Starting phenix.real_space_refine on Tue Nov 19 14:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jet_36195/11_2024/8jet_36195.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jet_36195/11_2024/8jet_36195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jet_36195/11_2024/8jet_36195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jet_36195/11_2024/8jet_36195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jet_36195/11_2024/8jet_36195.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jet_36195/11_2024/8jet_36195.cif" } resolution = 3.1 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= 0.003 sd= 0.076 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 84 5.16 5 C 12702 2.51 5 N 3308 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19526 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 652, 4876 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 18, 'TRANS': 633} Chain breaks: 2 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 256 Conformer: "B" Number of residues, atoms: 652, 4876 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 18, 'TRANS': 633} Chain breaks: 2 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 256 bond proxies already assigned to first conformer: 4968 Chain: "B" Number of atoms: 4878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 654, 4862 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 18, 'TRANS': 635} Chain breaks: 2 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 242 Conformer: "B" Number of residues, atoms: 654, 4862 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 18, 'TRANS': 635} Chain breaks: 2 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 242 bond proxies already assigned to first conformer: 4946 Chain: "C" Number of atoms: 4885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 652, 4876 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 18, 'TRANS': 633} Chain breaks: 2 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 256 Conformer: "B" Number of residues, atoms: 652, 4876 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 18, 'TRANS': 633} Chain breaks: 2 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 256 bond proxies already assigned to first conformer: 4968 Chain: "D" Number of atoms: 4878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 654, 4862 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 18, 'TRANS': 635} Chain breaks: 2 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 242 Conformer: "B" Number of residues, atoms: 654, 4862 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 18, 'TRANS': 635} Chain breaks: 2 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 242 bond proxies already assigned to first conformer: 4946 Time building chain proxies: 21.00, per 1000 atoms: 1.08 Number of scatterers: 19526 At special positions: 0 Unit cell: (106.05, 106.05, 184.83, 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 84 16.00 O 3432 8.00 N 3308 7.00 C 12702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 5.8 seconds 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 8 sheets defined 69.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 81 through 106 removed outlier: 3.975A pdb=" N ILE A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.576A pdb=" N GLN A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.880A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.579A pdb=" N TYR A 186 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 191 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 4.095A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.575A pdb=" N ALA A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 5.200A pdb=" N GLY A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.905A pdb=" N THR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 329 removed outlier: 3.832A pdb=" N PHE A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 353 through 369 removed outlier: 3.645A pdb=" N GLN A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.711A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Proline residue: A 396 - end of helix Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.688A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.561A pdb=" N ILE A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.622A pdb=" N ILE A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.608A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 559 removed outlier: 4.208A pdb=" N GLU A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.757A pdb=" N SER A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 592 removed outlier: 3.659A pdb=" N LEU A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 removed outlier: 3.685A pdb=" N THR A 597 " --> pdb=" O TYR A 593 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 removed outlier: 3.668A pdb=" N GLU A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 Processing helix chain 'A' and resid 644 through 656 removed outlier: 3.680A pdb=" N VAL A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 654 " --> pdb=" O CYS A 650 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.534A pdb=" N ARG A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.616A pdb=" N ILE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'B' and resid 81 through 105 removed outlier: 3.732A pdb=" N ILE B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 132 removed outlier: 3.513A pdb=" N GLN B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.738A pdb=" N ILE B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 167 Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.863A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.794A pdb=" N LEU B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 212 through 242 removed outlier: 3.516A pdb=" N LYS B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.808A pdb=" N GLU B 248 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 287 removed outlier: 3.854A pdb=" N THR B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 329 removed outlier: 3.614A pdb=" N PHE B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.519A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 350 " --> pdb=" O TYR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 370 removed outlier: 3.799A pdb=" N GLY B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.677A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.706A pdb=" N LYS B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.942A pdb=" N ILE B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 498 through 509 removed outlier: 3.698A pdb=" N ILE B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.876A pdb=" N ARG B 515 " --> pdb=" O HIS B 511 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.935A pdb=" N LYS B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.762A pdb=" N TYR B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.765A pdb=" N LEU B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.755A pdb=" N ARG B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 602 removed outlier: 3.688A pdb=" N LEU B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 removed outlier: 3.688A pdb=" N ALA B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 636 removed outlier: 3.846A pdb=" N ALA B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 655 removed outlier: 3.518A pdb=" N VAL B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 654 " --> pdb=" O CYS B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.619A pdb=" N ARG B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 666 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 removed outlier: 3.720A pdb=" N VAL B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 removed outlier: 3.646A pdb=" N ALA B 694 " --> pdb=" O PHE B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 740 removed outlier: 4.013A pdb=" N LEU B 729 " --> pdb=" O MET B 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 106 removed outlier: 3.944A pdb=" N ILE C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP C 92 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.581A pdb=" N GLN C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.842A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 160 " --> pdb=" O TYR C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.552A pdb=" N TYR C 186 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 187 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 191 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 207 removed outlier: 4.095A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 242 removed outlier: 3.618A pdb=" N ALA C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 5.202A pdb=" N GLY C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 3.801A pdb=" N THR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 329 removed outlier: 3.833A pdb=" N PHE C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'C' and resid 353 through 369 removed outlier: 3.642A pdb=" N GLN C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.665A pdb=" N LYS C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.685A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.613A pdb=" N ILE C 476 " --> pdb=" O GLY C 472 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.615A pdb=" N ILE C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.603A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 559 removed outlier: 4.225A pdb=" N GLU C 545 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 546 " --> pdb=" O SER C 542 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 removed outlier: 3.717A pdb=" N SER C 566 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.693A pdb=" N LEU C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 603 removed outlier: 3.687A pdb=" N THR C 597 " --> pdb=" O TYR C 593 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.517A pdb=" N GLU C 620 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 621 " --> pdb=" O PRO C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 Processing helix chain 'C' and resid 644 through 656 removed outlier: 3.519A pdb=" N ALA C 654 " --> pdb=" O CYS C 650 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 655 " --> pdb=" O THR C 651 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 666 removed outlier: 3.637A pdb=" N LEU C 664 " --> pdb=" O PHE C 660 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 666 " --> pdb=" O LYS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 691 through 699 removed outlier: 3.560A pdb=" N ILE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 696 " --> pdb=" O VAL C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 740 Processing helix chain 'D' and resid 81 through 105 removed outlier: 3.753A pdb=" N ILE D 91 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 92 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 114 through 132 removed outlier: 3.512A pdb=" N GLN D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.736A pdb=" N ILE D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 167 Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.864A pdb=" N ILE D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.812A pdb=" N LEU D 187 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 194 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 207 Processing helix chain 'D' and resid 212 through 242 removed outlier: 3.518A pdb=" N LYS D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.822A pdb=" N GLU D 248 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY D 249 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.585A pdb=" N THR D 276 " --> pdb=" O TRP D 272 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 329 removed outlier: 3.628A pdb=" N PHE D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.793A pdb=" N ASP D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN D 350 " --> pdb=" O TYR D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 370 removed outlier: 3.889A pdb=" N GLY D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 382 through 394 removed outlier: 3.680A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 3.693A pdb=" N LYS D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 408 through 417 removed outlier: 3.871A pdb=" N ILE D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 498 through 509 removed outlier: 3.702A pdb=" N ILE D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 509 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.822A pdb=" N ARG D 515 " --> pdb=" O HIS D 511 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 517 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 533 removed outlier: 3.973A pdb=" N LYS D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.569A pdb=" N HIS D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.743A pdb=" N LEU D 564 " --> pdb=" O ASP D 560 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 566 " --> pdb=" O TYR D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.772A pdb=" N ARG D 591 " --> pdb=" O LEU D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 602 removed outlier: 3.679A pdb=" N LEU D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 600 " --> pdb=" O ILE D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 624 removed outlier: 3.588A pdb=" N ASN D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 636 removed outlier: 3.875A pdb=" N ALA D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU D 632 " --> pdb=" O ARG D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 655 removed outlier: 3.529A pdb=" N VAL D 652 " --> pdb=" O PHE D 648 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA D 654 " --> pdb=" O CYS D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 667 removed outlier: 3.585A pdb=" N ARG D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 665 " --> pdb=" O LEU D 661 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN D 667 " --> pdb=" O ARG D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 removed outlier: 3.735A pdb=" N VAL D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 700 removed outlier: 3.646A pdb=" N ALA D 694 " --> pdb=" O PHE D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 Processing helix chain 'D' and resid 723 through 740 removed outlier: 4.012A pdb=" N LEU D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 424 removed outlier: 3.629A pdb=" N CYS A 492 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 441 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431 removed outlier: 6.881A pdb=" N VAL A 486 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.668A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG B 493 " --> pdb=" O CYS B 444 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 429 through 431 removed outlier: 6.354A pdb=" N VAL B 486 " --> pdb=" O ILE B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 420 through 424 removed outlier: 3.572A pdb=" N CYS C 492 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR C 441 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS C 469 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 429 through 431 removed outlier: 6.668A pdb=" N VAL C 486 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.686A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG D 493 " --> pdb=" O CYS D 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 429 through 431 removed outlier: 6.331A pdb=" N VAL D 486 " --> pdb=" O ILE D 430 " (cutoff:3.500A) 1122 hydrogen bonds defined for protein. 3157 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: 7.33 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6265 1.34 - 1.46: 4596 1.46 - 1.58: 8949 1.58 - 1.69: 0 1.69 - 1.81: 142 Bond restraints: 19952 Sorted by residual: bond pdb=" C LEU A 271 " pdb=" N TRP A 272 " ideal model delta sigma weight residual 1.335 1.320 0.016 1.34e-02 5.57e+03 1.36e+00 bond pdb=" C ARG A 274 " pdb=" N TYR A 275 " ideal model delta sigma weight residual 1.333 1.319 0.014 1.45e-02 4.76e+03 8.97e-01 bond pdb=" C THR A 277 " pdb=" N SER A 278 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.36e-02 5.41e+03 6.90e-01 bond pdb=" CA PHE D 266 " pdb=" CB PHE D 266 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.51e-02 4.39e+03 6.25e-01 bond pdb=" C ASP A 270 " pdb=" N LEU A 271 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.40e-02 5.10e+03 6.09e-01 ... (remaining 19947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 26708 1.28 - 2.56: 334 2.56 - 3.85: 94 3.85 - 5.13: 28 5.13 - 6.41: 4 Bond angle restraints: 27168 Sorted by residual: angle pdb=" N ILE A 253 " pdb=" CA ILE A 253 " pdb=" C ILE A 253 " ideal model delta sigma weight residual 112.96 109.68 3.28 1.00e+00 1.00e+00 1.08e+01 angle pdb=" N ILE C 253 " pdb=" CA ILE C 253 " pdb=" C ILE C 253 " ideal model delta sigma weight residual 112.96 109.75 3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" C ASP C 270 " pdb=" N LEU C 271 " pdb=" CA LEU C 271 " ideal model delta sigma weight residual 121.54 126.25 -4.71 1.91e+00 2.74e-01 6.08e+00 angle pdb=" N ASP C 260 " pdb=" CA ASP C 260 " pdb=" C ASP C 260 " ideal model delta sigma weight residual 114.56 111.44 3.12 1.27e+00 6.20e-01 6.04e+00 angle pdb=" CA GLU D 268 " pdb=" CB GLU D 268 " pdb=" CG GLU D 268 " ideal model delta sigma weight residual 114.10 118.44 -4.34 2.00e+00 2.50e-01 4.70e+00 ... (remaining 27163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 11080 15.83 - 31.66: 554 31.66 - 47.48: 86 47.48 - 63.31: 11 63.31 - 79.14: 5 Dihedral angle restraints: 11736 sinusoidal: 4050 harmonic: 7686 Sorted by residual: dihedral pdb=" CA GLY D 179 " pdb=" C GLY D 179 " pdb=" N GLU D 180 " pdb=" CA GLU D 180 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N GLU B 180 " pdb=" CA GLU B 180 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP B 270 " pdb=" C ASP B 270 " pdb=" N LEU B 271 " pdb=" CA LEU B 271 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 11733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1995 0.030 - 0.060: 868 0.060 - 0.090: 221 0.090 - 0.119: 85 0.119 - 0.149: 13 Chirality restraints: 3182 Sorted by residual: chirality pdb=" CA PHE D 266 " pdb=" N PHE D 266 " pdb=" C PHE D 266 " pdb=" CB PHE D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA PHE B 266 " pdb=" N PHE B 266 " pdb=" C PHE B 266 " pdb=" CB PHE B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 3179 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 266 " -0.011 2.00e-02 2.50e+03 1.23e-02 2.66e+00 pdb=" CG PHE B 266 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 266 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 266 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 266 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 266 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 266 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 266 " 0.011 2.00e-02 2.50e+03 1.21e-02 2.57e+00 pdb=" CG PHE D 266 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE D 266 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 266 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 266 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 266 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 266 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 680 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 681 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " -0.019 5.00e-02 4.00e+02 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5080 2.80 - 3.32: 19341 3.32 - 3.85: 29880 3.85 - 4.37: 34646 4.37 - 4.90: 59272 Nonbonded interactions: 148219 Sorted by model distance: nonbonded pdb=" O ARG C 663 " pdb=" OG SER C 666 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR A 676 " pdb=" OD2 ASP D 675 " model vdw 2.272 3.040 nonbonded pdb=" O ARG A 663 " pdb=" OG SER A 666 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP B 675 " pdb=" OH TYR C 676 " model vdw 2.282 3.040 nonbonded pdb=" O GLN D 414 " pdb=" NH1 ARG D 418 " model vdw 2.284 3.120 ... (remaining 148214 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 74 through 202 or resid 204 through 249 or resid 251 throu \ gh 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) or \ resid 352 through 358 or (resid 359 and (name N or name CA or name C or name O \ or name CB )) or resid 360 through 365 or (resid 366 and (name N or name CA or n \ ame C or name O or name CB )) or resid 367 through 369 or (resid 370 through 376 \ and (name N or name CA or name C or name O or name CB )) or resid 377 through 4 \ 07 or (resid 408 and (name N or name CA or name C or name O or name CB )) or res \ id 409 through 410 or (resid 411 and (name N or name CA or name C or name O or n \ ame CB )) or resid 412 through 413 or (resid 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 420 or (resid 421 through 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 424 o \ r (resid 425 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 26 through 427 or (resid 428 through 433 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 434 through 436 and (name N or name CA or name C or \ name O or name CB )) or (resid 439 and (name N or name CA or name C or name O or \ name CB )) or resid 440 through 449 or (resid 462 through 464 and (name N or na \ me CA or name C or name O or name CB )) or resid 465 through 468 or (resid 469 a \ nd (name N or name CA or name C or name O or name CB )) or resid 470 through 472 \ or (resid 473 through 477 and (name N or name CA or name C or name O or name CB \ )) or resid 478 through 481 or (resid 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 or (resid 484 through 492 and (name N or name C \ A or name C or name O or name CB )) or resid 493 through 494 or (resid 495 throu \ gh 496 and (name N or name CA or name C or name O or name CB )) or resid 497 thr \ ough 498 or (resid 499 through 501 and (name N or name CA or name C or name O or \ name CB )) or resid 502 or (resid 503 through 508 and (name N or name CA or nam \ e C or name O or name CB )) or resid 509 through 561 or (resid 562 and (name N o \ r name CA or name C or name O or name CB )) or resid 563 through 572 or (resid 5 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 574 through \ 575 or (resid 576 and (name N or name CA or name C or name O or name CB )) or r \ esid 577 through 602 or (resid 603 and (name N or name CA or name C or name O or \ name CB )) or resid 604 through 605 or (resid 606 and (name N or name CA or nam \ e C or name O or name CB )) or resid 607 through 638 or (resid 639 and (name N o \ r name CA or name C or name O or name CB )) or resid 640 through 654 or (resid 6 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 656 or (res \ id 657 and (name N or name CA or name C or name O or name CB )) or resid 658 thr \ ough 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) \ or resid 663 through 669 or (resid 670 and (name N or name CA or name C or name \ O or name CB )) or resid 671 or (resid 672 and (name N or name CA or name C or n \ ame O or name CB )) or resid 673 through 681 or (resid 682 and (name N or name C \ A or name C or name O or name CB )) or resid 683 through 686 or (resid 687 throu \ gh 688 and (name N or name CA or name C or name O or name CB )) or resid 689 or \ (resid 690 through 692 and (name N or name CA or name C or name O or name CB )) \ or resid 693 through 694 or (resid 695 and (name N or name CA or name C or name \ O or name CB )) or resid 696 through 697 or (resid 698 through 710 and (name N o \ r name CA or name C or name O or name CB )) or resid 711 through 740)) selection = (chain 'B' and ((resid 74 through 76 and (name N or name CA or name C or name O \ or name CB )) or resid 77 or (resid 78 through 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 134 or (resid 135 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 157 o \ r (resid 158 through 159 and (name N or name CA or name C or name O or name CB ) \ ) or resid 160 through 202 or resid 204 through 249 or resid 251 through 353 or \ (resid 354 and (name N or name CA or name C or name O or name CB )) or resid 355 \ through 370 or (resid 371 through 376 and (name N or name CA or name C or name \ O or name CB )) or resid 377 through 379 or (resid 380 and (name N or name CA or \ name C or name O or name CB )) or resid 381 through 387 or (resid 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 through 399 or (res \ id 400 and (name N or name CA or name C or name O or name CB )) or resid 401 thr \ ough 467 or (resid 468 through 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470 through 478 or (resid 479 and (name N or name CA or nam \ e C or name O or name CB )) or resid 480 through 510 or (resid 511 through 512 a \ nd (name N or name CA or name C or name O or name CB )) or resid 513 or (resid 5 \ 14 through 519 and (name N or name CA or name C or name O or name CB )) or resid \ 520 through 521 or (resid 522 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 529 through 537 and (name N or name CA or name C or name O or \ name CB )) or resid 538 through 539 or (resid 540 and (name N or name CA or name \ C or name O or name CB )) or resid 541 through 612 or (resid 613 and (name N or \ name CA or name C or name O or name CB )) or resid 614 through 625 or (resid 62 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 627 through \ 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) or re \ sid 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) o \ r resid 678 through 683 or (resid 684 through 688 and (name N or name CA or name \ C or name O or name CB )) or resid 689 through 708 or (resid 709 through 710 an \ d (name N or name CA or name C or name O or name CB )) or resid 711 through 739 \ or (resid 740 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 74 through 202 or resid 204 through 249 or resid 251 throu \ gh 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) or \ resid 352 through 358 or (resid 359 and (name N or name CA or name C or name O \ or name CB )) or resid 360 through 365 or (resid 366 and (name N or name CA or n \ ame C or name O or name CB )) or resid 367 through 369 or (resid 370 through 376 \ and (name N or name CA or name C or name O or name CB )) or resid 377 through 4 \ 07 or (resid 408 and (name N or name CA or name C or name O or name CB )) or res \ id 409 through 410 or (resid 411 and (name N or name CA or name C or name O or n \ ame CB )) or resid 412 through 413 or (resid 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 420 or (resid 421 through 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 424 o \ r (resid 425 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 26 through 427 or (resid 428 through 433 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 434 through 436 and (name N or name CA or name C or \ name O or name CB )) or (resid 439 and (name N or name CA or name C or name O or \ name CB )) or resid 440 through 449 or (resid 462 through 464 and (name N or na \ me CA or name C or name O or name CB )) or resid 465 through 468 or (resid 469 a \ nd (name N or name CA or name C or name O or name CB )) or resid 470 through 472 \ or (resid 473 through 477 and (name N or name CA or name C or name O or name CB \ )) or resid 478 through 481 or (resid 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 or (resid 484 through 492 and (name N or name C \ A or name C or name O or name CB )) or resid 493 through 494 or (resid 495 throu \ gh 496 and (name N or name CA or name C or name O or name CB )) or resid 497 thr \ ough 498 or (resid 499 through 501 and (name N or name CA or name C or name O or \ name CB )) or resid 502 or (resid 503 through 508 and (name N or name CA or nam \ e C or name O or name CB )) or resid 509 through 561 or (resid 562 and (name N o \ r name CA or name C or name O or name CB )) or resid 563 through 572 or (resid 5 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 574 through \ 575 or (resid 576 and (name N or name CA or name C or name O or name CB )) or r \ esid 577 through 602 or (resid 603 and (name N or name CA or name C or name O or \ name CB )) or resid 604 through 605 or (resid 606 and (name N or name CA or nam \ e C or name O or name CB )) or resid 607 through 638 or (resid 639 and (name N o \ r name CA or name C or name O or name CB )) or resid 640 through 654 or (resid 6 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 656 or (res \ id 657 and (name N or name CA or name C or name O or name CB )) or resid 658 thr \ ough 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) \ or resid 663 through 669 or (resid 670 and (name N or name CA or name C or name \ O or name CB )) or resid 671 or (resid 672 and (name N or name CA or name C or n \ ame O or name CB )) or resid 673 through 681 or (resid 682 and (name N or name C \ A or name C or name O or name CB )) or resid 683 through 686 or (resid 687 throu \ gh 688 and (name N or name CA or name C or name O or name CB )) or resid 689 or \ (resid 690 through 692 and (name N or name CA or name C or name O or name CB )) \ or resid 693 through 694 or (resid 695 and (name N or name CA or name C or name \ O or name CB )) or resid 696 through 697 or (resid 698 through 710 and (name N o \ r name CA or name C or name O or name CB )) or resid 711 through 740)) selection = (chain 'D' and ((resid 74 through 76 and (name N or name CA or name C or name O \ or name CB )) or resid 77 or (resid 78 through 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 134 or (resid 135 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 157 o \ r (resid 158 through 159 and (name N or name CA or name C or name O or name CB ) \ ) or resid 160 through 202 or resid 204 through 249 or resid 251 through 353 or \ (resid 354 and (name N or name CA or name C or name O or name CB )) or resid 355 \ through 370 or (resid 371 through 376 and (name N or name CA or name C or name \ O or name CB )) or resid 377 through 379 or (resid 380 and (name N or name CA or \ name C or name O or name CB )) or resid 381 through 387 or (resid 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 through 399 or (res \ id 400 and (name N or name CA or name C or name O or name CB )) or resid 401 thr \ ough 467 or (resid 468 through 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470 through 478 or (resid 479 and (name N or name CA or nam \ e C or name O or name CB )) or resid 480 through 510 or (resid 511 through 512 a \ nd (name N or name CA or name C or name O or name CB )) or resid 513 or (resid 5 \ 14 through 519 and (name N or name CA or name C or name O or name CB )) or resid \ 520 through 521 or (resid 522 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 529 through 537 and (name N or name CA or name C or name O or \ name CB )) or resid 538 through 539 or (resid 540 and (name N or name CA or name \ C or name O or name CB )) or resid 541 through 612 or (resid 613 and (name N or \ name CA or name C or name O or name CB )) or resid 614 through 625 or (resid 62 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 627 through \ 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) or re \ sid 676 or (resid 677 and (name N or name CA or name C or name O or name CB )) o \ r resid 678 through 683 or (resid 684 through 688 and (name N or name CA or name \ C or name O or name CB )) or resid 689 through 708 or (resid 709 through 710 an \ d (name N or name CA or name C or name O or name CB )) or resid 711 through 739 \ or (resid 740 and (name N or name CA or name C or name O or name CB )))) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 59.290 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.002 0.032 19952 Z= 0.111 Angle : 0.430 6.410 27168 Z= 0.230 Chirality : 0.037 0.149 3182 Planarity : 0.003 0.033 3430 Dihedral : 9.646 79.139 6792 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.54 % Allowed : 7.33 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.17), residues: 2594 helix: 0.05 (0.14), residues: 1490 sheet: 1.53 (0.62), residues: 52 loop : -0.07 (0.21), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 272 HIS 0.002 0.000 HIS D 76 PHE 0.029 0.001 PHE B 266 TYR 0.011 0.001 TYR C 280 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 1.492 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: A 279 MET cc_start: 0.9124 (tpt) cc_final: 0.8891 (tpt) REVERT: A 347 MET cc_start: 0.9080 (mtm) cc_final: 0.8876 (mtm) REVERT: A 431 MET cc_start: 0.7801 (mtt) cc_final: 0.7598 (mtm) REVERT: B 340 MET cc_start: 0.8950 (tpp) cc_final: 0.8614 (tpp) REVERT: C 347 MET cc_start: 0.9108 (mtm) cc_final: 0.8795 (mtp) REVERT: C 431 MET cc_start: 0.7492 (mtt) cc_final: 0.7290 (mtt) REVERT: D 340 MET cc_start: 0.9000 (tpp) cc_final: 0.8730 (tpp) REVERT: D 613 LEU cc_start: 0.8382 (mm) cc_final: 0.8096 (tt) outliers start: 26 outliers final: 7 residues processed: 255 average time/residue: 0.2365 time to fit residues: 89.5883 Evaluate side-chains 141 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 480 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 40.0000 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 0.2980 chunk 151 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 359 GLN A 433 GLN A 439 GLN A 445 HIS A 667 ASN B 247 GLN B 322 ASN B 391 GLN B 575 ASN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 359 GLN C 439 GLN C 445 HIS C 667 ASN D 247 GLN D 322 ASN D 363 HIS D 391 GLN D 575 ASN ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19952 Z= 0.178 Angle : 0.573 8.056 27168 Z= 0.304 Chirality : 0.041 0.160 3182 Planarity : 0.004 0.037 3430 Dihedral : 4.541 59.919 2878 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.54 % Allowed : 11.19 % Favored : 87.27 % 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: 0.53 (0.17), residues: 2594 helix: 0.71 (0.13), residues: 1622 sheet: 1.08 (0.63), residues: 52 loop : -0.16 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 272 HIS 0.005 0.001 HIS C 203 PHE 0.028 0.001 PHE B 266 TYR 0.024 0.001 TYR D 372 ARG 0.008 0.001 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.9159 (tpt) cc_final: 0.8848 (tpt) REVERT: B 352 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7642 (pp) REVERT: C 663 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6512 (mtp85) REVERT: D 343 ILE cc_start: 0.9401 (mm) cc_final: 0.8957 (tt) REVERT: D 344 MET cc_start: 0.8850 (mmm) cc_final: 0.8463 (mmm) REVERT: D 352 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7664 (pp) outliers start: 26 outliers final: 13 residues processed: 181 average time/residue: 0.3523 time to fit residues: 98.3303 Evaluate side-chains 142 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 660 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 0.0270 chunk 236 optimal weight: 6.9990 chunk 255 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19952 Z= 0.151 Angle : 0.542 10.723 27168 Z= 0.278 Chirality : 0.040 0.159 3182 Planarity : 0.004 0.043 3430 Dihedral : 4.123 55.835 2872 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.65 % Allowed : 11.80 % Favored : 86.55 % 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: 0.88 (0.17), residues: 2594 helix: 1.13 (0.13), residues: 1650 sheet: 1.11 (0.63), residues: 52 loop : -0.36 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 85 HIS 0.004 0.001 HIS C 683 PHE 0.028 0.001 PHE B 266 TYR 0.021 0.001 TYR D 156 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 2.338 Fit side-chains revert: symmetry clash REVERT: A 279 MET cc_start: 0.9186 (tpt) cc_final: 0.8889 (tpt) REVERT: A 655 LYS cc_start: 0.7136 (pttm) cc_final: 0.6908 (pttm) REVERT: A 663 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6745 (ttm170) REVERT: B 343 ILE cc_start: 0.9355 (mm) cc_final: 0.8884 (tt) REVERT: B 344 MET cc_start: 0.8862 (mmm) cc_final: 0.8535 (mmm) REVERT: B 693 LEU cc_start: 0.6420 (mm) cc_final: 0.6030 (tt) REVERT: C 196 HIS cc_start: 0.8145 (t-170) cc_final: 0.7890 (t-170) REVERT: C 431 MET cc_start: 0.7426 (mtt) cc_final: 0.6962 (mtt) REVERT: D 340 MET cc_start: 0.8896 (tpp) cc_final: 0.8403 (tpp) REVERT: D 343 ILE cc_start: 0.9342 (mm) cc_final: 0.8834 (tt) REVERT: D 344 MET cc_start: 0.8986 (mmm) cc_final: 0.7739 (mmm) REVERT: D 478 CYS cc_start: 0.7853 (m) cc_final: 0.7340 (t) REVERT: D 693 LEU cc_start: 0.6490 (mm) cc_final: 0.6113 (tt) outliers start: 28 outliers final: 19 residues processed: 170 average time/residue: 0.2979 time to fit residues: 80.7045 Evaluate side-chains 148 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 660 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 224 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19952 Z= 0.204 Angle : 0.564 10.402 27168 Z= 0.288 Chirality : 0.041 0.162 3182 Planarity : 0.004 0.045 3430 Dihedral : 4.191 55.740 2872 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.65 % Allowed : 12.51 % Favored : 85.83 % 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: 1.09 (0.17), residues: 2594 helix: 1.33 (0.13), residues: 1638 sheet: 1.06 (0.62), residues: 52 loop : -0.31 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 272 HIS 0.003 0.001 HIS A 363 PHE 0.032 0.002 PHE C 161 TYR 0.019 0.001 TYR D 156 ARG 0.004 0.000 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8049 (tpt) cc_final: 0.7842 (tpt) REVERT: A 279 MET cc_start: 0.9186 (tpt) cc_final: 0.8872 (tpt) REVERT: A 603 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6579 (tm-30) REVERT: B 344 MET cc_start: 0.8866 (mmm) cc_final: 0.8596 (mmm) REVERT: C 169 MET cc_start: 0.8101 (tpt) cc_final: 0.7895 (tpt) REVERT: C 431 MET cc_start: 0.7372 (mtt) cc_final: 0.6930 (mtt) REVERT: D 340 MET cc_start: 0.8856 (tpp) cc_final: 0.8623 (tpp) REVERT: D 343 ILE cc_start: 0.9365 (mm) cc_final: 0.8995 (tt) outliers start: 28 outliers final: 22 residues processed: 158 average time/residue: 0.2996 time to fit residues: 75.0347 Evaluate side-chains 142 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 660 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 214 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 225 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN C 683 HIS ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19952 Z= 0.274 Angle : 0.605 9.452 27168 Z= 0.313 Chirality : 0.042 0.165 3182 Planarity : 0.004 0.049 3430 Dihedral : 4.430 56.741 2870 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.65 % Allowed : 13.01 % Favored : 85.34 % 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: 1.04 (0.17), residues: 2594 helix: 1.30 (0.13), residues: 1632 sheet: 1.22 (0.57), residues: 64 loop : -0.37 (0.23), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 272 HIS 0.005 0.001 HIS A 363 PHE 0.033 0.002 PHE B 266 TYR 0.016 0.002 TYR D 372 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 MET cc_start: 0.9165 (tpt) cc_final: 0.8855 (tpt) REVERT: A 603 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: B 343 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.8892 (tt) REVERT: B 344 MET cc_start: 0.8921 (mmm) cc_final: 0.8482 (mmm) REVERT: C 302 MET cc_start: 0.9458 (mtt) cc_final: 0.9250 (mtt) REVERT: C 431 MET cc_start: 0.7605 (mtt) cc_final: 0.7157 (mtt) REVERT: D 340 MET cc_start: 0.8851 (tpp) cc_final: 0.8464 (tpp) REVERT: D 343 ILE cc_start: 0.9466 (mm) cc_final: 0.9070 (tt) outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 0.3016 time to fit residues: 73.4521 Evaluate side-chains 143 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN A 413 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN C 413 ASN C 445 HIS ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19952 Z= 0.169 Angle : 0.556 9.864 27168 Z= 0.278 Chirality : 0.040 0.163 3182 Planarity : 0.004 0.048 3430 Dihedral : 4.197 57.237 2870 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.49 % Allowed : 13.67 % Favored : 84.84 % 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: 1.19 (0.17), residues: 2594 helix: 1.49 (0.13), residues: 1638 sheet: 0.85 (0.63), residues: 52 loop : -0.45 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 85 HIS 0.003 0.001 HIS B 586 PHE 0.030 0.001 PHE B 266 TYR 0.017 0.001 TYR A 562 ARG 0.011 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 2.321 Fit side-chains revert: symmetry clash REVERT: A 279 MET cc_start: 0.9159 (tpt) cc_final: 0.8844 (tpt) REVERT: A 431 MET cc_start: 0.8010 (mtm) cc_final: 0.7668 (ptp) REVERT: A 539 PHE cc_start: 0.6170 (t80) cc_final: 0.5906 (t80) REVERT: A 603 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: A 663 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6905 (ttm170) REVERT: B 332 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (mmmt) REVERT: B 343 ILE cc_start: 0.9417 (mm) cc_final: 0.8869 (tt) REVERT: B 344 MET cc_start: 0.8918 (mmm) cc_final: 0.8419 (mmm) REVERT: C 431 MET cc_start: 0.7645 (mtt) cc_final: 0.7221 (mtt) REVERT: D 340 MET cc_start: 0.8859 (tpp) cc_final: 0.8559 (tpp) REVERT: D 343 ILE cc_start: 0.9406 (mm) cc_final: 0.9114 (tt) outliers start: 25 outliers final: 21 residues processed: 144 average time/residue: 0.3000 time to fit residues: 69.4809 Evaluate side-chains 144 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 250 optimal weight: 50.0000 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19952 Z= 0.240 Angle : 0.588 10.317 27168 Z= 0.297 Chirality : 0.041 0.163 3182 Planarity : 0.004 0.045 3430 Dihedral : 4.327 56.829 2870 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.87 % Allowed : 13.62 % Favored : 84.51 % 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 (0.17), residues: 2594 helix: 1.49 (0.13), residues: 1634 sheet: 1.07 (0.58), residues: 64 loop : -0.36 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 81 HIS 0.004 0.001 HIS A 363 PHE 0.031 0.002 PHE B 266 TYR 0.016 0.001 TYR D 372 ARG 0.006 0.000 ARG C 591 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 279 MET cc_start: 0.9172 (tpt) cc_final: 0.8882 (tpt) REVERT: A 431 MET cc_start: 0.8108 (mtm) cc_final: 0.7881 (ptp) REVERT: A 539 PHE cc_start: 0.6206 (t80) cc_final: 0.5946 (t80) REVERT: A 603 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: A 663 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7054 (mtt-85) REVERT: B 332 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8829 (mmmt) REVERT: B 343 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.8889 (tt) REVERT: B 344 MET cc_start: 0.8936 (mmm) cc_final: 0.8422 (mmm) REVERT: B 693 LEU cc_start: 0.6461 (mm) cc_final: 0.6139 (tp) REVERT: C 431 MET cc_start: 0.7743 (mtt) cc_final: 0.7314 (mtt) REVERT: C 591 ARG cc_start: 0.8533 (mmp80) cc_final: 0.8174 (mmp80) REVERT: C 642 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7318 (tt) REVERT: D 340 MET cc_start: 0.8892 (tpp) cc_final: 0.8673 (tpp) outliers start: 32 outliers final: 23 residues processed: 149 average time/residue: 0.3024 time to fit residues: 72.6317 Evaluate side-chains 148 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 0.0670 chunk 48 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19952 Z= 0.138 Angle : 0.543 10.340 27168 Z= 0.270 Chirality : 0.040 0.159 3182 Planarity : 0.003 0.041 3430 Dihedral : 4.111 57.105 2870 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.32 % Allowed : 14.33 % Favored : 84.34 % 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: 1.33 (0.17), residues: 2594 helix: 1.63 (0.13), residues: 1646 sheet: 0.85 (0.63), residues: 52 loop : -0.47 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 85 HIS 0.007 0.001 HIS D 586 PHE 0.029 0.001 PHE B 266 TYR 0.015 0.001 TYR D 372 ARG 0.003 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 PHE cc_start: 0.6182 (t80) cc_final: 0.5912 (t80) REVERT: A 603 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: A 663 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.6966 (mtp85) REVERT: B 343 ILE cc_start: 0.9395 (mm) cc_final: 0.8845 (tt) REVERT: B 344 MET cc_start: 0.8958 (mmm) cc_final: 0.8460 (mmm) REVERT: B 693 LEU cc_start: 0.6481 (mm) cc_final: 0.6162 (tp) REVERT: C 431 MET cc_start: 0.7663 (mtt) cc_final: 0.7225 (mtt) REVERT: C 539 PHE cc_start: 0.6030 (t80) cc_final: 0.5769 (t80) REVERT: C 591 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8273 (mmp80) REVERT: C 642 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7461 (tt) REVERT: C 648 PHE cc_start: 0.8031 (m-10) cc_final: 0.7817 (m-80) REVERT: D 340 MET cc_start: 0.8863 (tpp) cc_final: 0.8621 (tpp) REVERT: D 343 ILE cc_start: 0.9432 (mm) cc_final: 0.9109 (tt) REVERT: D 693 LEU cc_start: 0.6517 (mm) cc_final: 0.6187 (tp) outliers start: 22 outliers final: 17 residues processed: 146 average time/residue: 0.3062 time to fit residues: 71.6098 Evaluate side-chains 148 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 660 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 183 optimal weight: 0.0040 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 232 optimal weight: 40.0000 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19952 Z= 0.266 Angle : 0.605 10.140 27168 Z= 0.307 Chirality : 0.042 0.180 3182 Planarity : 0.004 0.041 3430 Dihedral : 4.356 56.854 2870 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.65 % Allowed : 13.89 % Favored : 84.45 % 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: 1.27 (0.18), residues: 2594 helix: 1.55 (0.13), residues: 1638 sheet: 0.64 (0.62), residues: 52 loop : -0.40 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 81 HIS 0.006 0.001 HIS D 586 PHE 0.031 0.002 PHE D 266 TYR 0.018 0.002 TYR A 562 ARG 0.004 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: A 279 MET cc_start: 0.9167 (tpt) cc_final: 0.8870 (tpt) REVERT: A 591 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8121 (mmm160) REVERT: A 603 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: A 663 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.6979 (mtp85) REVERT: B 332 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8840 (mmmt) REVERT: B 340 MET cc_start: 0.8868 (tpp) cc_final: 0.8518 (tpp) REVERT: B 344 MET cc_start: 0.8958 (mmm) cc_final: 0.8463 (mmm) REVERT: B 605 VAL cc_start: 0.3409 (OUTLIER) cc_final: 0.3191 (t) REVERT: B 693 LEU cc_start: 0.6381 (mm) cc_final: 0.6058 (tp) REVERT: C 431 MET cc_start: 0.7824 (mtt) cc_final: 0.7343 (mtt) REVERT: C 642 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7474 (tt) REVERT: D 340 MET cc_start: 0.8896 (tpp) cc_final: 0.8677 (tpp) REVERT: D 605 VAL cc_start: 0.3518 (OUTLIER) cc_final: 0.3305 (t) REVERT: D 693 LEU cc_start: 0.6368 (mm) cc_final: 0.5988 (tp) outliers start: 28 outliers final: 21 residues processed: 148 average time/residue: 0.2977 time to fit residues: 71.0864 Evaluate side-chains 149 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 609 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 171 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 644 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 ASN ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19952 Z= 0.140 Angle : 0.550 10.472 27168 Z= 0.273 Chirality : 0.040 0.173 3182 Planarity : 0.003 0.038 3430 Dihedral : 4.109 57.309 2870 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.21 % Allowed : 14.44 % Favored : 84.34 % 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: 1.39 (0.18), residues: 2594 helix: 1.68 (0.13), residues: 1648 sheet: 0.81 (0.63), residues: 52 loop : -0.46 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.005 0.001 HIS D 586 PHE 0.030 0.001 PHE B 266 TYR 0.020 0.001 TYR A 562 ARG 0.005 0.000 ARG C 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 2.290 Fit side-chains revert: symmetry clash REVERT: A 603 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: A 663 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.6900 (mtp85) REVERT: B 343 ILE cc_start: 0.9402 (mm) cc_final: 0.8851 (tt) REVERT: B 344 MET cc_start: 0.8958 (mmm) cc_final: 0.8453 (mmm) REVERT: B 693 LEU cc_start: 0.6477 (mm) cc_final: 0.6183 (tp) REVERT: C 431 MET cc_start: 0.7747 (mtt) cc_final: 0.7275 (mtt) REVERT: C 642 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7614 (tt) REVERT: D 340 MET cc_start: 0.8874 (tpp) cc_final: 0.8664 (tpp) REVERT: D 343 ILE cc_start: 0.9423 (mm) cc_final: 0.9103 (tt) outliers start: 20 outliers final: 17 residues processed: 149 average time/residue: 0.3050 time to fit residues: 72.4953 Evaluate side-chains 144 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 609 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.3980 chunk 219 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068427 restraints weight = 127741.988| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.45 r_work: 0.3075 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19952 Z= 0.170 Angle : 0.555 10.753 27168 Z= 0.277 Chirality : 0.040 0.169 3182 Planarity : 0.003 0.038 3430 Dihedral : 4.093 56.478 2870 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.32 % Allowed : 14.55 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.18), residues: 2594 helix: 1.71 (0.13), residues: 1648 sheet: 0.77 (0.63), residues: 52 loop : -0.46 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 81 HIS 0.005 0.001 HIS D 586 PHE 0.030 0.001 PHE B 266 TYR 0.020 0.001 TYR A 562 ARG 0.006 0.000 ARG A 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3765.37 seconds wall clock time: 121 minutes 23.05 seconds (7283.05 seconds total)