Starting phenix.real_space_refine on Sat May 24 05:19:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzp_18779/05_2025/8qzp_18779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzp_18779/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qzp_18779/05_2025/8qzp_18779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzp_18779/05_2025/8qzp_18779.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzp_18779/05_2025/8qzp_18779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzp_18779/05_2025/8qzp_18779.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} 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: 15.08, per 1000 atoms: 0.59 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: 6.53 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.67 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: 7.31 Time building geometry restraints manager: 7.33 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 53.100 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.140 ------------------------------------------------------------------------------- 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 : 22.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (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 TRP 0.021 0.002 TRP F 454 HIS 0.011 0.001 HIS E 302 PHE 0.031 0.002 PHE H 311 TYR 0.028 0.001 TYR E 428 ARG 0.010 0.001 ARG G 391 Details of bonding type rmsd hydrogen bonds : bond 0.17332 ( 1247) hydrogen bonds : angle 7.25202 ( 3621) covalent geometry : bond 0.00455 (26015) covalent geometry : angle 0.79895 (35311) *********************** 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 : 2.939 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 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: 0.8440 (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: 0.6651 (mmm160) REVERT: D 193 MET cc_start: 0.8605 (mmt) cc_final: 0.8118 (mmt) REVERT: D 334 LEU cc_start: 0.9150 (tt) cc_final: 0.8580 (tt) REVERT: D 336 MET cc_start: 0.8822 (tmm) cc_final: 0.8584 (ppp) REVERT: D 337 LEU cc_start: 0.7448 (tp) cc_final: 0.7080 (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: 0.8966 (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: 0.8563 (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: 0.7518 (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: 0.8400 (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: 0.5683 (mmm) outliers start: 32 outliers final: 13 residues processed: 490 average time/residue: 0.3585 time to fit residues: 274.2711 Evaluate side-chains 390 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 373 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 30.0000 chunk 245 optimal weight: 40.0000 chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 50.0000 chunk 131 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 189 optimal weight: 30.0000 chunk 294 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 294 ASN B 338 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 164 GLN E 177 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.138652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105941 restraints weight = 82398.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102611 restraints weight = 59231.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103293 restraints weight = 51706.686| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26015 Z= 0.213 Angle : 0.704 10.236 35311 Z= 0.363 Chirality : 0.043 0.197 3856 Planarity : 0.006 0.056 4594 Dihedral : 5.112 25.247 3636 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3245 helix: -0.25 (0.12), residues: 1827 sheet: -0.49 (1.86), residues: 10 loop : -1.82 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 158 HIS 0.008 0.001 HIS F 302 PHE 0.022 0.002 PHE B 422 TYR 0.024 0.002 TYR B 450 ARG 0.006 0.001 ARG F 486 Details of bonding type rmsd hydrogen bonds : bond 0.05201 ( 1247) hydrogen bonds : angle 5.84672 ( 3621) covalent geometry : bond 0.00480 (26015) covalent geometry : angle 0.70350 (35311) *********************** 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 465 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 2.636 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: 0.6507 (mmp) cc_final: 0.6016 (mmp) REVERT: A 422 PHE cc_start: 0.9271 (t80) cc_final: 0.8948 (t80) REVERT: B 179 MET cc_start: 0.8786 (mpp) cc_final: 0.8049 (mpp) REVERT: B 450 TYR cc_start: 0.8084 (m-80) cc_final: 0.7731 (m-80) REVERT: C 297 THR cc_start: 0.9121 (p) cc_final: 0.8482 (t) REVERT: C 350 ILE cc_start: 0.7745 (pt) cc_final: 0.7540 (pt) REVERT: C 450 TYR cc_start: 0.8140 (m-10) cc_final: 0.7748 (m-10) REVERT: C 466 MET cc_start: 0.8787 (pmm) cc_final: 0.8543 (pmm) REVERT: D 148 ASN cc_start: 0.8899 (t0) cc_final: 0.8505 (t0) REVERT: D 337 LEU cc_start: 0.7610 (tp) cc_final: 0.7302 (tp) REVERT: D 406 LEU cc_start: 0.8988 (pp) cc_final: 0.8547 (mt) REVERT: E 409 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8203 (pm20) REVERT: F 175 ILE cc_start: 0.9300 (mm) cc_final: 0.8970 (mm) REVERT: F 257 GLU cc_start: 0.8051 (pm20) cc_final: 0.7660 (pm20) REVERT: G 227 LEU cc_start: 0.8872 (tp) cc_final: 0.8578 (tp) REVERT: G 261 TYR cc_start: 0.8114 (t80) cc_final: 0.7724 (t80) REVERT: G 360 MET cc_start: 0.2178 (mmm) cc_final: 0.1817 (mmm) REVERT: H 379 ARG cc_start: 0.8676 (tmt-80) cc_final: 0.8082 (tpt90) REVERT: H 383 GLU cc_start: 0.8756 (pp20) cc_final: 0.8532 (pp20) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.3422 time to fit residues: 253.3671 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 : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 160 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 302 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 176 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** H 181 HIS H 200 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** 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 = 0.140697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105807 restraints weight = 82588.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.104994 restraints weight = 60163.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105609 restraints weight = 43443.011| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26015 Z= 0.164 Angle : 0.656 9.454 35311 Z= 0.335 Chirality : 0.043 0.151 3856 Planarity : 0.006 0.078 4594 Dihedral : 4.981 27.118 3636 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3245 helix: -0.13 (0.12), residues: 1839 sheet: -0.48 (1.90), residues: 10 loop : -1.73 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 454 HIS 0.008 0.001 HIS E 165 PHE 0.025 0.002 PHE H 438 TYR 0.021 0.001 TYR D 450 ARG 0.005 0.000 ARG H 414 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 1247) hydrogen bonds : angle 5.48830 ( 3621) covalent geometry : bond 0.00374 (26015) covalent geometry : angle 0.65581 (35311) *********************** 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 486 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 2.835 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 422 PHE cc_start: 0.9253 (t80) cc_final: 0.8922 (t80) REVERT: B 179 MET cc_start: 0.8585 (mpp) cc_final: 0.8079 (mpp) REVERT: B 447 MET cc_start: 0.8298 (ttm) cc_final: 0.8086 (ttm) REVERT: B 450 TYR cc_start: 0.8062 (m-80) cc_final: 0.7833 (m-80) REVERT: C 297 THR cc_start: 0.8952 (p) cc_final: 0.8289 (t) REVERT: C 365 HIS cc_start: 0.6588 (m-70) cc_final: 0.6070 (m90) REVERT: C 368 TYR cc_start: 0.8702 (m-10) cc_final: 0.8464 (m-80) REVERT: C 450 TYR cc_start: 0.8077 (m-10) cc_final: 0.7633 (m-10) REVERT: C 466 MET cc_start: 0.8725 (pmm) cc_final: 0.8377 (pmm) REVERT: D 112 CYS cc_start: 0.7480 (m) cc_final: 0.7220 (m) REVERT: D 148 ASN cc_start: 0.8743 (t0) cc_final: 0.8378 (t0) REVERT: D 257 GLU cc_start: 0.8760 (mp0) cc_final: 0.8544 (mp0) REVERT: D 337 LEU cc_start: 0.7500 (tp) cc_final: 0.6976 (pp) REVERT: D 406 LEU cc_start: 0.8981 (pp) cc_final: 0.8530 (mt) REVERT: D 466 MET cc_start: 0.8444 (pmm) cc_final: 0.8225 (pmm) REVERT: E 155 LEU cc_start: 0.8185 (tt) cc_final: 0.7810 (pp) REVERT: E 409 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8269 (pm20) REVERT: F 174 ASP cc_start: 0.9673 (m-30) cc_final: 0.9416 (m-30) REVERT: F 175 ILE cc_start: 0.9313 (mm) cc_final: 0.9015 (mm) REVERT: F 257 GLU cc_start: 0.7960 (pm20) cc_final: 0.7654 (pm20) REVERT: F 314 LEU cc_start: 0.9527 (mp) cc_final: 0.9292 (mp) REVERT: F 450 TYR cc_start: 0.8797 (m-80) cc_final: 0.8548 (m-80) REVERT: G 145 MET cc_start: 0.7802 (mmm) cc_final: 0.7331 (mmm) REVERT: G 227 LEU cc_start: 0.8822 (tp) cc_final: 0.8375 (tp) REVERT: G 261 TYR cc_start: 0.8190 (t80) cc_final: 0.7785 (t80) REVERT: G 360 MET cc_start: 0.2368 (mmm) cc_final: 0.2023 (mmm) REVERT: G 447 MET cc_start: 0.8285 (ptt) cc_final: 0.7530 (ptt) REVERT: G 450 TYR cc_start: 0.7982 (m-10) cc_final: 0.7621 (m-10) REVERT: H 379 ARG cc_start: 0.8617 (tmt-80) cc_final: 0.7938 (tpt90) REVERT: H 383 GLU cc_start: 0.8780 (pp20) cc_final: 0.8500 (pp20) REVERT: H 429 ARG cc_start: 0.7357 (tmt170) cc_final: 0.7087 (tpt90) REVERT: H 450 TYR cc_start: 0.8855 (m-10) cc_final: 0.8556 (m-80) outliers start: 1 outliers final: 0 residues processed: 485 average time/residue: 0.3449 time to fit residues: 266.3868 Evaluate side-chains 373 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 309 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 294 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 258 ASN ** 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 326 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN H 181 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103894 restraints weight = 82667.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103089 restraints weight = 67857.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.103302 restraints weight = 46462.342| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26015 Z= 0.191 Angle : 0.678 9.294 35311 Z= 0.345 Chirality : 0.043 0.175 3856 Planarity : 0.005 0.057 4594 Dihedral : 4.982 24.408 3636 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.07 % Favored : 91.83 % Rotamer: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3245 helix: -0.14 (0.12), residues: 1848 sheet: -0.63 (1.89), residues: 10 loop : -1.74 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 158 HIS 0.006 0.001 HIS F 302 PHE 0.027 0.002 PHE B 422 TYR 0.024 0.002 TYR A 142 ARG 0.004 0.000 ARG E 429 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1247) hydrogen bonds : angle 5.47225 ( 3621) covalent geometry : bond 0.00431 (26015) covalent geometry : angle 0.67763 (35311) *********************** 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 463 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 461 time to evaluate : 2.660 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 101 TYR cc_start: 0.8063 (m-80) cc_final: 0.7850 (m-10) REVERT: A 293 MET cc_start: 0.7243 (mmp) cc_final: 0.6758 (mmp) REVERT: A 422 PHE cc_start: 0.9264 (t80) cc_final: 0.8942 (t80) REVERT: B 164 GLN cc_start: 0.8285 (tp40) cc_final: 0.7969 (tp40) REVERT: B 179 MET cc_start: 0.8802 (mpp) cc_final: 0.8173 (mpp) REVERT: B 276 ARG cc_start: 0.8888 (mmp-170) cc_final: 0.8501 (mmp80) REVERT: B 447 MET cc_start: 0.8372 (ttm) cc_final: 0.8128 (ttm) REVERT: B 450 TYR cc_start: 0.8028 (m-80) cc_final: 0.7760 (m-80) REVERT: C 220 ASP cc_start: 0.8186 (m-30) cc_final: 0.7826 (m-30) REVERT: C 297 THR cc_start: 0.9000 (p) cc_final: 0.8451 (t) REVERT: C 365 HIS cc_start: 0.6666 (m-70) cc_final: 0.6398 (m90) REVERT: C 450 TYR cc_start: 0.8032 (m-10) cc_final: 0.7587 (m-10) REVERT: D 112 CYS cc_start: 0.7578 (m) cc_final: 0.7198 (m) REVERT: D 148 ASN cc_start: 0.8832 (t0) cc_final: 0.8412 (t0) REVERT: D 257 GLU cc_start: 0.8657 (mp0) cc_final: 0.8442 (mp0) REVERT: D 337 LEU cc_start: 0.7403 (tp) cc_final: 0.7021 (pp) REVERT: D 406 LEU cc_start: 0.9005 (pp) cc_final: 0.8540 (mt) REVERT: E 155 LEU cc_start: 0.8410 (tt) cc_final: 0.8064 (pp) REVERT: E 297 THR cc_start: 0.8619 (m) cc_final: 0.8047 (p) REVERT: E 409 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8293 (pm20) REVERT: F 174 ASP cc_start: 0.9692 (m-30) cc_final: 0.9447 (m-30) REVERT: F 175 ILE cc_start: 0.9272 (mm) cc_final: 0.9004 (mm) REVERT: F 217 GLN cc_start: 0.9309 (pp30) cc_final: 0.9104 (pp30) REVERT: F 257 GLU cc_start: 0.8100 (pm20) cc_final: 0.7687 (pm20) REVERT: G 145 MET cc_start: 0.7823 (mmm) cc_final: 0.7600 (mmm) REVERT: G 227 LEU cc_start: 0.8821 (tp) cc_final: 0.8385 (tp) REVERT: G 261 TYR cc_start: 0.8244 (t80) cc_final: 0.7975 (t80) REVERT: G 360 MET cc_start: 0.2226 (mmm) cc_final: 0.1824 (mmm) REVERT: G 447 MET cc_start: 0.8443 (ptt) cc_final: 0.8003 (ptt) REVERT: G 450 TYR cc_start: 0.8126 (m-10) cc_final: 0.7713 (m-10) REVERT: H 379 ARG cc_start: 0.8650 (tmt-80) cc_final: 0.7973 (tpt90) REVERT: H 383 GLU cc_start: 0.8807 (pp20) cc_final: 0.8549 (pp20) REVERT: H 429 ARG cc_start: 0.7560 (tmt170) cc_final: 0.7206 (tpt90) outliers start: 2 outliers final: 1 residues processed: 463 average time/residue: 0.3415 time to fit residues: 251.3210 Evaluate side-chains 365 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 286 optimal weight: 30.0000 chunk 270 optimal weight: 20.0000 chunk 235 optimal weight: 0.4980 chunk 194 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- 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 258 ASN ** 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** D 210 GLN D 291 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN E 302 HIS F 177 GLN ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** 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 = 0.4202 r_free = 0.4202 target = 0.138470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.104759 restraints weight = 83264.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103047 restraints weight = 53112.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.103530 restraints weight = 49673.561| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26015 Z= 0.209 Angle : 0.698 10.031 35311 Z= 0.354 Chirality : 0.044 0.187 3856 Planarity : 0.005 0.057 4594 Dihedral : 5.043 24.449 3636 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.14 % Favored : 91.77 % Rotamer: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3245 helix: -0.19 (0.12), residues: 1850 sheet: -0.65 (1.89), residues: 10 loop : -1.75 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 454 HIS 0.009 0.001 HIS E 302 PHE 0.031 0.002 PHE A 285 TYR 0.043 0.002 TYR F 450 ARG 0.010 0.001 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 1247) hydrogen bonds : angle 5.48987 ( 3621) covalent geometry : bond 0.00470 (26015) covalent geometry : angle 0.69777 (35311) *********************** 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 465 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 2.642 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: A 422 PHE cc_start: 0.9183 (t80) cc_final: 0.8912 (t80) REVERT: B 164 GLN cc_start: 0.8287 (tp40) cc_final: 0.7994 (tp40) REVERT: B 179 MET cc_start: 0.8894 (mpp) cc_final: 0.8164 (mpp) REVERT: B 276 ARG cc_start: 0.8868 (mmp-170) cc_final: 0.8478 (mmp80) REVERT: B 447 MET cc_start: 0.8485 (ttm) cc_final: 0.8210 (ttm) REVERT: B 450 TYR cc_start: 0.7971 (m-10) cc_final: 0.7709 (m-80) REVERT: C 297 THR cc_start: 0.9037 (p) cc_final: 0.8526 (t) REVERT: C 450 TYR cc_start: 0.8092 (m-10) cc_final: 0.7676 (m-10) REVERT: D 112 CYS cc_start: 0.7500 (m) cc_final: 0.7126 (m) REVERT: D 337 LEU cc_start: 0.7499 (tp) cc_final: 0.7186 (tp) REVERT: D 406 LEU cc_start: 0.9024 (pp) cc_final: 0.8531 (mt) REVERT: D 466 MET cc_start: 0.8487 (pmm) cc_final: 0.8267 (pmm) REVERT: E 155 LEU cc_start: 0.8818 (tt) cc_final: 0.8575 (pp) REVERT: E 193 MET cc_start: 0.8600 (tmm) cc_final: 0.8269 (tmm) REVERT: E 297 THR cc_start: 0.8650 (m) cc_final: 0.8167 (p) REVERT: F 174 ASP cc_start: 0.9663 (m-30) cc_final: 0.9420 (m-30) REVERT: F 175 ILE cc_start: 0.9274 (mm) cc_final: 0.9048 (mm) REVERT: F 257 GLU cc_start: 0.8205 (pm20) cc_final: 0.7728 (pm20) REVERT: G 261 TYR cc_start: 0.8298 (t80) cc_final: 0.7959 (t80) REVERT: G 262 MET cc_start: 0.8272 (ppp) cc_final: 0.7957 (ppp) REVERT: G 360 MET cc_start: 0.2303 (mmm) cc_final: 0.1635 (mmm) REVERT: G 447 MET cc_start: 0.8508 (ptt) cc_final: 0.7961 (ptt) REVERT: G 450 TYR cc_start: 0.8051 (m-10) cc_final: 0.7680 (m-80) REVERT: H 121 LEU cc_start: 0.8225 (tp) cc_final: 0.7902 (tp) REVERT: H 379 ARG cc_start: 0.8680 (tmt-80) cc_final: 0.8045 (tpt90) REVERT: H 429 ARG cc_start: 0.7491 (tmt170) cc_final: 0.7078 (tpt90) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.3387 time to fit residues: 249.4710 Evaluate side-chains 365 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 208 optimal weight: 40.0000 chunk 175 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** 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 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN F 177 GLN G 222 GLN H 181 HIS ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.139418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104385 restraints weight = 82096.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103217 restraints weight = 63168.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103657 restraints weight = 47795.089| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26015 Z= 0.185 Angle : 0.696 11.222 35311 Z= 0.350 Chirality : 0.044 0.164 3856 Planarity : 0.005 0.058 4594 Dihedral : 4.999 23.655 3636 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 0.04 % Allowed : 2.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3245 helix: -0.14 (0.12), residues: 1856 sheet: -0.68 (1.80), residues: 10 loop : -1.73 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 158 HIS 0.006 0.001 HIS F 302 PHE 0.029 0.002 PHE H 438 TYR 0.034 0.002 TYR F 450 ARG 0.013 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 1247) hydrogen bonds : angle 5.40534 ( 3621) covalent geometry : bond 0.00420 (26015) covalent geometry : angle 0.69585 (35311) *********************** 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 473 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 3.047 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: symmetry clash REVERT: A 422 PHE cc_start: 0.9228 (t80) cc_final: 0.8949 (t80) REVERT: B 164 GLN cc_start: 0.8195 (tp40) cc_final: 0.7904 (tp40) REVERT: B 179 MET cc_start: 0.8925 (mpp) cc_final: 0.8098 (mpp) REVERT: B 447 MET cc_start: 0.8417 (ttm) cc_final: 0.8177 (ttm) REVERT: B 450 TYR cc_start: 0.7998 (m-10) cc_final: 0.7763 (m-80) REVERT: C 220 ASP cc_start: 0.8195 (m-30) cc_final: 0.7861 (m-30) REVERT: C 297 THR cc_start: 0.8908 (p) cc_final: 0.8321 (p) REVERT: C 450 TYR cc_start: 0.8078 (m-10) cc_final: 0.7594 (m-10) REVERT: D 112 CYS cc_start: 0.7536 (m) cc_final: 0.7162 (m) REVERT: D 148 ASN cc_start: 0.8694 (t0) cc_final: 0.8324 (t0) REVERT: D 337 LEU cc_start: 0.7474 (tp) cc_final: 0.7082 (pp) REVERT: D 406 LEU cc_start: 0.8991 (pp) cc_final: 0.8501 (mt) REVERT: E 297 THR cc_start: 0.8670 (m) cc_final: 0.8283 (p) REVERT: F 174 ASP cc_start: 0.9651 (m-30) cc_final: 0.9376 (m-30) REVERT: F 175 ILE cc_start: 0.9265 (mm) cc_final: 0.9050 (mm) REVERT: F 193 MET cc_start: 0.8729 (ptp) cc_final: 0.8427 (ptp) REVERT: F 257 GLU cc_start: 0.8204 (pm20) cc_final: 0.7696 (pm20) REVERT: F 392 ASP cc_start: 0.8024 (m-30) cc_final: 0.7822 (m-30) REVERT: G 261 TYR cc_start: 0.8310 (t80) cc_final: 0.8009 (t80) REVERT: G 360 MET cc_start: 0.2377 (mmm) cc_final: 0.1846 (mmm) REVERT: G 447 MET cc_start: 0.8501 (ptt) cc_final: 0.8004 (ptt) REVERT: G 450 TYR cc_start: 0.8089 (m-10) cc_final: 0.7717 (m-80) REVERT: H 276 ARG cc_start: 0.8411 (mmp80) cc_final: 0.8182 (mmp80) REVERT: H 348 ASP cc_start: 0.8797 (t70) cc_final: 0.8462 (m-30) REVERT: H 379 ARG cc_start: 0.8619 (tmt-80) cc_final: 0.8082 (tpt90) REVERT: H 383 GLU cc_start: 0.8641 (pp20) cc_final: 0.8413 (pp20) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3563 time to fit residues: 266.6623 Evaluate side-chains 366 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 322 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 274 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- 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 258 ASN ** 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 355 ASN ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN H 181 HIS ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.139953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.105213 restraints weight = 82731.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103626 restraints weight = 63161.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.104060 restraints weight = 48427.524| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2226 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= 0.175 Angle : 0.686 12.133 35311 Z= 0.345 Chirality : 0.043 0.186 3856 Planarity : 0.005 0.057 4594 Dihedral : 4.952 23.612 3636 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.07 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3245 helix: -0.08 (0.12), residues: 1849 sheet: -0.59 (1.84), residues: 10 loop : -1.69 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 454 HIS 0.006 0.001 HIS G 326 PHE 0.029 0.002 PHE A 285 TYR 0.033 0.001 TYR F 450 ARG 0.007 0.000 ARG F 240 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 1247) hydrogen bonds : angle 5.34818 ( 3621) covalent geometry : bond 0.00402 (26015) covalent geometry : angle 0.68592 (35311) *********************** 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 466 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 2.606 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 293 MET cc_start: 0.7263 (mmp) cc_final: 0.6796 (mmp) REVERT: A 422 PHE cc_start: 0.9222 (t80) cc_final: 0.8936 (t80) REVERT: B 179 MET cc_start: 0.8931 (mpp) cc_final: 0.8070 (mpp) REVERT: B 447 MET cc_start: 0.8403 (ttm) cc_final: 0.8116 (ttm) REVERT: B 450 TYR cc_start: 0.8002 (m-10) cc_final: 0.7750 (m-80) REVERT: C 220 ASP cc_start: 0.8181 (m-30) cc_final: 0.7821 (m-30) REVERT: C 297 THR cc_start: 0.8953 (p) cc_final: 0.8289 (p) REVERT: C 450 TYR cc_start: 0.8110 (m-10) cc_final: 0.7618 (m-10) REVERT: D 148 ASN cc_start: 0.8568 (t0) cc_final: 0.8325 (t0) REVERT: D 337 LEU cc_start: 0.7551 (tp) cc_final: 0.7069 (pp) REVERT: D 397 VAL cc_start: 0.8852 (t) cc_final: 0.8619 (t) REVERT: D 406 LEU cc_start: 0.9007 (pp) cc_final: 0.8528 (mt) REVERT: E 297 THR cc_start: 0.8714 (m) cc_final: 0.8419 (p) REVERT: F 174 ASP cc_start: 0.9663 (m-30) cc_final: 0.9390 (m-30) REVERT: F 175 ILE cc_start: 0.9286 (mm) cc_final: 0.9086 (mm) REVERT: F 314 LEU cc_start: 0.9588 (mp) cc_final: 0.9331 (mp) REVERT: G 261 TYR cc_start: 0.8341 (t80) cc_final: 0.8053 (t80) REVERT: G 262 MET cc_start: 0.8354 (ppp) cc_final: 0.8090 (ppp) REVERT: G 447 MET cc_start: 0.8527 (ptt) cc_final: 0.8051 (ptt) REVERT: G 450 TYR cc_start: 0.8121 (m-10) cc_final: 0.7739 (m-80) REVERT: H 276 ARG cc_start: 0.8439 (mmp80) cc_final: 0.8214 (mmp80) REVERT: H 379 ARG cc_start: 0.8634 (tmt-80) cc_final: 0.8076 (tpt90) REVERT: H 383 GLU cc_start: 0.8657 (pp20) cc_final: 0.8364 (pp20) REVERT: H 429 ARG cc_start: 0.7369 (tmt170) cc_final: 0.6935 (tpt90) REVERT: H 450 TYR cc_start: 0.8856 (m-10) cc_final: 0.8584 (m-80) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.3422 time to fit residues: 252.1153 Evaluate side-chains 363 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 62 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 296 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 260 optimal weight: 40.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 HIS C 469 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS H 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.140875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106958 restraints weight = 81480.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105257 restraints weight = 50425.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106276 restraints weight = 42351.076| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26015 Z= 0.151 Angle : 0.675 13.228 35311 Z= 0.339 Chirality : 0.043 0.189 3856 Planarity : 0.005 0.057 4594 Dihedral : 4.867 24.518 3636 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3245 helix: 0.05 (0.12), residues: 1840 sheet: -0.38 (1.84), residues: 10 loop : -1.64 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 454 HIS 0.006 0.001 HIS G 291 PHE 0.027 0.002 PHE H 438 TYR 0.033 0.001 TYR F 450 ARG 0.007 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1247) hydrogen bonds : angle 5.22491 ( 3621) covalent geometry : bond 0.00348 (26015) covalent geometry : angle 0.67538 (35311) *********************** 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 474 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 2.702 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: A 117 ASP cc_start: 0.8470 (m-30) cc_final: 0.7341 (p0) REVERT: A 422 PHE cc_start: 0.9197 (t80) cc_final: 0.8927 (t80) REVERT: A 483 LEU cc_start: 0.8844 (mm) cc_final: 0.8494 (tt) REVERT: B 179 MET cc_start: 0.8616 (mpp) cc_final: 0.8231 (mpp) REVERT: C 220 ASP cc_start: 0.8116 (m-30) cc_final: 0.7852 (m-30) REVERT: C 262 MET cc_start: 0.8005 (mtm) cc_final: 0.7617 (mtt) REVERT: C 297 THR cc_start: 0.8927 (p) cc_final: 0.8202 (p) REVERT: C 365 HIS cc_start: 0.6459 (m-70) cc_final: 0.6209 (m90) REVERT: C 450 TYR cc_start: 0.8021 (m-10) cc_final: 0.7530 (m-10) REVERT: D 148 ASN cc_start: 0.8590 (t0) cc_final: 0.8232 (t0) REVERT: D 325 LEU cc_start: 0.9288 (mm) cc_final: 0.8931 (pt) REVERT: D 337 LEU cc_start: 0.7540 (tp) cc_final: 0.7066 (pp) REVERT: D 397 VAL cc_start: 0.8838 (t) cc_final: 0.8598 (t) REVERT: D 406 LEU cc_start: 0.8977 (pp) cc_final: 0.8522 (mt) REVERT: E 297 THR cc_start: 0.8743 (m) cc_final: 0.8498 (p) REVERT: E 409 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8312 (pm20) REVERT: E 466 MET cc_start: 0.6873 (pmm) cc_final: 0.6562 (pmm) REVERT: F 174 ASP cc_start: 0.9661 (m-30) cc_final: 0.9380 (m-30) REVERT: F 175 ILE cc_start: 0.9252 (mm) cc_final: 0.8869 (mm) REVERT: G 261 TYR cc_start: 0.8310 (t80) cc_final: 0.7987 (t80) REVERT: G 447 MET cc_start: 0.8551 (ptt) cc_final: 0.8078 (ptt) REVERT: G 450 TYR cc_start: 0.8165 (m-10) cc_final: 0.7747 (m-80) REVERT: H 348 ASP cc_start: 0.8731 (t70) cc_final: 0.8387 (m-30) REVERT: H 379 ARG cc_start: 0.8518 (tmt-80) cc_final: 0.8006 (tpt90) REVERT: H 383 GLU cc_start: 0.8632 (pp20) cc_final: 0.8384 (pp20) REVERT: H 450 TYR cc_start: 0.8848 (m-10) cc_final: 0.8570 (m-80) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.3478 time to fit residues: 261.5999 Evaluate side-chains 368 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 87 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 244 optimal weight: 40.0000 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 239 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.139415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106136 restraints weight = 82977.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.104377 restraints weight = 50183.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.105459 restraints weight = 45548.933| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26015 Z= 0.200 Angle : 0.723 13.373 35311 Z= 0.363 Chirality : 0.044 0.216 3856 Planarity : 0.006 0.074 4594 Dihedral : 4.970 24.485 3636 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.26 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3245 helix: -0.06 (0.12), residues: 1856 sheet: -0.05 (1.95), residues: 10 loop : -1.68 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 454 HIS 0.006 0.001 HIS A 184 PHE 0.028 0.002 PHE D 437 TYR 0.033 0.002 TYR F 450 ARG 0.013 0.001 ARG H 414 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 1247) hydrogen bonds : angle 5.39585 ( 3621) covalent geometry : bond 0.00458 (26015) covalent geometry : angle 0.72342 (35311) *********************** 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 451 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 2.649 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: A 422 PHE cc_start: 0.9187 (t80) cc_final: 0.8927 (t80) REVERT: B 179 MET cc_start: 0.8727 (mpp) cc_final: 0.8207 (mpp) REVERT: B 447 MET cc_start: 0.8393 (ttm) cc_final: 0.8156 (ttm) REVERT: B 450 TYR cc_start: 0.8079 (m-80) cc_final: 0.7781 (m-80) REVERT: C 220 ASP cc_start: 0.8358 (m-30) cc_final: 0.8023 (m-30) REVERT: C 262 MET cc_start: 0.8118 (mtm) cc_final: 0.7775 (mtt) REVERT: C 297 THR cc_start: 0.8990 (p) cc_final: 0.8321 (p) REVERT: C 450 TYR cc_start: 0.8059 (m-10) cc_final: 0.7650 (m-10) REVERT: D 148 ASN cc_start: 0.8608 (t0) cc_final: 0.8306 (t0) REVERT: D 325 LEU cc_start: 0.9292 (mm) cc_final: 0.8924 (pt) REVERT: D 337 LEU cc_start: 0.7653 (tp) cc_final: 0.7189 (pp) REVERT: D 397 VAL cc_start: 0.8864 (t) cc_final: 0.8635 (t) REVERT: D 406 LEU cc_start: 0.9064 (pp) cc_final: 0.8558 (mt) REVERT: E 297 THR cc_start: 0.8729 (m) cc_final: 0.8471 (p) REVERT: E 409 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8255 (pm20) REVERT: E 466 MET cc_start: 0.6812 (pmm) cc_final: 0.6590 (pmm) REVERT: F 143 LEU cc_start: 0.9284 (tt) cc_final: 0.8958 (tp) REVERT: F 174 ASP cc_start: 0.9683 (m-30) cc_final: 0.9388 (m-30) REVERT: F 175 ILE cc_start: 0.9265 (mm) cc_final: 0.8878 (mm) REVERT: G 261 TYR cc_start: 0.8360 (t80) cc_final: 0.8005 (t80) REVERT: G 262 MET cc_start: 0.8460 (ppp) cc_final: 0.8189 (ppp) REVERT: G 447 MET cc_start: 0.8642 (ptt) cc_final: 0.7848 (ptt) REVERT: G 450 TYR cc_start: 0.8038 (m-10) cc_final: 0.7677 (m-80) REVERT: H 348 ASP cc_start: 0.8677 (t70) cc_final: 0.8326 (m-30) REVERT: H 379 ARG cc_start: 0.8651 (tmt-80) cc_final: 0.8090 (tpt90) REVERT: H 383 GLU cc_start: 0.8631 (pp20) cc_final: 0.8391 (pp20) REVERT: H 429 ARG cc_start: 0.7560 (tmt170) cc_final: 0.7055 (tmt170) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.3401 time to fit residues: 243.5937 Evaluate side-chains 361 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 297 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 321 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 304 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.142101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.109368 restraints weight = 82283.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.105938 restraints weight = 62312.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.106793 restraints weight = 51447.496| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26015 Z= 0.140 Angle : 0.693 13.444 35311 Z= 0.345 Chirality : 0.043 0.212 3856 Planarity : 0.005 0.064 4594 Dihedral : 4.841 23.396 3636 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.00 % Favored : 92.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3245 helix: 0.12 (0.12), residues: 1846 sheet: 0.05 (1.95), residues: 10 loop : -1.56 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 158 HIS 0.008 0.001 HIS C 365 PHE 0.024 0.002 PHE H 438 TYR 0.036 0.001 TYR F 450 ARG 0.008 0.000 ARG H 429 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 1247) hydrogen bonds : angle 5.18452 ( 3621) covalent geometry : bond 0.00327 (26015) covalent geometry : angle 0.69346 (35311) ********************** 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 477 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 2.646 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: A 117 ASP cc_start: 0.8369 (m-30) cc_final: 0.7267 (p0) REVERT: A 293 MET cc_start: 0.7016 (mmp) cc_final: 0.6776 (mmp) REVERT: A 483 LEU cc_start: 0.8862 (mm) cc_final: 0.8540 (tt) REVERT: B 179 MET cc_start: 0.8574 (mpp) cc_final: 0.8191 (mpp) REVERT: B 232 THR cc_start: 0.9197 (p) cc_final: 0.8960 (t) REVERT: B 244 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8507 (mmm160) REVERT: B 450 TYR cc_start: 0.8033 (m-80) cc_final: 0.7754 (m-80) REVERT: C 220 ASP cc_start: 0.8097 (m-30) cc_final: 0.7868 (m-30) REVERT: C 262 MET cc_start: 0.7979 (mtm) cc_final: 0.7687 (mtt) REVERT: C 297 THR cc_start: 0.8850 (p) cc_final: 0.8039 (p) REVERT: C 450 TYR cc_start: 0.7954 (m-10) cc_final: 0.7498 (m-10) REVERT: D 148 ASN cc_start: 0.8596 (t0) cc_final: 0.8138 (t0) REVERT: D 325 LEU cc_start: 0.9306 (mm) cc_final: 0.8964 (pt) REVERT: D 337 LEU cc_start: 0.7590 (tp) cc_final: 0.7002 (pp) REVERT: D 397 VAL cc_start: 0.8766 (t) cc_final: 0.8533 (t) REVERT: D 406 LEU cc_start: 0.9016 (pp) cc_final: 0.8561 (mt) REVERT: E 297 THR cc_start: 0.8644 (m) cc_final: 0.8431 (p) REVERT: E 409 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8273 (pm20) REVERT: E 450 TYR cc_start: 0.8496 (m-10) cc_final: 0.7911 (m-80) REVERT: F 143 LEU cc_start: 0.9162 (tt) cc_final: 0.8704 (tp) REVERT: F 174 ASP cc_start: 0.9649 (m-30) cc_final: 0.9443 (m-30) REVERT: F 175 ILE cc_start: 0.9280 (mm) cc_final: 0.8954 (mm) REVERT: G 164 GLN cc_start: 0.9066 (pp30) cc_final: 0.8833 (pp30) REVERT: G 261 TYR cc_start: 0.8300 (t80) cc_final: 0.7968 (t80) REVERT: G 447 MET cc_start: 0.8528 (ptt) cc_final: 0.8147 (ptt) REVERT: G 450 TYR cc_start: 0.8029 (m-10) cc_final: 0.7640 (m-80) REVERT: H 276 ARG cc_start: 0.8396 (mmp80) cc_final: 0.8158 (mmp80) REVERT: H 348 ASP cc_start: 0.8691 (t70) cc_final: 0.8339 (m-30) REVERT: H 355 ASN cc_start: 0.8531 (m-40) cc_final: 0.8263 (m110) REVERT: H 379 ARG cc_start: 0.8648 (tmt-80) cc_final: 0.8109 (tpt90) REVERT: H 383 GLU cc_start: 0.8624 (pp20) cc_final: 0.8389 (pp20) REVERT: H 429 ARG cc_start: 0.7515 (tmt170) cc_final: 0.7128 (tmt170) REVERT: H 450 TYR cc_start: 0.8640 (m-10) cc_final: 0.8332 (m-80) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.3500 time to fit residues: 261.8427 Evaluate side-chains 370 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 264 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 277 optimal weight: 30.0000 chunk 291 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.140912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107373 restraints weight = 81819.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104945 restraints weight = 53543.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105867 restraints weight = 44960.438| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2622 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= 0.170 Angle : 0.714 14.432 35311 Z= 0.357 Chirality : 0.044 0.208 3856 Planarity : 0.005 0.061 4594 Dihedral : 4.864 23.458 3636 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.83 % Favored : 92.08 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3245 helix: 0.08 (0.12), residues: 1862 sheet: -0.01 (1.96), residues: 10 loop : -1.60 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 158 HIS 0.014 0.001 HIS A 365 PHE 0.037 0.002 PHE E 160 TYR 0.035 0.002 TYR F 450 ARG 0.010 0.001 ARG H 356 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 1247) hydrogen bonds : angle 5.26736 ( 3621) covalent geometry : bond 0.00394 (26015) covalent geometry : angle 0.71399 (35311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7864.50 seconds wall clock time: 138 minutes 51.49 seconds (8331.49 seconds total)