Starting phenix.real_space_refine on Fri Sep 19 10:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzp_18779/09_2025/8qzp_18779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzp_18779/09_2025/8qzp_18779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qzp_18779/09_2025/8qzp_18779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzp_18779/09_2025/8qzp_18779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qzp_18779/09_2025/8qzp_18779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzp_18779/09_2025/8qzp_18779.map" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.107 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 16273 2.51 5 N 4419 2.21 5 O 4589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25393 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3201 Classifications: {'peptide': 413} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 26, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3208 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 387} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3217 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 389} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3407 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 414} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3112 Classifications: {'peptide': 401} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3090 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 24, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 370} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3090 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 24, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.64, per 1000 atoms: 0.22 Number of scatterers: 25393 At special positions: 0 Unit cell: (104.64, 150.42, 149.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4589 8.00 N 4419 7.00 C 16273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 944.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 13 sheets defined 63.5% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.628A pdb=" N VAL A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.751A pdb=" N LEU A 207 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.956A pdb=" N ARG A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.599A pdb=" N ALA A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.631A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.562A pdb=" N ALA A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.581A pdb=" N HIS A 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.943A pdb=" N GLY A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.905A pdb=" N SER A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 419 through 432 removed outlier: 3.619A pdb=" N TYR A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.974A pdb=" N LEU A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 447 through 460 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.677A pdb=" N LEU B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 200 through 208 Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 215 through 243 removed outlier: 3.633A pdb=" N ARG B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.902A pdb=" N ALA B 242 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 294 through 306 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 327 Proline residue: B 324 - end of helix removed outlier: 3.808A pdb=" N GLY B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 327' Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.869A pdb=" N VAL B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 372 through 390 removed outlier: 4.084A pdb=" N LYS B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.577A pdb=" N SER B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 419 through 432 removed outlier: 4.354A pdb=" N TYR B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 459 removed outlier: 3.957A pdb=" N LEU B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 4.425A pdb=" N ALA B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.829A pdb=" N ARG B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 507 " --> pdb=" O THR B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 507' Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 151 through 165 Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.836A pdb=" N LEU C 173 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 removed outlier: 3.576A pdb=" N VAL C 188 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.974A pdb=" N TYR C 213 " --> pdb=" O GLN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 242 Proline residue: C 231 - end of helix removed outlier: 3.681A pdb=" N ALA C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 329 through 341 removed outlier: 4.024A pdb=" N VAL C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 345 through 355 removed outlier: 3.623A pdb=" N PHE C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 389 removed outlier: 3.872A pdb=" N LYS C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU C 383 " --> pdb=" O ARG C 379 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.932A pdb=" N GLU C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.649A pdb=" N ILE C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 431 removed outlier: 3.799A pdb=" N TYR C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 443 Proline residue: C 439 - end of helix Processing helix chain 'C' and resid 444 through 445 No H-bonds generated for 'chain 'C' and resid 444 through 445' Processing helix chain 'C' and resid 446 through 458 removed outlier: 4.694A pdb=" N ALA C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 4.050A pdb=" N ARG C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 136 through 147 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 169 through 179 removed outlier: 3.934A pdb=" N LEU D 173 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.722A pdb=" N HIS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 211 through 214 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 231 - end of helix Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.763A pdb=" N ASP D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 294 through 305 Processing helix chain 'D' and resid 309 through 321 removed outlier: 3.909A pdb=" N ALA D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 4.046A pdb=" N GLY D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 355 removed outlier: 3.731A pdb=" N PHE D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 390 removed outlier: 3.707A pdb=" N LYS D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 407 removed outlier: 3.993A pdb=" N GLU D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 419 through 431 removed outlier: 3.816A pdb=" N TYR D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 436 No H-bonds generated for 'chain 'D' and resid 434 through 436' Processing helix chain 'D' and resid 437 through 442 removed outlier: 3.836A pdb=" N LEU D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 460 removed outlier: 4.462A pdb=" N ALA D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 457 " --> pdb=" O HIS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 486 removed outlier: 3.876A pdb=" N GLU D 485 " --> pdb=" O PRO D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 136 through 147 Processing helix chain 'E' and resid 151 through 164 removed outlier: 3.584A pdb=" N TRP E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 178 removed outlier: 3.800A pdb=" N LEU E 173 " --> pdb=" O PRO E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 200 Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 211 through 214 removed outlier: 3.555A pdb=" N LYS E 214 " --> pdb=" O ASP E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 214' Processing helix chain 'E' and resid 215 through 242 removed outlier: 3.688A pdb=" N ARG E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Proline residue: E 231 - end of helix Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 274 through 288 Processing helix chain 'E' and resid 294 through 306 removed outlier: 3.792A pdb=" N HIS E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 323 removed outlier: 4.256A pdb=" N GLY E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 342 through 345 Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'E' and resid 365 through 369 removed outlier: 4.255A pdb=" N LYS E 369 " --> pdb=" O ARG E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 390 removed outlier: 4.166A pdb=" N LYS E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 408 Processing helix chain 'E' and resid 408 through 414 removed outlier: 3.937A pdb=" N ILE E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 431 removed outlier: 3.594A pdb=" N TYR E 423 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 436 No H-bonds generated for 'chain 'E' and resid 434 through 436' Processing helix chain 'E' and resid 437 through 442 removed outlier: 4.035A pdb=" N LEU E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 459 removed outlier: 4.029A pdb=" N GLY E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG E 455 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 3.993A pdb=" N ARG E 506 " --> pdb=" O ASN E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 removed outlier: 4.148A pdb=" N SER F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 151 through 165 removed outlier: 3.563A pdb=" N HIS F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 200 through 203 Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.589A pdb=" N ARG F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 209' Processing helix chain 'F' and resid 210 through 214 Processing helix chain 'F' and resid 215 through 242 Proline residue: F 231 - end of helix removed outlier: 3.907A pdb=" N ALA F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 274 through 288 removed outlier: 4.026A pdb=" N HIS F 288 " --> pdb=" O LEU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 Processing helix chain 'F' and resid 309 through 320 removed outlier: 3.843A pdb=" N ALA F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 323 No H-bonds generated for 'chain 'F' and resid 321 through 323' Processing helix chain 'F' and resid 328 through 341 removed outlier: 3.602A pdb=" N GLY F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 345 through 355 removed outlier: 3.656A pdb=" N LYS F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 390 removed outlier: 3.810A pdb=" N LYS F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 408 removed outlier: 3.940A pdb=" N LEU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER F 407 " --> pdb=" O LYS F 403 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 408 " --> pdb=" O ALA F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 removed outlier: 3.880A pdb=" N ILE F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 431 removed outlier: 3.944A pdb=" N TYR F 423 " --> pdb=" O ASN F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 436 No H-bonds generated for 'chain 'F' and resid 434 through 436' Processing helix chain 'F' and resid 437 through 460 Proline residue: F 445 - end of helix removed outlier: 4.761A pdb=" N ALA F 448 " --> pdb=" O ILE F 444 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 136 through 147 Processing helix chain 'G' and resid 151 through 165 removed outlier: 3.734A pdb=" N HIS G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 177 removed outlier: 3.530A pdb=" N GLN G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 197 Processing helix chain 'G' and resid 215 through 229 removed outlier: 4.450A pdb=" N LYS G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 234 Processing helix chain 'G' and resid 237 through 243 removed outlier: 3.582A pdb=" N LEU G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 264 Processing helix chain 'G' and resid 276 through 288 removed outlier: 3.843A pdb=" N VAL G 280 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE G 285 " --> pdb=" O LEU G 281 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 307 removed outlier: 3.851A pdb=" N ALA G 299 " --> pdb=" O CYS G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.909A pdb=" N TYR G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 340 removed outlier: 3.780A pdb=" N LEU G 334 " --> pdb=" O ASN G 330 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS G 335 " --> pdb=" O GLU G 331 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G 336 " --> pdb=" O ALA G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 344 No H-bonds generated for 'chain 'G' and resid 342 through 344' Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.598A pdb=" N PHE G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 390 removed outlier: 3.771A pdb=" N LYS G 376 " --> pdb=" O ASP G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 406 Processing helix chain 'G' and resid 408 through 414 Processing helix chain 'G' and resid 419 through 431 removed outlier: 4.023A pdb=" N TYR G 423 " --> pdb=" O ASN G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 458 removed outlier: 3.780A pdb=" N ILE G 444 " --> pdb=" O VAL G 440 " (cutoff:3.500A) Proline residue: G 445 - end of helix removed outlier: 4.389A pdb=" N ALA G 448 " --> pdb=" O ILE G 444 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY G 449 " --> pdb=" O PRO G 445 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 486 Processing helix chain 'G' and resid 502 through 508 Processing helix chain 'H' and resid 127 through 134 removed outlier: 3.516A pdb=" N LEU H 131 " --> pdb=" O PRO H 127 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'H' and resid 151 through 165 Processing helix chain 'H' and resid 171 through 176 Processing helix chain 'H' and resid 184 through 200 removed outlier: 4.337A pdb=" N VAL H 188 " --> pdb=" O HIS H 184 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 230 removed outlier: 4.118A pdb=" N VAL H 230 " --> pdb=" O ILE H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.909A pdb=" N ALA H 236 " --> pdb=" O THR H 232 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG H 240 " --> pdb=" O ALA H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 262 Processing helix chain 'H' and resid 275 through 288 Processing helix chain 'H' and resid 296 through 302 Processing helix chain 'H' and resid 302 through 307 removed outlier: 4.245A pdb=" N SER H 306 " --> pdb=" O HIS H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 332 through 338 removed outlier: 4.146A pdb=" N MET H 336 " --> pdb=" O ALA H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 355 removed outlier: 3.754A pdb=" N LYS H 354 " --> pdb=" O ILE H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 387 removed outlier: 4.450A pdb=" N LYS H 376 " --> pdb=" O ASP H 372 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL H 377 " --> pdb=" O PRO H 373 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 387 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 405 removed outlier: 3.747A pdb=" N GLU H 396 " --> pdb=" O ASP H 392 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 397 " --> pdb=" O PRO H 393 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 414 Processing helix chain 'H' and resid 419 through 432 removed outlier: 3.711A pdb=" N GLY H 432 " --> pdb=" O TYR H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 460 removed outlier: 3.754A pdb=" N ALA H 448 " --> pdb=" O ILE H 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.631A pdb=" N VAL B 471 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AA7, first strand: chain 'C' and resid 471 through 472 removed outlier: 5.664A pdb=" N VAL C 471 " --> pdb=" O SER D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 115 Processing sheet with id=AA9, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AB1, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.601A pdb=" N TYR F 126 " --> pdb=" O TYR F 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 122 through 123 Processing sheet with id=AB3, first strand: chain 'G' and resid 471 through 472 removed outlier: 6.866A pdb=" N VAL G 471 " --> pdb=" O SER H 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 113 through 114 1247 hydrogen bonds defined for protein. 3621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5696 1.33 - 1.45: 5667 1.45 - 1.57: 14452 1.57 - 1.69: 0 1.69 - 1.82: 200 Bond restraints: 26015 Sorted by residual: bond pdb=" CA ALA B 234 " pdb=" C ALA B 234 " ideal model delta sigma weight residual 1.524 1.437 0.088 1.28e-02 6.10e+03 4.71e+01 bond pdb=" CA ALA B 236 " pdb=" C ALA B 236 " ideal model delta sigma weight residual 1.524 1.448 0.075 1.44e-02 4.82e+03 2.74e+01 bond pdb=" CA THR B 232 " pdb=" C THR B 232 " ideal model delta sigma weight residual 1.524 1.459 0.065 1.26e-02 6.30e+03 2.65e+01 bond pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.05e-02 9.07e+03 2.20e+01 bond pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.24e-02 6.50e+03 1.95e+01 ... (remaining 26010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 34412 2.17 - 4.33: 714 4.33 - 6.50: 124 6.50 - 8.67: 45 8.67 - 10.83: 16 Bond angle restraints: 35311 Sorted by residual: angle pdb=" N ALA E 156 " pdb=" CA ALA E 156 " pdb=" C ALA E 156 " ideal model delta sigma weight residual 111.07 100.40 10.67 1.07e+00 8.73e-01 9.95e+01 angle pdb=" N GLU B 485 " pdb=" CA GLU B 485 " pdb=" C GLU B 485 " ideal model delta sigma weight residual 112.54 102.94 9.60 1.22e+00 6.72e-01 6.19e+01 angle pdb=" N GLU A 485 " pdb=" CA GLU A 485 " pdb=" C GLU A 485 " ideal model delta sigma weight residual 112.72 103.92 8.80 1.14e+00 7.69e-01 5.96e+01 angle pdb=" N SER F 197 " pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 110.97 103.56 7.41 1.09e+00 8.42e-01 4.62e+01 angle pdb=" N GLN B 484 " pdb=" CA GLN B 484 " pdb=" C GLN B 484 " ideal model delta sigma weight residual 113.12 104.96 8.16 1.25e+00 6.40e-01 4.26e+01 ... (remaining 35306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14150 17.89 - 35.79: 1235 35.79 - 53.68: 196 53.68 - 71.58: 42 71.58 - 89.47: 28 Dihedral angle restraints: 15651 sinusoidal: 6126 harmonic: 9525 Sorted by residual: dihedral pdb=" CA LEU H 325 " pdb=" C LEU H 325 " pdb=" N HIS H 326 " pdb=" CA HIS H 326 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLU C 292 " pdb=" C GLU C 292 " pdb=" N MET C 293 " pdb=" CA MET C 293 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP B 493 " pdb=" C ASP B 493 " pdb=" N LYS B 494 " pdb=" CA LYS B 494 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 15648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3467 0.072 - 0.144: 367 0.144 - 0.215: 20 0.215 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASN C 148 " pdb=" N ASN C 148 " pdb=" C ASN C 148 " pdb=" CB ASN C 148 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE C 395 " pdb=" CA ILE C 395 " pdb=" CG1 ILE C 395 " pdb=" CG2 ILE C 395 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3853 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 227 " -0.026 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C LEU B 227 " 0.093 2.00e-02 2.50e+03 pdb=" O LEU B 227 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY B 228 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 414 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C ARG F 414 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG F 414 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS F 415 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 430 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ALA D 430 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA D 430 " -0.024 2.00e-02 2.50e+03 pdb=" N MET D 431 " -0.021 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3061 2.74 - 3.28: 29111 3.28 - 3.82: 44265 3.82 - 4.36: 51423 4.36 - 4.90: 81496 Nonbonded interactions: 209356 Sorted by model distance: nonbonded pdb=" OG1 THR B 342 " pdb=" OD1 ASN B 345 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR G 261 " pdb=" O ARG G 269 " model vdw 2.208 3.040 nonbonded pdb=" O TRP D 454 " pdb=" OG SER D 457 " model vdw 2.214 3.040 nonbonded pdb=" O HIS G 302 " pdb=" OG SER G 305 " model vdw 2.220 3.040 nonbonded pdb=" O MET C 179 " pdb=" NH2 ARG C 240 " model vdw 2.222 3.120 ... (remaining 209351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'B' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'C' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'D' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'E' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 501 or (resid 502 and (name N or name CA or name C or name O )) or resid 503 \ through 508)) selection = (chain 'F' and (resid 106 through 460 or resid 464 through 486 or resid 488 thro \ ugh 496 or (resid 497 through 498 and (name N or name CA or name C or name O )) \ or resid 499 through 504)) selection = (chain 'G' and (resid 106 through 486 or resid 488 through 496 or (resid 497 thr \ ough 498 and (name N or name CA or name C or name O )) or resid 499 through 504) \ ) selection = (chain 'H' and (resid 106 through 460 or resid 464 through 486 or resid 488 thro \ ugh 496 or (resid 497 through 498 and (name N or name CA or name C or name O )) \ or resid 499 through 504)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.005 0.088 26015 Z= 0.269 Angle : 0.799 10.835 35311 Z= 0.440 Chirality : 0.044 0.359 3856 Planarity : 0.006 0.091 4594 Dihedral : 14.084 89.469 9561 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.04 % Favored : 91.40 % Rotamer: Outliers : 1.23 % Allowed : 0.61 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3245 helix: -0.36 (0.12), residues: 1778 sheet: -0.73 (1.70), residues: 10 loop : -1.78 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 391 TYR 0.028 0.001 TYR E 428 PHE 0.031 0.002 PHE H 311 TRP 0.021 0.002 TRP F 454 HIS 0.011 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00455 (26015) covalent geometry : angle 0.79895 (35311) hydrogen bonds : bond 0.17332 ( 1247) hydrogen bonds : angle 7.25202 ( 3621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 462 time to evaluate : 0.878 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: 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 152 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8522 (mmtt) REVERT: A 179 MET cc_start: 0.8498 (mmm) cc_final: 0.8182 (mmm) REVERT: A 293 MET cc_start: 0.6366 (mmp) cc_final: 0.6089 (mmp) REVERT: A 422 PHE cc_start: 0.9236 (t80) cc_final: 0.8950 (t80) REVERT: C 124 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6252 (tpp80) REVERT: C 229 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8357 (mptt) REVERT: C 297 THR cc_start: 0.9071 (p) cc_final: 0.8439 (p) REVERT: C 450 TYR cc_start: 0.8103 (m-10) cc_final: 0.7660 (m-10) REVERT: D 124 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6668 (mmm160) REVERT: D 193 MET cc_start: 0.8605 (mmt) cc_final: 0.8119 (mmt) REVERT: D 337 LEU cc_start: 0.7448 (tp) cc_final: 0.7030 (tp) REVERT: E 409 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8128 (pm20) REVERT: F 175 ILE cc_start: 0.9274 (mm) cc_final: 0.8967 (mm) REVERT: F 217 GLN cc_start: 0.9407 (pt0) cc_final: 0.9140 (tp40) REVERT: F 220 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8785 (m-30) REVERT: G 227 LEU cc_start: 0.8839 (tp) cc_final: 0.8564 (tp) REVERT: G 261 TYR cc_start: 0.7833 (t80) cc_final: 0.7374 (t80) REVERT: G 262 MET cc_start: 0.8016 (ppp) cc_final: 0.7520 (ppp) REVERT: H 276 ARG cc_start: 0.8296 (mmp80) cc_final: 0.8068 (mmp80) REVERT: H 379 ARG cc_start: 0.8625 (tmt-80) cc_final: 0.8392 (tpt90) REVERT: H 383 GLU cc_start: 0.8725 (pp20) cc_final: 0.7960 (tp30) REVERT: H 431 MET cc_start: 0.6026 (mmp) cc_final: 0.5687 (mmm) outliers start: 32 outliers final: 14 residues processed: 490 average time/residue: 0.1654 time to fit residues: 128.1161 Evaluate side-chains 389 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 371 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 338 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN F 177 GLN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 HIS H 181 HIS H 204 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.136782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102729 restraints weight = 83052.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100823 restraints weight = 48903.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101864 restraints weight = 43484.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101912 restraints weight = 37846.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102030 restraints weight = 35217.210| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 26015 Z= 0.270 Angle : 0.758 9.765 35311 Z= 0.391 Chirality : 0.045 0.198 3856 Planarity : 0.006 0.059 4594 Dihedral : 5.297 25.093 3636 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.44 % Favored : 91.43 % Rotamer: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.14), residues: 3245 helix: -0.46 (0.11), residues: 1835 sheet: -0.62 (1.83), residues: 10 loop : -1.89 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 486 TYR 0.024 0.002 TYR B 450 PHE 0.025 0.002 PHE B 422 TRP 0.018 0.002 TRP A 158 HIS 0.009 0.002 HIS F 302 Details of bonding type rmsd covalent geometry : bond 0.00600 (26015) covalent geometry : angle 0.75770 (35311) hydrogen bonds : bond 0.05525 ( 1247) hydrogen bonds : angle 6.05251 ( 3621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 0.925 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.9206 (t80) cc_final: 0.8921 (t80) REVERT: B 164 GLN cc_start: 0.8518 (mm110) cc_final: 0.8085 (tp40) REVERT: B 179 MET cc_start: 0.8898 (mpp) cc_final: 0.8074 (mpp) REVERT: B 257 GLU cc_start: 0.8550 (pt0) cc_final: 0.8319 (pt0) REVERT: B 447 MET cc_start: 0.8559 (ttm) cc_final: 0.8292 (ttm) REVERT: B 450 TYR cc_start: 0.8005 (m-80) cc_final: 0.7602 (m-80) REVERT: C 193 MET cc_start: 0.8777 (mmm) cc_final: 0.8576 (mmm) REVERT: C 297 THR cc_start: 0.9077 (p) cc_final: 0.8581 (t) REVERT: C 350 ILE cc_start: 0.7722 (pt) cc_final: 0.7478 (pt) REVERT: C 450 TYR cc_start: 0.8186 (m-10) cc_final: 0.7708 (m-10) REVERT: D 337 LEU cc_start: 0.7593 (tp) cc_final: 0.7143 (tt) REVERT: D 406 LEU cc_start: 0.8993 (pp) cc_final: 0.8530 (mt) REVERT: E 145 MET cc_start: 0.7637 (ptt) cc_final: 0.7371 (ptt) REVERT: E 409 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8196 (pm20) REVERT: F 175 ILE cc_start: 0.9304 (mm) cc_final: 0.8956 (mm) REVERT: F 257 GLU cc_start: 0.8154 (pm20) cc_final: 0.7738 (pm20) REVERT: G 261 TYR cc_start: 0.8094 (t80) cc_final: 0.7722 (t80) REVERT: G 262 MET cc_start: 0.8199 (ppp) cc_final: 0.7737 (ppp) REVERT: G 360 MET cc_start: 0.2237 (mmm) cc_final: 0.1883 (mmm) REVERT: H 137 TYR cc_start: 0.7859 (t80) cc_final: 0.7640 (t80) REVERT: H 379 ARG cc_start: 0.8663 (tmt-80) cc_final: 0.8052 (tpt90) REVERT: H 383 GLU cc_start: 0.8750 (pp20) cc_final: 0.8543 (pp20) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.1524 time to fit residues: 111.2399 Evaluate side-chains 356 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 230 optimal weight: 40.0000 chunk 118 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 HIS D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS D 469 GLN E 177 GLN E 204 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN H 200 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.140859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.106858 restraints weight = 82725.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105604 restraints weight = 62842.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.106143 restraints weight = 45676.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.107090 restraints weight = 39409.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107348 restraints weight = 34290.358| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26015 Z= 0.152 Angle : 0.657 10.086 35311 Z= 0.334 Chirality : 0.042 0.153 3856 Planarity : 0.005 0.074 4594 Dihedral : 5.026 28.294 3636 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.81 % Favored : 93.07 % Rotamer: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.14), residues: 3245 helix: -0.18 (0.12), residues: 1839 sheet: -0.54 (1.90), residues: 10 loop : -1.74 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 240 TYR 0.019 0.001 TYR D 450 PHE 0.025 0.002 PHE H 438 TRP 0.013 0.001 TRP G 454 HIS 0.008 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00344 (26015) covalent geometry : angle 0.65652 (35311) hydrogen bonds : bond 0.04603 ( 1247) hydrogen bonds : angle 5.46756 ( 3621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 497 time to evaluate : 0.979 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.9191 (t80) cc_final: 0.8899 (t80) REVERT: B 179 MET cc_start: 0.8569 (mpp) cc_final: 0.8025 (mpp) REVERT: B 450 TYR cc_start: 0.7971 (m-80) cc_final: 0.7733 (m-80) REVERT: C 297 THR cc_start: 0.8897 (p) cc_final: 0.8250 (p) REVERT: C 365 HIS cc_start: 0.6453 (m-70) cc_final: 0.6167 (m90) REVERT: C 450 TYR cc_start: 0.7992 (m-10) cc_final: 0.7576 (m-10) REVERT: D 112 CYS cc_start: 0.7525 (m) cc_final: 0.7160 (m) REVERT: D 148 ASN cc_start: 0.8692 (t0) cc_final: 0.8344 (t0) REVERT: D 193 MET cc_start: 0.8998 (mmp) cc_final: 0.8727 (mmt) REVERT: D 257 GLU cc_start: 0.8685 (mp0) cc_final: 0.8472 (mp0) REVERT: D 337 LEU cc_start: 0.7609 (tp) cc_final: 0.7258 (tp) REVERT: D 406 LEU cc_start: 0.8964 (pp) cc_final: 0.8505 (mt) REVERT: E 155 LEU cc_start: 0.8332 (tt) cc_final: 0.7909 (pp) REVERT: E 409 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8263 (pm20) REVERT: F 174 ASP cc_start: 0.9659 (m-30) cc_final: 0.9407 (m-30) REVERT: F 175 ILE cc_start: 0.9310 (mm) cc_final: 0.8975 (mm) REVERT: F 217 GLN cc_start: 0.9373 (pt0) cc_final: 0.9106 (tp40) REVERT: F 257 GLU cc_start: 0.8003 (pm20) cc_final: 0.7678 (pm20) REVERT: F 450 TYR cc_start: 0.8726 (m-80) cc_final: 0.8505 (m-80) REVERT: G 227 LEU cc_start: 0.8833 (tp) cc_final: 0.8427 (tp) REVERT: G 261 TYR cc_start: 0.8127 (t80) cc_final: 0.7754 (t80) REVERT: G 360 MET cc_start: 0.2505 (mmm) cc_final: 0.2064 (mmm) REVERT: G 447 MET cc_start: 0.8275 (ptt) cc_final: 0.7557 (ptt) REVERT: G 450 TYR cc_start: 0.7917 (m-10) cc_final: 0.7555 (m-10) REVERT: H 276 ARG cc_start: 0.8377 (mmp80) cc_final: 0.8155 (mmp80) REVERT: H 379 ARG cc_start: 0.8626 (tmt-80) cc_final: 0.7939 (tpt90) REVERT: H 383 GLU cc_start: 0.8769 (pp20) cc_final: 0.8505 (pp20) REVERT: H 429 ARG cc_start: 0.7405 (tmt170) cc_final: 0.7079 (tpt90) outliers start: 4 outliers final: 0 residues processed: 499 average time/residue: 0.1541 time to fit residues: 123.3549 Evaluate side-chains 376 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 25 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 40.0000 chunk 315 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 271 optimal weight: 30.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 291 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.138096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104166 restraints weight = 83616.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.102514 restraints weight = 49035.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103517 restraints weight = 43128.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103645 restraints weight = 36629.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.103747 restraints weight = 35111.035| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 26015 Z= 0.239 Angle : 0.727 11.000 35311 Z= 0.371 Chirality : 0.044 0.170 3856 Planarity : 0.006 0.063 4594 Dihedral : 5.175 24.127 3636 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.14), residues: 3245 helix: -0.33 (0.12), residues: 1841 sheet: -0.80 (1.84), residues: 10 loop : -1.80 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 414 TYR 0.028 0.002 TYR A 142 PHE 0.030 0.002 PHE B 422 TRP 0.019 0.002 TRP G 158 HIS 0.007 0.001 HIS F 302 Details of bonding type rmsd covalent geometry : bond 0.00538 (26015) covalent geometry : angle 0.72746 (35311) hydrogen bonds : bond 0.04831 ( 1247) hydrogen bonds : angle 5.65269 ( 3621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 456 time to evaluate : 1.012 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7172 (mmp) cc_final: 0.6713 (mmp) REVERT: A 422 PHE cc_start: 0.9269 (t80) cc_final: 0.8959 (t80) REVERT: B 164 GLN cc_start: 0.8233 (tp40) cc_final: 0.7943 (tp40) REVERT: B 179 MET cc_start: 0.8849 (mpp) cc_final: 0.8145 (mpp) REVERT: B 276 ARG cc_start: 0.8865 (mmp-170) cc_final: 0.8494 (mmp80) REVERT: B 447 MET cc_start: 0.8459 (ttm) cc_final: 0.8156 (ttm) REVERT: B 450 TYR cc_start: 0.7971 (m-80) cc_final: 0.7675 (m-80) REVERT: C 297 THR cc_start: 0.9015 (p) cc_final: 0.8510 (t) REVERT: C 450 TYR cc_start: 0.8133 (m-10) cc_final: 0.7621 (m-10) REVERT: D 429 ARG cc_start: 0.8234 (tmt170) cc_final: 0.7739 (tmt-80) REVERT: E 155 LEU cc_start: 0.8408 (tt) cc_final: 0.8030 (pp) REVERT: E 409 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8269 (pm20) REVERT: F 174 ASP cc_start: 0.9686 (m-30) cc_final: 0.9440 (m-30) REVERT: F 175 ILE cc_start: 0.9302 (mm) cc_final: 0.8994 (mm) REVERT: F 217 GLN cc_start: 0.9320 (pt0) cc_final: 0.9044 (tp40) REVERT: F 257 GLU cc_start: 0.8184 (pm20) cc_final: 0.7749 (pm20) REVERT: G 145 MET cc_start: 0.7746 (mmm) cc_final: 0.7545 (mmm) REVERT: G 261 TYR cc_start: 0.8281 (t80) cc_final: 0.7835 (t80) REVERT: G 262 MET cc_start: 0.8250 (ppp) cc_final: 0.7869 (ppp) REVERT: G 360 MET cc_start: 0.2295 (mmm) cc_final: 0.1823 (mmm) REVERT: H 121 LEU cc_start: 0.8284 (tp) cc_final: 0.7941 (tp) REVERT: H 379 ARG cc_start: 0.8668 (tmt-80) cc_final: 0.7994 (tpt90) REVERT: H 429 ARG cc_start: 0.7520 (tmt170) cc_final: 0.7120 (tpt90) outliers start: 2 outliers final: 1 residues processed: 458 average time/residue: 0.1582 time to fit residues: 115.9451 Evaluate side-chains 354 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 288 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 205 optimal weight: 30.0000 chunk 297 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 302 HIS F 177 GLN H 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.140030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105859 restraints weight = 82104.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.103945 restraints weight = 62529.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.104431 restraints weight = 48647.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105470 restraints weight = 41375.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.105604 restraints weight = 35438.371| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26015 Z= 0.166 Angle : 0.670 9.556 35311 Z= 0.338 Chirality : 0.043 0.186 3856 Planarity : 0.005 0.062 4594 Dihedral : 4.985 25.701 3636 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.58 % Favored : 92.30 % Rotamer: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.14), residues: 3245 helix: -0.20 (0.12), residues: 1853 sheet: -0.64 (1.87), residues: 10 loop : -1.73 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 225 TYR 0.025 0.001 TYR H 428 PHE 0.026 0.002 PHE H 438 TRP 0.013 0.001 TRP G 454 HIS 0.009 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00381 (26015) covalent geometry : angle 0.67045 (35311) hydrogen bonds : bond 0.04416 ( 1247) hydrogen bonds : angle 5.38111 ( 3621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.867 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.9265 (t80) cc_final: 0.8956 (t80) REVERT: B 164 GLN cc_start: 0.8266 (tp40) cc_final: 0.7952 (tp40) REVERT: B 179 MET cc_start: 0.8858 (mpp) cc_final: 0.8113 (mpp) REVERT: B 276 ARG cc_start: 0.8889 (mmp-170) cc_final: 0.8556 (mmp80) REVERT: B 409 GLU cc_start: 0.8986 (pp20) cc_final: 0.8700 (pp20) REVERT: B 447 MET cc_start: 0.8351 (ttm) cc_final: 0.8084 (ttm) REVERT: B 450 TYR cc_start: 0.7970 (m-10) cc_final: 0.7725 (m-80) REVERT: C 297 THR cc_start: 0.8964 (p) cc_final: 0.8312 (p) REVERT: C 450 TYR cc_start: 0.8012 (m-10) cc_final: 0.7522 (m-10) REVERT: D 148 ASN cc_start: 0.8690 (t0) cc_final: 0.8302 (t0) REVERT: D 186 MET cc_start: 0.8668 (mmm) cc_final: 0.8349 (mmm) REVERT: D 429 ARG cc_start: 0.8126 (tmt170) cc_final: 0.7567 (tmt-80) REVERT: E 155 LEU cc_start: 0.8651 (tt) cc_final: 0.8339 (pp) REVERT: E 179 MET cc_start: 0.7398 (mmt) cc_final: 0.7111 (mmt) REVERT: E 297 THR cc_start: 0.8684 (m) cc_final: 0.8181 (p) REVERT: F 174 ASP cc_start: 0.9649 (m-30) cc_final: 0.9405 (m-30) REVERT: F 175 ILE cc_start: 0.9281 (mm) cc_final: 0.9029 (mm) REVERT: F 257 GLU cc_start: 0.8126 (pm20) cc_final: 0.7667 (pm20) REVERT: G 261 TYR cc_start: 0.8321 (t80) cc_final: 0.7975 (t80) REVERT: G 262 MET cc_start: 0.8254 (ppp) cc_final: 0.7926 (ppp) REVERT: G 360 MET cc_start: 0.2227 (mmm) cc_final: 0.1802 (mmm) REVERT: G 447 MET cc_start: 0.8330 (ptt) cc_final: 0.7993 (ptt) REVERT: H 379 ARG cc_start: 0.8609 (tmt-80) cc_final: 0.8237 (ttp80) REVERT: H 429 ARG cc_start: 0.7408 (tmt170) cc_final: 0.7058 (tpt90) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.1537 time to fit residues: 117.9050 Evaluate side-chains 358 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 85 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 200 optimal weight: 0.2980 chunk 180 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 257 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN F 177 GLN G 222 GLN H 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.140324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105964 restraints weight = 83299.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104701 restraints weight = 65157.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.104855 restraints weight = 50404.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105877 restraints weight = 43261.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.105979 restraints weight = 37309.945| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26015 Z= 0.162 Angle : 0.672 10.671 35311 Z= 0.337 Chirality : 0.043 0.180 3856 Planarity : 0.005 0.061 4594 Dihedral : 4.907 23.500 3636 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.15), residues: 3245 helix: -0.11 (0.12), residues: 1850 sheet: -0.54 (1.83), residues: 10 loop : -1.63 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 240 TYR 0.046 0.002 TYR F 450 PHE 0.031 0.002 PHE H 438 TRP 0.014 0.001 TRP F 454 HIS 0.006 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00372 (26015) covalent geometry : angle 0.67157 (35311) hydrogen bonds : bond 0.04276 ( 1247) hydrogen bonds : angle 5.29976 ( 3621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 0.945 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7081 (mmp) cc_final: 0.6662 (mmp) REVERT: A 422 PHE cc_start: 0.9239 (t80) cc_final: 0.8935 (t80) REVERT: B 154 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: B 164 GLN cc_start: 0.8204 (tp40) cc_final: 0.7859 (tp40) REVERT: B 179 MET cc_start: 0.8856 (mpp) cc_final: 0.8055 (mpp) REVERT: B 409 GLU cc_start: 0.8990 (pp20) cc_final: 0.8637 (pp20) REVERT: B 450 TYR cc_start: 0.7960 (m-10) cc_final: 0.7715 (m-80) REVERT: C 262 MET cc_start: 0.7376 (mtm) cc_final: 0.6907 (mtt) REVERT: C 297 THR cc_start: 0.8940 (p) cc_final: 0.8270 (p) REVERT: C 450 TYR cc_start: 0.7992 (m-10) cc_final: 0.7520 (m-10) REVERT: D 148 ASN cc_start: 0.8639 (t0) cc_final: 0.8276 (t0) REVERT: D 186 MET cc_start: 0.8645 (mmm) cc_final: 0.8375 (mmm) REVERT: D 337 LEU cc_start: 0.7959 (tp) cc_final: 0.7363 (pp) REVERT: D 397 VAL cc_start: 0.8842 (t) cc_final: 0.8613 (t) REVERT: E 155 LEU cc_start: 0.8792 (tt) cc_final: 0.8567 (pp) REVERT: E 179 MET cc_start: 0.7467 (mmt) cc_final: 0.6972 (mmt) REVERT: E 297 THR cc_start: 0.8658 (m) cc_final: 0.8208 (p) REVERT: E 466 MET cc_start: 0.6826 (pmm) cc_final: 0.6621 (pmm) REVERT: F 174 ASP cc_start: 0.9642 (m-30) cc_final: 0.9372 (m-30) REVERT: F 175 ILE cc_start: 0.9267 (mm) cc_final: 0.9021 (mm) REVERT: F 193 MET cc_start: 0.8816 (ptp) cc_final: 0.8587 (ptp) REVERT: G 447 MET cc_start: 0.8164 (ptt) cc_final: 0.7904 (ptt) REVERT: G 450 TYR cc_start: 0.8114 (t80) cc_final: 0.7189 (t80) REVERT: G 451 LEU cc_start: 0.9092 (mt) cc_final: 0.8891 (mt) REVERT: H 348 ASP cc_start: 0.8782 (t70) cc_final: 0.8456 (m-30) REVERT: H 379 ARG cc_start: 0.8611 (tmt-80) cc_final: 0.8049 (tpt90) REVERT: H 383 GLU cc_start: 0.8622 (pp20) cc_final: 0.8357 (pp20) REVERT: H 429 ARG cc_start: 0.7437 (tmt170) cc_final: 0.6938 (tpt90) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.1608 time to fit residues: 119.8633 Evaluate side-chains 363 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 101 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 288 HIS ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN C 365 HIS D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN H 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.107819 restraints weight = 83007.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105442 restraints weight = 53952.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.106593 restraints weight = 44571.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106968 restraints weight = 38280.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107100 restraints weight = 34833.760| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26015 Z= 0.155 Angle : 0.667 10.927 35311 Z= 0.334 Chirality : 0.042 0.165 3856 Planarity : 0.005 0.059 4594 Dihedral : 4.848 24.114 3636 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 3245 helix: -0.02 (0.12), residues: 1845 sheet: -0.08 (1.94), residues: 10 loop : -1.59 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 429 TYR 0.038 0.001 TYR F 450 PHE 0.027 0.002 PHE H 438 TRP 0.024 0.002 TRP F 454 HIS 0.006 0.001 HIS G 291 Details of bonding type rmsd covalent geometry : bond 0.00358 (26015) covalent geometry : angle 0.66727 (35311) hydrogen bonds : bond 0.04194 ( 1247) hydrogen bonds : angle 5.24730 ( 3621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.865 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7222 (mmp) cc_final: 0.6802 (mmp) REVERT: A 422 PHE cc_start: 0.9138 (t80) cc_final: 0.8902 (t80) REVERT: B 164 GLN cc_start: 0.8124 (tp40) cc_final: 0.7902 (tp40) REVERT: B 179 MET cc_start: 0.8508 (mpp) cc_final: 0.8085 (mpp) REVERT: B 409 GLU cc_start: 0.8932 (pp20) cc_final: 0.8650 (pp20) REVERT: B 450 TYR cc_start: 0.7980 (m-10) cc_final: 0.7744 (m-80) REVERT: C 297 THR cc_start: 0.8906 (p) cc_final: 0.8246 (p) REVERT: C 450 TYR cc_start: 0.7980 (m-10) cc_final: 0.7527 (m-10) REVERT: D 148 ASN cc_start: 0.8514 (t0) cc_final: 0.8300 (t0) REVERT: D 186 MET cc_start: 0.8526 (mmm) cc_final: 0.8289 (mmm) REVERT: D 325 LEU cc_start: 0.9251 (mm) cc_final: 0.8964 (pt) REVERT: D 337 LEU cc_start: 0.7904 (tp) cc_final: 0.7260 (pp) REVERT: D 397 VAL cc_start: 0.8867 (t) cc_final: 0.8654 (t) REVERT: D 429 ARG cc_start: 0.7809 (tmt-80) cc_final: 0.7460 (tmt-80) REVERT: E 179 MET cc_start: 0.7605 (mmt) cc_final: 0.7107 (mmt) REVERT: E 193 MET cc_start: 0.8597 (tmm) cc_final: 0.8324 (tmm) REVERT: E 297 THR cc_start: 0.8640 (m) cc_final: 0.8279 (p) REVERT: F 145 MET cc_start: 0.7604 (ptm) cc_final: 0.6994 (tmm) REVERT: F 174 ASP cc_start: 0.9648 (m-30) cc_final: 0.9348 (m-30) REVERT: F 175 ILE cc_start: 0.9255 (mm) cc_final: 0.9007 (mm) REVERT: F 314 LEU cc_start: 0.9577 (mp) cc_final: 0.9329 (mp) REVERT: G 145 MET cc_start: 0.7658 (mmm) cc_final: 0.7045 (mmm) REVERT: G 261 TYR cc_start: 0.8156 (t80) cc_final: 0.7701 (t80) REVERT: G 360 MET cc_start: 0.2370 (mmm) cc_final: 0.2163 (mmm) REVERT: H 379 ARG cc_start: 0.8529 (tmt-80) cc_final: 0.8002 (tpt90) REVERT: H 383 GLU cc_start: 0.8583 (pp20) cc_final: 0.8356 (pp20) REVERT: H 429 ARG cc_start: 0.7413 (tmt170) cc_final: 0.6895 (tpt90) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.1576 time to fit residues: 118.7548 Evaluate side-chains 367 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 165 optimal weight: 50.0000 chunk 91 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 310 optimal weight: 50.0000 chunk 289 optimal weight: 10.0000 chunk 282 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN C 365 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN H 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.140095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.106243 restraints weight = 82997.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104558 restraints weight = 49372.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.105708 restraints weight = 43354.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.105881 restraints weight = 36697.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106019 restraints weight = 34342.570| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26015 Z= 0.169 Angle : 0.692 12.439 35311 Z= 0.347 Chirality : 0.043 0.173 3856 Planarity : 0.005 0.058 4594 Dihedral : 4.883 24.514 3636 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.15), residues: 3245 helix: -0.00 (0.12), residues: 1838 sheet: -0.01 (1.97), residues: 10 loop : -1.60 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 429 TYR 0.037 0.001 TYR A 142 PHE 0.042 0.002 PHE H 411 TRP 0.062 0.002 TRP B 158 HIS 0.005 0.001 HIS G 291 Details of bonding type rmsd covalent geometry : bond 0.00390 (26015) covalent geometry : angle 0.69160 (35311) hydrogen bonds : bond 0.04267 ( 1247) hydrogen bonds : angle 5.30395 ( 3621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.842 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.6404 (mmp) cc_final: 0.6046 (mmp) REVERT: A 422 PHE cc_start: 0.9190 (t80) cc_final: 0.8930 (t80) REVERT: B 179 MET cc_start: 0.8563 (mpp) cc_final: 0.8084 (mpp) REVERT: B 409 GLU cc_start: 0.8877 (pp20) cc_final: 0.8518 (pp20) REVERT: B 413 LYS cc_start: 0.8600 (mppt) cc_final: 0.8295 (mmtm) REVERT: C 262 MET cc_start: 0.7414 (mtm) cc_final: 0.6915 (mtt) REVERT: C 297 THR cc_start: 0.8951 (p) cc_final: 0.8295 (p) REVERT: C 450 TYR cc_start: 0.7986 (m-10) cc_final: 0.7494 (m-10) REVERT: D 148 ASN cc_start: 0.8614 (t0) cc_final: 0.8301 (t0) REVERT: D 186 MET cc_start: 0.8584 (mmm) cc_final: 0.8364 (mmm) REVERT: D 325 LEU cc_start: 0.9285 (mm) cc_final: 0.8987 (pt) REVERT: D 337 LEU cc_start: 0.7940 (tp) cc_final: 0.7290 (pp) REVERT: D 397 VAL cc_start: 0.8866 (t) cc_final: 0.8635 (t) REVERT: E 179 MET cc_start: 0.7673 (mmt) cc_final: 0.7156 (mmt) REVERT: E 297 THR cc_start: 0.8664 (m) cc_final: 0.8392 (p) REVERT: E 409 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8325 (pm20) REVERT: F 145 MET cc_start: 0.7508 (ptm) cc_final: 0.6786 (tmm) REVERT: F 174 ASP cc_start: 0.9672 (m-30) cc_final: 0.9454 (m-30) REVERT: F 175 ILE cc_start: 0.9256 (mm) cc_final: 0.8864 (mm) REVERT: F 179 MET cc_start: 0.8784 (mpp) cc_final: 0.8547 (mpp) REVERT: G 145 MET cc_start: 0.7636 (mmm) cc_final: 0.7338 (mmm) REVERT: G 261 TYR cc_start: 0.8265 (t80) cc_final: 0.7767 (t80) REVERT: G 360 MET cc_start: 0.2225 (mmm) cc_final: 0.1953 (mmm) REVERT: H 348 ASP cc_start: 0.8731 (t70) cc_final: 0.8360 (m-30) REVERT: H 379 ARG cc_start: 0.8586 (tmt-80) cc_final: 0.8050 (tpt90) REVERT: H 383 GLU cc_start: 0.8608 (pp20) cc_final: 0.8362 (pp20) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.1538 time to fit residues: 115.2420 Evaluate side-chains 367 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 274 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 271 optimal weight: 40.0000 chunk 71 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 HIS C 469 GLN D 210 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN H 181 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.141016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.107796 restraints weight = 82291.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.106230 restraints weight = 49177.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107194 restraints weight = 45057.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.107678 restraints weight = 36669.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108058 restraints weight = 33917.404| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26015 Z= 0.155 Angle : 0.691 12.686 35311 Z= 0.345 Chirality : 0.043 0.196 3856 Planarity : 0.005 0.058 4594 Dihedral : 4.827 24.480 3636 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3245 helix: -0.00 (0.12), residues: 1850 sheet: -0.15 (1.92), residues: 10 loop : -1.57 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.036 0.001 TYR F 450 PHE 0.026 0.002 PHE H 411 TRP 0.037 0.002 TRP B 158 HIS 0.005 0.001 HIS G 288 Details of bonding type rmsd covalent geometry : bond 0.00360 (26015) covalent geometry : angle 0.69138 (35311) hydrogen bonds : bond 0.04172 ( 1247) hydrogen bonds : angle 5.25792 ( 3621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 1.017 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: 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 240 ARG cc_start: 0.7441 (ttt180) cc_final: 0.6863 (tmt170) REVERT: B 179 MET cc_start: 0.8619 (mpp) cc_final: 0.8133 (mpp) REVERT: B 413 LYS cc_start: 0.8661 (mppt) cc_final: 0.8431 (mmtt) REVERT: B 450 TYR cc_start: 0.7995 (m-80) cc_final: 0.7729 (m-80) REVERT: C 262 MET cc_start: 0.7417 (mtm) cc_final: 0.6942 (mtt) REVERT: C 297 THR cc_start: 0.8896 (p) cc_final: 0.8169 (p) REVERT: C 450 TYR cc_start: 0.7950 (m-10) cc_final: 0.7530 (m-10) REVERT: D 148 ASN cc_start: 0.8536 (t0) cc_final: 0.8233 (t0) REVERT: D 257 GLU cc_start: 0.8470 (mp0) cc_final: 0.8214 (mp0) REVERT: D 325 LEU cc_start: 0.9243 (mm) cc_final: 0.8942 (pt) REVERT: D 337 LEU cc_start: 0.7883 (tp) cc_final: 0.7228 (pp) REVERT: D 397 VAL cc_start: 0.8827 (t) cc_final: 0.8592 (t) REVERT: D 429 ARG cc_start: 0.7897 (tmt-80) cc_final: 0.7465 (tmt-80) REVERT: D 438 PHE cc_start: 0.7852 (m-10) cc_final: 0.7551 (m-10) REVERT: E 179 MET cc_start: 0.7692 (mmt) cc_final: 0.7184 (mmt) REVERT: E 297 THR cc_start: 0.8657 (m) cc_final: 0.8413 (p) REVERT: E 409 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8283 (pm20) REVERT: E 466 MET cc_start: 0.6861 (pmm) cc_final: 0.6441 (pmm) REVERT: F 145 MET cc_start: 0.7426 (ptm) cc_final: 0.6806 (tmm) REVERT: F 174 ASP cc_start: 0.9659 (m-30) cc_final: 0.9457 (m-30) REVERT: G 145 MET cc_start: 0.7639 (mmm) cc_final: 0.7381 (mmm) REVERT: G 261 TYR cc_start: 0.8228 (t80) cc_final: 0.7724 (t80) REVERT: H 348 ASP cc_start: 0.8669 (t70) cc_final: 0.8311 (m-30) REVERT: H 379 ARG cc_start: 0.8621 (tmt-80) cc_final: 0.8081 (tpt90) REVERT: H 383 GLU cc_start: 0.8633 (pp20) cc_final: 0.8393 (pp20) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1554 time to fit residues: 115.9463 Evaluate side-chains 372 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 17 optimal weight: 0.0070 chunk 239 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 203 optimal weight: 50.0000 chunk 206 optimal weight: 50.0000 chunk 35 optimal weight: 0.9990 chunk 308 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS B 288 HIS ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 177 GLN H 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.143801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.109139 restraints weight = 81227.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107735 restraints weight = 57020.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108567 restraints weight = 45682.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.109221 restraints weight = 37991.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109862 restraints weight = 32774.553| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26015 Z= 0.129 Angle : 0.684 12.925 35311 Z= 0.338 Chirality : 0.043 0.182 3856 Planarity : 0.005 0.059 4594 Dihedral : 4.680 22.905 3636 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 3245 helix: 0.15 (0.12), residues: 1847 sheet: -0.42 (1.85), residues: 10 loop : -1.48 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 429 TYR 0.039 0.001 TYR F 450 PHE 0.025 0.002 PHE B 442 TRP 0.032 0.002 TRP B 158 HIS 0.005 0.001 HIS H 302 Details of bonding type rmsd covalent geometry : bond 0.00296 (26015) covalent geometry : angle 0.68436 (35311) hydrogen bonds : bond 0.03953 ( 1247) hydrogen bonds : angle 5.03917 ( 3621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.704 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8388 (m-30) cc_final: 0.7332 (p0) REVERT: A 186 MET cc_start: 0.8973 (ttm) cc_final: 0.8728 (ttm) REVERT: A 422 PHE cc_start: 0.9199 (t80) cc_final: 0.8893 (t80) REVERT: A 483 LEU cc_start: 0.8924 (mm) cc_final: 0.8624 (tt) REVERT: B 179 MET cc_start: 0.8690 (mpp) cc_final: 0.8050 (mpp) REVERT: B 409 GLU cc_start: 0.8928 (pp20) cc_final: 0.8696 (pp20) REVERT: B 413 LYS cc_start: 0.8800 (mppt) cc_final: 0.8551 (mmtt) REVERT: B 450 TYR cc_start: 0.8073 (m-80) cc_final: 0.7807 (m-80) REVERT: C 262 MET cc_start: 0.7530 (mtm) cc_final: 0.7044 (mtt) REVERT: D 148 ASN cc_start: 0.8503 (t0) cc_final: 0.8234 (t0) REVERT: D 325 LEU cc_start: 0.9338 (mm) cc_final: 0.9061 (pt) REVERT: D 337 LEU cc_start: 0.7954 (tp) cc_final: 0.7459 (pp) REVERT: D 429 ARG cc_start: 0.7897 (tmt-80) cc_final: 0.7473 (tmt-80) REVERT: E 179 MET cc_start: 0.7481 (mmt) cc_final: 0.6998 (mmt) REVERT: E 186 MET cc_start: 0.8567 (ttt) cc_final: 0.8181 (tmm) REVERT: E 297 THR cc_start: 0.8723 (m) cc_final: 0.8369 (p) REVERT: E 409 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8324 (pm20) REVERT: E 450 TYR cc_start: 0.8549 (m-10) cc_final: 0.7971 (m-80) REVERT: F 145 MET cc_start: 0.7625 (ptm) cc_final: 0.6572 (tmm) REVERT: F 175 ILE cc_start: 0.9312 (mm) cc_final: 0.9000 (mm) REVERT: F 179 MET cc_start: 0.8748 (mpp) cc_final: 0.8541 (mpp) REVERT: G 145 MET cc_start: 0.7710 (mmm) cc_final: 0.7472 (mmm) REVERT: G 261 TYR cc_start: 0.8275 (t80) cc_final: 0.7685 (t80) REVERT: H 337 LEU cc_start: 0.4112 (tt) cc_final: 0.3361 (pp) REVERT: H 360 MET cc_start: 0.6574 (mpp) cc_final: 0.5461 (tpp) REVERT: H 379 ARG cc_start: 0.8546 (tmt-80) cc_final: 0.8029 (tpt90) REVERT: H 383 GLU cc_start: 0.8644 (pp20) cc_final: 0.8378 (pp20) REVERT: H 450 TYR cc_start: 0.8832 (m-10) cc_final: 0.8519 (m-80) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1599 time to fit residues: 127.1942 Evaluate side-chains 387 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 149 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 204 optimal weight: 50.0000 chunk 156 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.141555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.108225 restraints weight = 82273.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105315 restraints weight = 54327.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106416 restraints weight = 44519.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106810 restraints weight = 38497.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.107098 restraints weight = 35116.043| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26015 Z= 0.171 Angle : 0.707 14.043 35311 Z= 0.352 Chirality : 0.044 0.183 3856 Planarity : 0.005 0.060 4594 Dihedral : 4.720 23.447 3636 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3245 helix: 0.11 (0.12), residues: 1865 sheet: -0.61 (1.84), residues: 10 loop : -1.52 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 429 TYR 0.036 0.002 TYR F 450 PHE 0.043 0.002 PHE B 438 TRP 0.027 0.002 TRP F 454 HIS 0.010 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00393 (26015) covalent geometry : angle 0.70715 (35311) hydrogen bonds : bond 0.04055 ( 1247) hydrogen bonds : angle 5.16252 ( 3621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4181.22 seconds wall clock time: 73 minutes 18.76 seconds (4398.76 seconds total)