc_final: 0.8455 (tmm) REVERT: F 217 GLN cc_start: 0.5740 (tp-100) cc_final: 0.5378 (mm-40) REVERT: F 339 TYR cc_start: 0.6435 (t80) cc_final: 0.6022 (t80) REVERT: F 412 PHE cc_start: 0.9145 (m-80) cc_final: 0.8747 (m-80) REVERT: F 442 MET cc_start: 0.8857 (mtm) cc_final: 0.8036 (mmt) REVERT: F 489 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7274 (tpt170) REVERT: H 137 MET cc_start: 0.8849 (ttp) cc_final: 0.8435 (tmm) REVERT: H 217 GLN cc_start: 0.5762 (tp-100) cc_final: 0.5389 (mm-40) REVERT: H 339 TYR cc_start: 0.6470 (t80) cc_final: 0.6085 (t80) REVERT: H 412 PHE cc_start: 0.9099 (m-80) cc_final: 0.8761 (m-80) REVERT: H 489 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7300 (tpt170) outliers start: 53 outliers final: 49 residues processed: 489 average time/residue: 0.3115 time to fit residues: 234.3666 Evaluate side-chains 497 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 448 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.1503 > 50: distance: 25 - 33: 3.070 distance: 80 - 82: 17.716 distance: 82 - 83: 13.842 distance: 83 - 84: 10.755 distance: 84 - 85: 17.055 distance: 84 - 86: 15.864 distance: 86 - 87: 8.864 distance: 87 - 88: 6.405 distance: 87 - 90: 16.153 distance: 88 - 89: 13.801 distance: 88 - 95: 15.840 distance: 90 - 91: 6.392 distance: 91 - 92: 9.577 distance: 92 - 93: 10.645 distance: 93 - 94: 17.927 distance: 95 - 96: 8.718 distance: 96 - 97: 21.909 distance: 97 - 103: 4.458 distance: 98 - 120: 22.985 distance: 99 - 100: 11.225 distance: 99 - 101: 13.648 distance: 100 - 102: 14.188 distance: 103 - 104: 17.299 distance: 104 - 105: 15.688 distance: 104 - 107: 19.558 distance: 105 - 106: 9.765 distance: 105 - 110: 10.332 distance: 106 - 128: 28.378 distance: 107 - 108: 6.642 distance: 107 - 109: 4.009 distance: 110 - 111: 12.389 distance: 111 - 112: 24.501 distance: 112 - 113: 23.641 distance: 112 - 114: 15.803 distance: 113 - 134: 32.453 distance: 114 - 115: 19.913 distance: 115 - 116: 12.374 distance: 115 - 118: 18.576 distance: 116 - 117: 29.947 distance: 116 - 120: 14.178 distance: 118 - 119: 14.404 distance: 120 - 121: 6.837 distance: 121 - 122: 22.305 distance: 121 - 124: 12.390 distance: 122 - 123: 10.166 distance: 122 - 128: 3.921 distance: 123 - 147: 20.965 distance: 124 - 125: 9.377 distance: 125 - 126: 30.496 distance: 125 - 127: 37.158 distance: 128 - 129: 9.024 distance: 129 - 130: 9.292 distance: 129 - 132: 11.841 distance: 130 - 134: 15.125 distance: 131 - 152: 8.891 distance: 132 - 133: 18.182 distance: 134 - 135: 11.860 distance: 135 - 136: 16.746 distance: 135 - 138: 14.127 distance: 136 - 137: 5.051 distance: 136 - 139: 20.245 distance: 137 - 156: 14.629 distance: 139 - 140: 13.947 distance: 140 - 141: 15.893 distance: 140 - 143: 9.892 distance: 141 - 142: 13.291 distance: 141 - 147: 8.956 distance: 143 - 144: 13.580 distance: 143 - 145: 14.709 distance: 144 - 146: 16.504