Starting phenix.real_space_refine on Thu May 29 01:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0e_18790/05_2025/8r0e_18790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0e_18790/05_2025/8r0e_18790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0e_18790/05_2025/8r0e_18790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0e_18790/05_2025/8r0e_18790.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0e_18790/05_2025/8r0e_18790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0e_18790/05_2025/8r0e_18790.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 138 5.16 5 C 19954 2.51 5 N 5808 2.21 5 O 6156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32056 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "B" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "C" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "D" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5344 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "E" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5344 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Chain: "F" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5342 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 711} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 318 Time building chain proxies: 17.78, per 1000 atoms: 0.55 Number of scatterers: 32056 At special positions: 0 Unit cell: (176.3, 178.02, 118.68, 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 138 16.00 O 6156 8.00 N 5808 7.00 C 19954 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: 8.51 Conformation dependent library (CDL) restraints added in 4.6 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 48.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN A 90 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.018A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.836A pdb=" N GLY A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.587A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.866A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.586A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 716 Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN B 90 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.751A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.019A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.836A pdb=" N GLY B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.588A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.866A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.517A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 609 removed outlier: 3.576A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.635A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.609A pdb=" N ASN C 90 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 removed outlier: 3.984A pdb=" N GLU C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.018A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.837A pdb=" N GLY C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.073A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.559A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 427 removed outlier: 4.284A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.588A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.867A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 609 removed outlier: 3.583A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.924A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.635A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 765 removed outlier: 3.776A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.607A pdb=" N ASN D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.711A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.019A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.837A pdb=" N GLY D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 349 through 353' Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.790A pdb=" N GLU D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU D 440 " --> pdb=" O THR D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.588A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.866A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.517A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 609 removed outlier: 3.617A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 678 removed outlier: 3.720A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN E 90 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.711A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.019A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.836A pdb=" N GLY E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU E 433 " --> pdb=" O LEU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU E 440 " --> pdb=" O THR E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.587A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.867A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 609 removed outlier: 3.562A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.807A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 716 Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 765 removed outlier: 3.775A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.608A pdb=" N ASN F 90 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.751A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 5.018A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.836A pdb=" N GLY F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 278 through 296 removed outlier: 4.162A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.074A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 334 removed outlier: 3.608A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.560A pdb=" N SER F 352 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 349 through 353' Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 407 through 427 removed outlier: 4.285A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 433 removed outlier: 3.789A pdb=" N GLU F 433 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 removed outlier: 4.112A pdb=" N GLU F 440 " --> pdb=" O THR F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.587A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.391A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.867A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.810A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.518A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 removed outlier: 3.591A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.923A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.808A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 678 removed outlier: 3.719A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.636A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 765 removed outlier: 3.776A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.749A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 240 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.750A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 240 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.749A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY C 240 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 27 through 29 Processing sheet with id=AB5, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.750A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 240 " --> pdb=" O PHE D 363 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.668A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AB9, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.748A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY E 240 " --> pdb=" O PHE E 363 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.669A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AC4, first strand: chain 'F' and resid 58 through 60 Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.749A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY F 240 " --> pdb=" O PHE F 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.668A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1408 hydrogen bonds defined for protein. 3990 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: 10.71 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7127 1.33 - 1.45: 6572 1.45 - 1.57: 18571 1.57 - 1.69: 2 1.69 - 1.81: 234 Bond restraints: 32506 Sorted by residual: bond pdb=" C LEU C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.44e-02 4.82e+03 1.89e+01 bond pdb=" C LEU D 117 " pdb=" N PRO D 118 " ideal model delta sigma weight residual 1.326 1.389 -0.062 1.44e-02 4.82e+03 1.88e+01 bond pdb=" C LEU A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.44e-02 4.82e+03 1.85e+01 bond pdb=" C LEU B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.44e-02 4.82e+03 1.84e+01 bond pdb=" C LEU E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.44e-02 4.82e+03 1.84e+01 ... (remaining 32501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 42716 2.91 - 5.83: 1179 5.83 - 8.74: 177 8.74 - 11.66: 39 11.66 - 14.57: 7 Bond angle restraints: 44118 Sorted by residual: angle pdb=" N LYS E 190 " pdb=" CA LYS E 190 " pdb=" C LYS E 190 " ideal model delta sigma weight residual 108.78 118.93 -10.15 8.20e-01 1.49e+00 1.53e+02 angle pdb=" N GLU C 200 " pdb=" CA GLU C 200 " pdb=" C GLU C 200 " ideal model delta sigma weight residual 111.52 96.95 14.57 1.40e+00 5.10e-01 1.08e+02 angle pdb=" N LYS B 190 " pdb=" CA LYS B 190 " pdb=" C LYS B 190 " ideal model delta sigma weight residual 108.75 118.37 -9.62 9.60e-01 1.09e+00 1.00e+02 angle pdb=" N LYS F 190 " pdb=" CA LYS F 190 " pdb=" C LYS F 190 " ideal model delta sigma weight residual 108.75 117.94 -9.19 9.60e-01 1.09e+00 9.16e+01 angle pdb=" C LEU E 117 " pdb=" N PRO E 118 " pdb=" CA PRO E 118 " ideal model delta sigma weight residual 120.98 111.66 9.32 1.07e+00 8.73e-01 7.59e+01 ... (remaining 44113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 17867 16.98 - 33.96: 1686 33.96 - 50.94: 284 50.94 - 67.92: 79 67.92 - 84.90: 48 Dihedral angle restraints: 19964 sinusoidal: 6962 harmonic: 13002 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N PRO A 170 " pdb=" CA PRO A 170 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP D 169 " pdb=" C ASP D 169 " pdb=" N PRO D 170 " pdb=" CA PRO D 170 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP B 169 " pdb=" C ASP B 169 " pdb=" N PRO B 170 " pdb=" CA PRO B 170 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 19961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 5100 0.339 - 0.678: 8 0.678 - 1.017: 0 1.017 - 1.357: 0 1.357 - 1.696: 6 Chirality restraints: 5114 Sorted by residual: chirality pdb=" CG LEU B 222 " pdb=" CB LEU B 222 " pdb=" CD1 LEU B 222 " pdb=" CD2 LEU B 222 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" CG LEU E 222 " pdb=" CB LEU E 222 " pdb=" CD1 LEU E 222 " pdb=" CD2 LEU E 222 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.18e+01 chirality pdb=" CG LEU F 222 " pdb=" CB LEU F 222 " pdb=" CD1 LEU F 222 " pdb=" CD2 LEU F 222 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.17e+01 ... (remaining 5111 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 371 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO D 372 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 371 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.62e+00 pdb=" N PRO A 372 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 371 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.62e+00 pdb=" N PRO F 372 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO F 372 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 372 " 0.042 5.00e-02 4.00e+02 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 177 2.57 - 3.15: 26105 3.15 - 3.74: 44697 3.74 - 4.32: 61209 4.32 - 4.90: 101740 Nonbonded interactions: 233928 Sorted by model distance: nonbonded pdb=" O ARG E 313 " pdb=" OG1 THR E 316 " model vdw 1.990 3.040 nonbonded pdb=" O ARG F 313 " pdb=" OG1 THR F 316 " model vdw 1.991 3.040 nonbonded pdb=" O ARG B 313 " pdb=" OG1 THR B 316 " model vdw 1.991 3.040 nonbonded pdb=" O ARG D 313 " pdb=" OG1 THR D 316 " model vdw 1.991 3.040 nonbonded pdb=" O ARG A 313 " pdb=" OG1 THR A 316 " model vdw 1.991 3.040 ... (remaining 233923 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 774)) selection = (chain 'E' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 774)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.060 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 66.550 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.012 0.164 32506 Z= 0.483 Angle : 1.204 14.569 44118 Z= 0.703 Chirality : 0.089 1.696 5114 Planarity : 0.008 0.078 5976 Dihedral : 14.995 84.898 11516 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.10), residues: 4512 helix: -2.88 (0.09), residues: 1992 sheet: -0.27 (0.24), residues: 438 loop : -3.92 (0.11), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 454 HIS 0.009 0.002 HIS C 406 PHE 0.030 0.003 PHE C 575 TYR 0.014 0.002 TYR D 244 ARG 0.008 0.001 ARG C 708 Details of bonding type rmsd hydrogen bonds : bond 0.17550 ( 1408) hydrogen bonds : angle 6.86657 ( 3990) covalent geometry : bond 0.01236 (32506) covalent geometry : angle 1.20445 (44118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 543 time to evaluate : 3.705 Fit side-chains REVERT: A 211 LYS cc_start: 0.7056 (mtpt) cc_final: 0.6834 (mtmm) REVERT: A 295 LYS cc_start: 0.6466 (mttp) cc_final: 0.6143 (mmtt) REVERT: A 742 PHE cc_start: 0.6763 (m-10) cc_final: 0.6267 (m-80) REVERT: A 753 ARG cc_start: 0.6163 (mtm110) cc_final: 0.5869 (mmp80) REVERT: B 225 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.6306 (ttp80) REVERT: B 295 LYS cc_start: 0.6700 (mttp) cc_final: 0.6239 (mmtt) REVERT: B 340 HIS cc_start: 0.6506 (m90) cc_final: 0.6133 (m-70) REVERT: B 753 ARG cc_start: 0.6180 (mtm110) cc_final: 0.5763 (mmp80) REVERT: C 560 ARG cc_start: 0.6907 (ttm170) cc_final: 0.6544 (ttm-80) REVERT: C 753 ARG cc_start: 0.6045 (mtm110) cc_final: 0.5807 (mmp80) REVERT: D 211 LYS cc_start: 0.6954 (mtpt) cc_final: 0.6624 (mmpt) REVERT: D 753 ARG cc_start: 0.6161 (mtm110) cc_final: 0.5609 (mmp80) REVERT: E 225 ARG cc_start: 0.6523 (ttm-80) cc_final: 0.6232 (ttp80) REVERT: E 285 ASN cc_start: 0.6817 (m110) cc_final: 0.6611 (m110) REVERT: E 295 LYS cc_start: 0.6707 (mttp) cc_final: 0.6238 (mmtt) REVERT: E 340 HIS cc_start: 0.6593 (m90) cc_final: 0.6261 (m-70) REVERT: E 560 ARG cc_start: 0.6809 (ttm170) cc_final: 0.6451 (ttm-80) REVERT: E 753 ARG cc_start: 0.6045 (mtm110) cc_final: 0.5806 (mmp80) REVERT: F 560 ARG cc_start: 0.7016 (ttm170) cc_final: 0.6643 (ttm-80) REVERT: F 753 ARG cc_start: 0.6052 (mtm110) cc_final: 0.5779 (mmp80) outliers start: 2 outliers final: 0 residues processed: 545 average time/residue: 1.8693 time to fit residues: 1156.6854 Evaluate side-chains 403 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 50.0000 chunk 341 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 230 optimal weight: 0.0070 chunk 182 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 214 optimal weight: 0.0970 chunk 262 optimal weight: 0.0980 chunk 408 optimal weight: 1.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 340 HIS C 260 ASN C 533 ASN C 624 ASN D 285 ASN D 340 HIS F 260 ASN F 533 ASN F 624 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.220153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.193469 restraints weight = 32661.238| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.08 r_work: 0.3766 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32506 Z= 0.138 Angle : 0.621 6.754 44118 Z= 0.332 Chirality : 0.045 0.205 5114 Planarity : 0.004 0.045 5976 Dihedral : 5.182 24.545 4800 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.94 % Allowed : 11.39 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.12), residues: 4512 helix: -0.56 (0.11), residues: 1932 sheet: -0.08 (0.24), residues: 522 loop : -3.09 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 454 HIS 0.006 0.001 HIS C 317 PHE 0.020 0.001 PHE D 265 TYR 0.012 0.001 TYR D 203 ARG 0.004 0.000 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 1408) hydrogen bonds : angle 4.73574 ( 3990) covalent geometry : bond 0.00277 (32506) covalent geometry : angle 0.62071 (44118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 428 time to evaluate : 3.923 Fit side-chains REVERT: A 295 LYS cc_start: 0.6258 (mttp) cc_final: 0.5917 (mmtt) REVERT: A 442 MET cc_start: 0.4834 (ptp) cc_final: 0.3988 (tmm) REVERT: A 678 MET cc_start: 0.6340 (mmp) cc_final: 0.6018 (mpm) REVERT: A 742 PHE cc_start: 0.6855 (m-10) cc_final: 0.6018 (m-80) REVERT: A 753 ARG cc_start: 0.6337 (mtm110) cc_final: 0.6023 (mmp80) REVERT: B 256 ARG cc_start: 0.7458 (mpt-90) cc_final: 0.7179 (mpp80) REVERT: B 295 LYS cc_start: 0.6431 (mttp) cc_final: 0.6201 (mmtm) REVERT: B 324 ILE cc_start: 0.8120 (tt) cc_final: 0.7863 (tp) REVERT: B 340 HIS cc_start: 0.6542 (m90) cc_final: 0.6039 (m-70) REVERT: B 554 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 568 GLN cc_start: 0.7509 (mm110) cc_final: 0.7287 (mt0) REVERT: B 720 MET cc_start: 0.2711 (OUTLIER) cc_final: 0.2267 (mpm) REVERT: B 742 PHE cc_start: 0.6832 (m-10) cc_final: 0.6093 (m-80) REVERT: C 256 ARG cc_start: 0.7372 (mpt-90) cc_final: 0.7059 (mpt-90) REVERT: C 508 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7144 (ttt) REVERT: C 560 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7189 (ttm-80) REVERT: D 210 ARG cc_start: 0.5695 (tpm170) cc_final: 0.5253 (ttp-110) REVERT: D 256 ARG cc_start: 0.7404 (mpt-90) cc_final: 0.7111 (mpp80) REVERT: D 275 MET cc_start: 0.8561 (mmm) cc_final: 0.8349 (mmm) REVERT: D 288 LYS cc_start: 0.7520 (mttt) cc_final: 0.7130 (mmmt) REVERT: D 295 LYS cc_start: 0.6430 (mttp) cc_final: 0.6133 (mmtt) REVERT: D 442 MET cc_start: 0.4791 (ptp) cc_final: 0.3928 (tmm) REVERT: D 508 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7145 (ttt) REVERT: D 753 ARG cc_start: 0.6190 (mtm110) cc_final: 0.5854 (mmp80) REVERT: E 256 ARG cc_start: 0.7451 (mpt-90) cc_final: 0.7189 (mpp80) REVERT: E 295 LYS cc_start: 0.6443 (mttp) cc_final: 0.6220 (mmtm) REVERT: E 324 ILE cc_start: 0.8130 (tt) cc_final: 0.7882 (tp) REVERT: E 340 HIS cc_start: 0.6560 (m90) cc_final: 0.6061 (m-70) REVERT: E 554 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: E 568 GLN cc_start: 0.7528 (mm110) cc_final: 0.7302 (mt0) REVERT: E 720 MET cc_start: 0.2699 (OUTLIER) cc_final: 0.2235 (mpm) REVERT: E 742 PHE cc_start: 0.6824 (m-10) cc_final: 0.6093 (m-80) REVERT: F 219 MET cc_start: 0.7815 (mtt) cc_final: 0.7543 (mtm) REVERT: F 256 ARG cc_start: 0.7422 (mpt-90) cc_final: 0.7120 (mpt-90) REVERT: F 295 LYS cc_start: 0.6420 (mttp) cc_final: 0.6216 (mmtm) REVERT: F 508 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7130 (ttt) REVERT: F 560 ARG cc_start: 0.7438 (ttm170) cc_final: 0.7201 (ttm-80) outliers start: 55 outliers final: 19 residues processed: 458 average time/residue: 1.8127 time to fit residues: 949.0658 Evaluate side-chains 386 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 360 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 741 ARG Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 161 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 386 optimal weight: 0.6980 chunk 425 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 367 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 320 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 227 optimal weight: 30.0000 chunk 315 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN C 285 ASN C 327 GLN E 260 ASN E 285 ASN F 285 ASN F 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.213582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.188903 restraints weight = 32419.683| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.02 r_work: 0.3727 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32506 Z= 0.199 Angle : 0.719 8.154 44118 Z= 0.380 Chirality : 0.050 0.201 5114 Planarity : 0.005 0.042 5976 Dihedral : 5.180 23.527 4800 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.86 % Allowed : 13.08 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.94 (0.12), residues: 4512 helix: -0.26 (0.11), residues: 2016 sheet: 0.25 (0.24), residues: 522 loop : -2.90 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 476 HIS 0.006 0.001 HIS E 317 PHE 0.023 0.002 PHE D 265 TYR 0.021 0.002 TYR D 203 ARG 0.004 0.001 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.07295 ( 1408) hydrogen bonds : angle 4.86117 ( 3990) covalent geometry : bond 0.00466 (32506) covalent geometry : angle 0.71881 (44118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 386 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6680 (mmpt) REVERT: A 295 LYS cc_start: 0.6373 (mttp) cc_final: 0.6037 (mmtt) REVERT: A 427 MET cc_start: 0.5285 (mpm) cc_final: 0.4516 (mmt) REVERT: A 442 MET cc_start: 0.5105 (ptp) cc_final: 0.4270 (tmm) REVERT: A 599 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8175 (ptm160) REVERT: A 641 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.7025 (mt0) REVERT: A 678 MET cc_start: 0.6536 (mmp) cc_final: 0.6218 (mpm) REVERT: A 742 PHE cc_start: 0.7112 (m-10) cc_final: 0.6269 (m-80) REVERT: B 256 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7645 (mpp80) REVERT: B 340 HIS cc_start: 0.6677 (m90) cc_final: 0.6170 (m-70) REVERT: B 554 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 568 GLN cc_start: 0.7793 (mm110) cc_final: 0.7585 (mm110) REVERT: B 611 MET cc_start: 0.7962 (ptt) cc_final: 0.7606 (ptp) REVERT: B 641 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6963 (mt0) REVERT: B 663 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7129 (mtmm) REVERT: B 720 MET cc_start: 0.3053 (OUTLIER) cc_final: 0.2403 (mpm) REVERT: B 742 PHE cc_start: 0.6956 (m-10) cc_final: 0.6244 (m-80) REVERT: C 218 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: C 256 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7418 (mpt-90) REVERT: C 283 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 417 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: C 508 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7319 (ttt) REVERT: C 560 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7818 (ttp80) REVERT: D 256 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7445 (mpp80) REVERT: D 295 LYS cc_start: 0.6508 (mttp) cc_final: 0.6160 (mmtt) REVERT: D 442 MET cc_start: 0.4973 (ptp) cc_final: 0.4347 (tmm) REVERT: D 641 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: D 678 MET cc_start: 0.6781 (mmp) cc_final: 0.6327 (mpm) REVERT: D 742 PHE cc_start: 0.7125 (m-10) cc_final: 0.6359 (m-80) REVERT: D 751 ASP cc_start: 0.7039 (m-30) cc_final: 0.6824 (m-30) REVERT: D 753 ARG cc_start: 0.6518 (mtm110) cc_final: 0.6165 (mmp80) REVERT: E 256 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7648 (mpp80) REVERT: E 554 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: E 560 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: E 568 GLN cc_start: 0.7783 (mm110) cc_final: 0.7578 (mm110) REVERT: E 611 MET cc_start: 0.7960 (ptt) cc_final: 0.7590 (ptp) REVERT: E 641 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: E 720 MET cc_start: 0.2953 (OUTLIER) cc_final: 0.2330 (mpm) REVERT: E 742 PHE cc_start: 0.6997 (m-10) cc_final: 0.6265 (m-80) REVERT: F 218 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: F 256 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7401 (mpt-90) REVERT: F 283 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7154 (mt-10) REVERT: F 417 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: F 442 MET cc_start: 0.5157 (ptp) cc_final: 0.4473 (mmp) REVERT: F 508 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7275 (ttt) REVERT: F 560 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7826 (ttp80) outliers start: 81 outliers final: 23 residues processed: 436 average time/residue: 1.8005 time to fit residues: 895.2340 Evaluate side-chains 410 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 364 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 641 GLN Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 641 GLN Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 641 GLN Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 641 GLN Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 615 LYS Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 203 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 444 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN C 327 GLN C 624 ASN D 327 GLN D 624 ASN E 260 ASN F 327 GLN F 624 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.213284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183348 restraints weight = 32631.137| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.33 r_work: 0.3546 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32506 Z= 0.142 Angle : 0.603 7.130 44118 Z= 0.320 Chirality : 0.046 0.205 5114 Planarity : 0.004 0.044 5976 Dihedral : 4.719 20.980 4800 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.32 % Allowed : 14.78 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.34 (0.12), residues: 4512 helix: 0.31 (0.12), residues: 1974 sheet: 0.56 (0.25), residues: 522 loop : -2.61 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 454 HIS 0.003 0.001 HIS E 317 PHE 0.022 0.002 PHE D 265 TYR 0.015 0.001 TYR D 203 ARG 0.005 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.05661 ( 1408) hydrogen bonds : angle 4.53311 ( 3990) covalent geometry : bond 0.00323 (32506) covalent geometry : angle 0.60270 (44118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 376 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6003 (mm-30) REVERT: A 427 MET cc_start: 0.5263 (mpm) cc_final: 0.4317 (mmt) REVERT: A 599 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8072 (ptm160) REVERT: A 608 MET cc_start: 0.8745 (mtm) cc_final: 0.8541 (mtm) REVERT: A 678 MET cc_start: 0.6483 (mmp) cc_final: 0.5986 (mpm) REVERT: A 742 PHE cc_start: 0.6992 (m-80) cc_final: 0.6168 (m-80) REVERT: A 756 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6033 (mt-10) REVERT: B 211 LYS cc_start: 0.6922 (mtpt) cc_final: 0.6472 (tmtt) REVERT: B 256 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7437 (mpp80) REVERT: B 340 HIS cc_start: 0.6706 (m90) cc_final: 0.6118 (m-70) REVERT: B 534 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 554 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 568 GLN cc_start: 0.7529 (mm110) cc_final: 0.7215 (mt0) REVERT: B 611 MET cc_start: 0.7969 (ptt) cc_final: 0.7630 (ptp) REVERT: B 720 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.2277 (mpm) REVERT: B 742 PHE cc_start: 0.6873 (m-10) cc_final: 0.6030 (m-80) REVERT: B 772 ARG cc_start: 0.6728 (mmm160) cc_final: 0.6515 (mmt180) REVERT: C 218 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: C 256 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7215 (mpt-90) REVERT: C 283 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6874 (mt-10) REVERT: C 364 ASP cc_start: 0.7738 (p0) cc_final: 0.7457 (p0) REVERT: C 417 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7067 (tp30) REVERT: C 427 MET cc_start: 0.5418 (mmt) cc_final: 0.4319 (mmt) REVERT: C 508 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7139 (ttt) REVERT: C 560 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7679 (ttp80) REVERT: D 211 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6579 (tptt) REVERT: D 256 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7358 (mpp80) REVERT: D 295 LYS cc_start: 0.6374 (mttp) cc_final: 0.6046 (mmtt) REVERT: D 427 MET cc_start: 0.5205 (mpm) cc_final: 0.4237 (mmt) REVERT: D 678 MET cc_start: 0.6726 (mmp) cc_final: 0.6224 (mpm) REVERT: D 742 PHE cc_start: 0.7134 (m-80) cc_final: 0.6303 (m-80) REVERT: D 753 ARG cc_start: 0.6549 (mtm110) cc_final: 0.6271 (mtm-85) REVERT: E 211 LYS cc_start: 0.6934 (mtpt) cc_final: 0.6466 (tmtt) REVERT: E 256 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7443 (mpp80) REVERT: E 554 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: E 560 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7913 (ttm170) REVERT: E 568 GLN cc_start: 0.7570 (mm110) cc_final: 0.7247 (mt0) REVERT: E 611 MET cc_start: 0.7976 (ptt) cc_final: 0.7627 (ptp) REVERT: E 720 MET cc_start: 0.2849 (OUTLIER) cc_final: 0.2271 (mpm) REVERT: E 742 PHE cc_start: 0.6891 (m-10) cc_final: 0.6029 (m-80) REVERT: E 772 ARG cc_start: 0.6708 (mmm160) cc_final: 0.6489 (mmt180) REVERT: F 218 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: F 283 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6872 (mt-10) REVERT: F 364 ASP cc_start: 0.7739 (p0) cc_final: 0.7451 (p0) REVERT: F 417 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7087 (tp30) REVERT: F 427 MET cc_start: 0.5400 (mmt) cc_final: 0.4316 (mmt) REVERT: F 508 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7145 (ttt) REVERT: F 560 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7685 (ttp80) outliers start: 94 outliers final: 34 residues processed: 431 average time/residue: 1.6949 time to fit residues: 833.2616 Evaluate side-chains 418 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 217 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 446 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 chunk 320 optimal weight: 0.9980 chunk 228 optimal weight: 40.0000 chunk 243 optimal weight: 0.0060 chunk 221 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 44 optimal weight: 0.0270 overall best weight: 1.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.214562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182999 restraints weight = 32575.790| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.27 r_work: 0.3579 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32506 Z= 0.115 Angle : 0.537 8.685 44118 Z= 0.285 Chirality : 0.045 0.200 5114 Planarity : 0.004 0.044 5976 Dihedral : 4.277 19.659 4800 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.39 % Allowed : 15.98 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.67 (0.13), residues: 4512 helix: 0.92 (0.12), residues: 1944 sheet: 0.73 (0.25), residues: 522 loop : -2.22 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.001 0.000 HIS B 317 PHE 0.019 0.001 PHE D 265 TYR 0.012 0.001 TYR D 203 ARG 0.004 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 1408) hydrogen bonds : angle 4.25514 ( 3990) covalent geometry : bond 0.00256 (32506) covalent geometry : angle 0.53700 (44118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 384 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6483 (mmpt) REVERT: A 321 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6143 (mm-30) REVERT: A 427 MET cc_start: 0.5391 (mpm) cc_final: 0.4420 (mmt) REVERT: A 599 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8131 (ptm160) REVERT: A 608 MET cc_start: 0.8862 (mtm) cc_final: 0.8636 (mtm) REVERT: A 674 PHE cc_start: 0.7061 (t80) cc_final: 0.6697 (t80) REVERT: A 678 MET cc_start: 0.6472 (mmp) cc_final: 0.5891 (mpm) REVERT: A 742 PHE cc_start: 0.7047 (m-80) cc_final: 0.6131 (m-80) REVERT: A 756 GLU cc_start: 0.6746 (mm-30) cc_final: 0.5757 (mt-10) REVERT: A 757 MET cc_start: 0.6783 (mtt) cc_final: 0.6167 (mmt) REVERT: B 211 LYS cc_start: 0.6858 (mtpt) cc_final: 0.6228 (tptm) REVERT: B 288 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7590 (mppt) REVERT: B 315 LYS cc_start: 0.5285 (mmmt) cc_final: 0.5059 (mmtt) REVERT: B 340 HIS cc_start: 0.6788 (m90) cc_final: 0.6224 (m-70) REVERT: B 487 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7519 (ttp80) REVERT: B 554 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: B 568 GLN cc_start: 0.7628 (mm110) cc_final: 0.7156 (mt0) REVERT: B 720 MET cc_start: 0.2768 (OUTLIER) cc_final: 0.2118 (mpm) REVERT: B 742 PHE cc_start: 0.6743 (m-80) cc_final: 0.5771 (m-80) REVERT: B 754 LYS cc_start: 0.7358 (mtmt) cc_final: 0.7084 (mtpp) REVERT: C 218 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: C 283 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6683 (mm-30) REVERT: C 288 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7336 (mptp) REVERT: C 417 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: C 427 MET cc_start: 0.5437 (mmt) cc_final: 0.4309 (mmt) REVERT: C 508 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7318 (ttt) REVERT: C 554 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 560 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7861 (ttm-80) REVERT: C 611 MET cc_start: 0.7933 (ptt) cc_final: 0.7514 (ptm) REVERT: C 651 LYS cc_start: 0.7193 (mppt) cc_final: 0.6979 (mptt) REVERT: D 211 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6351 (tptt) REVERT: D 427 MET cc_start: 0.5256 (mpm) cc_final: 0.4477 (mmt) REVERT: D 608 MET cc_start: 0.8835 (mtm) cc_final: 0.8623 (mtm) REVERT: D 678 MET cc_start: 0.6758 (mmp) cc_final: 0.6016 (mpm) REVERT: D 742 PHE cc_start: 0.7047 (m-80) cc_final: 0.6110 (m-80) REVERT: D 753 ARG cc_start: 0.6602 (mtm110) cc_final: 0.5932 (mtm-85) REVERT: D 756 GLU cc_start: 0.6790 (mm-30) cc_final: 0.5759 (mt-10) REVERT: D 757 MET cc_start: 0.6789 (mtt) cc_final: 0.6119 (mmt) REVERT: E 211 LYS cc_start: 0.6865 (mtpt) cc_final: 0.6227 (tptm) REVERT: E 256 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7568 (mpp80) REVERT: E 288 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7566 (mppt) REVERT: E 315 LYS cc_start: 0.5324 (mmmt) cc_final: 0.5104 (mmtt) REVERT: E 554 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: E 568 GLN cc_start: 0.7649 (mm110) cc_final: 0.7189 (mt0) REVERT: E 720 MET cc_start: 0.2743 (OUTLIER) cc_final: 0.2096 (mpm) REVERT: E 742 PHE cc_start: 0.6766 (m-80) cc_final: 0.5787 (m-80) REVERT: E 754 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7076 (mtpp) REVERT: F 218 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: F 283 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6662 (mm-30) REVERT: F 288 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7329 (mptp) REVERT: F 417 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: F 427 MET cc_start: 0.5448 (mmt) cc_final: 0.4325 (mmt) REVERT: F 508 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7317 (ttt) REVERT: F 554 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7849 (mt-10) REVERT: F 560 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7912 (ttm-80) REVERT: F 611 MET cc_start: 0.7902 (ptt) cc_final: 0.7486 (ptm) outliers start: 96 outliers final: 36 residues processed: 441 average time/residue: 1.7357 time to fit residues: 875.9727 Evaluate side-chains 424 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 369 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 315 optimal weight: 0.0010 chunk 54 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 283 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 234 optimal weight: 30.0000 chunk 329 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 392 optimal weight: 30.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN B 760 GLN C 327 GLN D 327 GLN E 327 GLN E 760 GLN F 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.210304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180076 restraints weight = 32481.366| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.27 r_work: 0.3524 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 32506 Z= 0.245 Angle : 0.752 8.056 44118 Z= 0.399 Chirality : 0.052 0.204 5114 Planarity : 0.006 0.049 5976 Dihedral : 5.051 25.332 4800 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.10 % Allowed : 15.88 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4512 helix: 0.18 (0.11), residues: 1986 sheet: 1.33 (0.26), residues: 450 loop : -2.52 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 476 HIS 0.004 0.001 HIS E 317 PHE 0.023 0.002 PHE C 265 TYR 0.021 0.003 TYR D 203 ARG 0.007 0.001 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.07812 ( 1408) hydrogen bonds : angle 4.80951 ( 3990) covalent geometry : bond 0.00588 (32506) covalent geometry : angle 0.75150 (44118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 367 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6597 (mmpt) REVERT: A 295 LYS cc_start: 0.6480 (mttp) cc_final: 0.6119 (mmtt) REVERT: A 321 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6458 (mm-30) REVERT: A 448 THR cc_start: 0.6972 (p) cc_final: 0.6638 (t) REVERT: A 599 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8300 (ptm160) REVERT: A 608 MET cc_start: 0.8914 (mtm) cc_final: 0.8690 (mtm) REVERT: A 678 MET cc_start: 0.6497 (mmp) cc_final: 0.5822 (mpm) REVERT: A 742 PHE cc_start: 0.7126 (m-80) cc_final: 0.6206 (m-80) REVERT: B 211 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6507 (tptt) REVERT: B 288 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7689 (mppt) REVERT: B 315 LYS cc_start: 0.5129 (mmmt) cc_final: 0.4862 (mmpt) REVERT: B 321 GLU cc_start: 0.7681 (mp0) cc_final: 0.7266 (mm-30) REVERT: B 534 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: B 554 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: B 560 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: B 568 GLN cc_start: 0.7912 (mm110) cc_final: 0.7579 (mm110) REVERT: B 641 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: B 742 PHE cc_start: 0.6879 (m-80) cc_final: 0.5879 (m-80) REVERT: B 754 LYS cc_start: 0.7307 (mtmt) cc_final: 0.7020 (mtpp) REVERT: C 218 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: C 283 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6948 (mt-10) REVERT: C 288 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7434 (mptp) REVERT: C 295 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6314 (mmpt) REVERT: C 359 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7032 (ttm170) REVERT: C 364 ASP cc_start: 0.7830 (p0) cc_final: 0.7539 (OUTLIER) REVERT: C 417 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: C 560 ARG cc_start: 0.8248 (ttm170) cc_final: 0.8003 (ttp80) REVERT: C 730 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6886 (tt0) REVERT: D 211 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6492 (tptt) REVERT: D 295 LYS cc_start: 0.6547 (mttp) cc_final: 0.6184 (mmtt) REVERT: D 321 GLU cc_start: 0.7638 (mp0) cc_final: 0.7407 (mm-30) REVERT: D 534 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: D 658 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7871 (mtmt) REVERT: D 678 MET cc_start: 0.6699 (mmp) cc_final: 0.5968 (mpm) REVERT: D 742 PHE cc_start: 0.7134 (m-80) cc_final: 0.6234 (m-80) REVERT: D 753 ARG cc_start: 0.6592 (mtm110) cc_final: 0.6148 (mtm-85) REVERT: E 211 LYS cc_start: 0.7110 (mtpt) cc_final: 0.6500 (tptt) REVERT: E 256 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7554 (mpp80) REVERT: E 288 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7011 (mppt) REVERT: E 292 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: E 315 LYS cc_start: 0.5146 (mmmt) cc_final: 0.4876 (mmpt) REVERT: E 321 GLU cc_start: 0.7697 (mp0) cc_final: 0.7272 (mm-30) REVERT: E 534 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: E 554 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: E 560 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8233 (ttm170) REVERT: E 568 GLN cc_start: 0.7894 (mm110) cc_final: 0.7564 (mm110) REVERT: E 641 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7253 (mt0) REVERT: E 742 PHE cc_start: 0.6904 (m-80) cc_final: 0.5901 (m-80) REVERT: E 754 LYS cc_start: 0.7296 (mtmt) cc_final: 0.7015 (mtpp) REVERT: F 218 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: F 283 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6930 (mt-10) REVERT: F 288 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7373 (mptp) REVERT: F 359 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7037 (ttm170) REVERT: F 364 ASP cc_start: 0.7858 (p0) cc_final: 0.7562 (OUTLIER) REVERT: F 417 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: F 560 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7985 (ttp80) REVERT: F 611 MET cc_start: 0.8115 (ptt) cc_final: 0.7663 (ptm) REVERT: F 730 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6874 (tt0) REVERT: F 757 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6060 (mtt) outliers start: 116 outliers final: 46 residues processed: 446 average time/residue: 1.8028 time to fit residues: 916.6688 Evaluate side-chains 432 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 360 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain B residue 641 GLN Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 641 GLN Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 757 MET Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 385 optimal weight: 50.0000 chunk 180 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 381 optimal weight: 20.0000 chunk 162 optimal weight: 50.0000 chunk 445 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 362 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 760 GLN D 327 GLN D 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.212718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182698 restraints weight = 32685.719| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.25 r_work: 0.3558 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32506 Z= 0.137 Angle : 0.585 6.706 44118 Z= 0.311 Chirality : 0.046 0.203 5114 Planarity : 0.004 0.045 5976 Dihedral : 4.543 20.806 4800 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.54 % Allowed : 16.90 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.81 (0.13), residues: 4512 helix: 0.71 (0.12), residues: 1944 sheet: 1.47 (0.26), residues: 450 loop : -2.31 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 454 HIS 0.002 0.001 HIS D 404 PHE 0.021 0.002 PHE C 265 TYR 0.014 0.001 TYR D 203 ARG 0.004 0.000 ARG E 256 Details of bonding type rmsd hydrogen bonds : bond 0.05521 ( 1408) hydrogen bonds : angle 4.43644 ( 3990) covalent geometry : bond 0.00312 (32506) covalent geometry : angle 0.58452 (44118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 362 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6495 (mmpt) REVERT: A 288 LYS cc_start: 0.8018 (mttt) cc_final: 0.7727 (mptp) REVERT: A 321 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6344 (mm-30) REVERT: A 427 MET cc_start: 0.5896 (mmm) cc_final: 0.4846 (mmt) REVERT: A 599 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8180 (ptm160) REVERT: A 608 MET cc_start: 0.8883 (mtm) cc_final: 0.8674 (mtm) REVERT: A 678 MET cc_start: 0.6504 (mmp) cc_final: 0.5791 (mpm) REVERT: A 742 PHE cc_start: 0.7031 (m-80) cc_final: 0.6112 (m-80) REVERT: A 757 MET cc_start: 0.6759 (mtt) cc_final: 0.6147 (mmt) REVERT: A 760 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6210 (tt0) REVERT: B 211 LYS cc_start: 0.6970 (mtpt) cc_final: 0.6366 (tptt) REVERT: B 288 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7646 (mppt) REVERT: B 315 LYS cc_start: 0.5125 (mmmt) cc_final: 0.4850 (mmtt) REVERT: B 359 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7183 (ttm170) REVERT: B 534 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: B 554 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: B 568 GLN cc_start: 0.7742 (mm110) cc_final: 0.7279 (mt0) REVERT: B 678 MET cc_start: 0.6644 (mmp) cc_final: 0.6358 (mmm) REVERT: B 742 PHE cc_start: 0.6782 (m-80) cc_final: 0.5807 (m-80) REVERT: B 754 LYS cc_start: 0.7295 (mtmt) cc_final: 0.7000 (mtpp) REVERT: C 218 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: C 283 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6780 (mt-10) REVERT: C 288 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7361 (mptp) REVERT: C 295 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6163 (mmpt) REVERT: C 417 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: C 427 MET cc_start: 0.5599 (mmt) cc_final: 0.4463 (mmt) REVERT: C 508 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7270 (ttt) REVERT: C 534 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: C 560 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7886 (ttm-80) REVERT: C 611 MET cc_start: 0.8041 (ptt) cc_final: 0.7696 (ptm) REVERT: D 211 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6447 (tptt) REVERT: D 359 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7097 (ttm170) REVERT: D 427 MET cc_start: 0.5878 (mmm) cc_final: 0.4830 (mmt) REVERT: D 658 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8037 (mtmt) REVERT: D 678 MET cc_start: 0.6737 (mmp) cc_final: 0.6022 (mpm) REVERT: D 742 PHE cc_start: 0.6988 (m-80) cc_final: 0.6132 (m-80) REVERT: D 753 ARG cc_start: 0.6568 (mtm110) cc_final: 0.5927 (mtm-85) REVERT: D 757 MET cc_start: 0.6700 (mtt) cc_final: 0.6140 (mmt) REVERT: D 760 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: E 211 LYS cc_start: 0.6960 (mtpt) cc_final: 0.6346 (tptt) REVERT: E 256 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7618 (mpp80) REVERT: E 288 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7616 (mppt) REVERT: E 315 LYS cc_start: 0.5122 (mmmt) cc_final: 0.4871 (mmtt) REVERT: E 348 ASN cc_start: 0.8538 (t0) cc_final: 0.8331 (t0) REVERT: E 534 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: E 554 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: E 560 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8207 (ttm170) REVERT: E 568 GLN cc_start: 0.7745 (mm110) cc_final: 0.7299 (mt0) REVERT: E 678 MET cc_start: 0.6624 (mmp) cc_final: 0.6328 (mmm) REVERT: E 742 PHE cc_start: 0.6815 (m-80) cc_final: 0.5855 (m-80) REVERT: E 754 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6996 (mtpp) REVERT: F 218 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: F 283 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6738 (mt-10) REVERT: F 288 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7304 (mptp) REVERT: F 417 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: F 427 MET cc_start: 0.5602 (mmt) cc_final: 0.4462 (mmt) REVERT: F 508 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7249 (ttt) REVERT: F 534 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: F 560 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7907 (ttm-80) REVERT: F 611 MET cc_start: 0.8029 (ptt) cc_final: 0.7674 (ptm) REVERT: F 651 LYS cc_start: 0.7237 (mppt) cc_final: 0.6986 (mptt) outliers start: 100 outliers final: 43 residues processed: 425 average time/residue: 1.8750 time to fit residues: 909.4874 Evaluate side-chains 427 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 356 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 760 GLN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 760 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 130 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 428 optimal weight: 6.9990 chunk 364 optimal weight: 0.1980 chunk 275 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 327 GLN D 760 GLN F 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.212491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181889 restraints weight = 32655.859| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.23 r_work: 0.3557 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32506 Z= 0.138 Angle : 0.579 5.705 44118 Z= 0.307 Chirality : 0.046 0.203 5114 Planarity : 0.004 0.046 5976 Dihedral : 4.442 20.700 4800 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.64 % Allowed : 17.33 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.68 (0.13), residues: 4512 helix: 0.84 (0.12), residues: 1944 sheet: 1.50 (0.26), residues: 450 loop : -2.25 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 454 HIS 0.002 0.001 HIS A 404 PHE 0.020 0.001 PHE C 265 TYR 0.014 0.001 TYR D 203 ARG 0.004 0.000 ARG F 753 Details of bonding type rmsd hydrogen bonds : bond 0.05500 ( 1408) hydrogen bonds : angle 4.38999 ( 3990) covalent geometry : bond 0.00314 (32506) covalent geometry : angle 0.57918 (44118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 362 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6536 (mmpt) REVERT: A 288 LYS cc_start: 0.8053 (mttt) cc_final: 0.7764 (mptp) REVERT: A 321 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6317 (mm-30) REVERT: A 359 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7129 (ttm170) REVERT: A 427 MET cc_start: 0.5976 (mmm) cc_final: 0.4879 (mmt) REVERT: A 534 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: A 599 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8181 (ptm160) REVERT: A 608 MET cc_start: 0.8902 (mtm) cc_final: 0.8664 (mtm) REVERT: A 678 MET cc_start: 0.6568 (mmp) cc_final: 0.5852 (mpm) REVERT: A 742 PHE cc_start: 0.7074 (m-80) cc_final: 0.6165 (m-80) REVERT: A 757 MET cc_start: 0.6784 (mtt) cc_final: 0.6208 (mmt) REVERT: B 211 LYS cc_start: 0.7019 (mtpt) cc_final: 0.6439 (tptt) REVERT: B 288 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7702 (mppt) REVERT: B 315 LYS cc_start: 0.5171 (mmmt) cc_final: 0.4937 (mmtt) REVERT: B 359 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7185 (ttm170) REVERT: B 534 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: B 554 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 568 GLN cc_start: 0.7776 (mm110) cc_final: 0.7313 (mt0) REVERT: B 720 MET cc_start: 0.2614 (OUTLIER) cc_final: 0.2016 (mpm) REVERT: B 742 PHE cc_start: 0.6841 (m-80) cc_final: 0.5801 (m-80) REVERT: B 754 LYS cc_start: 0.7308 (mtmt) cc_final: 0.7036 (mtpp) REVERT: C 218 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: C 283 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6837 (mm-30) REVERT: C 288 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7410 (mptp) REVERT: C 295 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.6159 (mmpt) REVERT: C 417 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: C 427 MET cc_start: 0.5555 (mmt) cc_final: 0.4477 (mmt) REVERT: C 508 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7353 (ttt) REVERT: C 534 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: C 554 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7839 (mt-10) REVERT: C 560 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7925 (ttm-80) REVERT: C 611 MET cc_start: 0.8002 (ptt) cc_final: 0.7659 (ptm) REVERT: D 211 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6506 (tptt) REVERT: D 359 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7161 (ttm170) REVERT: D 427 MET cc_start: 0.5950 (mmm) cc_final: 0.4882 (mmt) REVERT: D 658 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8043 (mtmt) REVERT: D 678 MET cc_start: 0.6828 (mmp) cc_final: 0.6115 (mpm) REVERT: D 742 PHE cc_start: 0.7051 (m-80) cc_final: 0.6141 (m-80) REVERT: D 753 ARG cc_start: 0.6634 (mtm110) cc_final: 0.5973 (mtm-85) REVERT: D 757 MET cc_start: 0.6701 (mtt) cc_final: 0.6147 (mmt) REVERT: D 760 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6218 (tt0) REVERT: E 211 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6378 (tptm) REVERT: E 256 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7558 (mpp80) REVERT: E 288 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7021 (mppt) REVERT: E 292 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: E 315 LYS cc_start: 0.5179 (mmmt) cc_final: 0.4936 (mmtt) REVERT: E 348 ASN cc_start: 0.8560 (t0) cc_final: 0.8357 (t0) REVERT: E 359 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7157 (ttm170) REVERT: E 534 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: E 554 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: E 560 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8230 (ttm170) REVERT: E 568 GLN cc_start: 0.7773 (mm110) cc_final: 0.7326 (mt0) REVERT: E 720 MET cc_start: 0.2551 (OUTLIER) cc_final: 0.1950 (mpm) REVERT: E 742 PHE cc_start: 0.6903 (m-80) cc_final: 0.5869 (m-80) REVERT: E 754 LYS cc_start: 0.7321 (mtmt) cc_final: 0.7060 (mtpp) REVERT: F 218 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: F 283 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6829 (mm-30) REVERT: F 288 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7365 (mptp) REVERT: F 417 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: F 427 MET cc_start: 0.5557 (mmt) cc_final: 0.4477 (mmt) REVERT: F 508 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7322 (ttt) REVERT: F 534 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: F 554 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7844 (mt-10) REVERT: F 560 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7928 (ttm-80) REVERT: F 611 MET cc_start: 0.8008 (ptt) cc_final: 0.7673 (ptm) outliers start: 103 outliers final: 46 residues processed: 433 average time/residue: 1.7825 time to fit residues: 884.9616 Evaluate side-chains 434 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 355 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 760 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 9.9990 chunk 282 optimal weight: 0.9990 chunk 139 optimal weight: 0.0050 chunk 322 optimal weight: 4.9990 chunk 243 optimal weight: 0.0770 chunk 265 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 302 optimal weight: 20.0000 chunk 331 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.9756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 760 GLN D 327 GLN D 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.215708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.185605 restraints weight = 32832.514| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.27 r_work: 0.3596 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32506 Z= 0.102 Angle : 0.509 5.094 44118 Z= 0.270 Chirality : 0.044 0.206 5114 Planarity : 0.003 0.045 5976 Dihedral : 4.010 19.794 4800 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.76 % Allowed : 18.35 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.21 (0.13), residues: 4512 helix: 1.29 (0.12), residues: 1944 sheet: 1.51 (0.26), residues: 456 loop : -2.01 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 454 HIS 0.001 0.000 HIS D 404 PHE 0.018 0.001 PHE F 265 TYR 0.011 0.001 TYR D 203 ARG 0.005 0.000 ARG C 753 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 1408) hydrogen bonds : angle 4.08531 ( 3990) covalent geometry : bond 0.00228 (32506) covalent geometry : angle 0.50892 (44118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 375 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6505 (mmpt) REVERT: A 288 LYS cc_start: 0.8002 (mttt) cc_final: 0.7530 (mmmt) REVERT: A 321 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: A 427 MET cc_start: 0.6054 (mmm) cc_final: 0.4932 (mmt) REVERT: A 534 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: A 599 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8117 (ptm160) REVERT: A 611 MET cc_start: 0.7794 (ptt) cc_final: 0.7246 (ptm) REVERT: A 674 PHE cc_start: 0.7152 (t80) cc_final: 0.6779 (t80) REVERT: A 678 MET cc_start: 0.6545 (mmp) cc_final: 0.5838 (mpm) REVERT: A 742 PHE cc_start: 0.6993 (m-80) cc_final: 0.6122 (m-80) REVERT: A 756 GLU cc_start: 0.6855 (mm-30) cc_final: 0.5851 (mt-10) REVERT: A 757 MET cc_start: 0.6807 (mtt) cc_final: 0.6177 (mmt) REVERT: B 211 LYS cc_start: 0.6880 (mtpt) cc_final: 0.6296 (tptm) REVERT: B 315 LYS cc_start: 0.5168 (mmmt) cc_final: 0.4915 (mmtt) REVERT: B 340 HIS cc_start: 0.6928 (m90) cc_final: 0.6301 (m-70) REVERT: B 427 MET cc_start: 0.5624 (mmt) cc_final: 0.4727 (mmt) REVERT: B 534 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: B 568 GLN cc_start: 0.7612 (mm110) cc_final: 0.7143 (mt0) REVERT: B 678 MET cc_start: 0.6853 (mmp) cc_final: 0.6527 (mmm) REVERT: B 720 MET cc_start: 0.2561 (OUTLIER) cc_final: 0.1961 (mpm) REVERT: B 742 PHE cc_start: 0.6788 (m-80) cc_final: 0.5714 (m-80) REVERT: B 754 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6991 (mtpp) REVERT: C 218 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: C 283 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6597 (mm-30) REVERT: C 288 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7232 (mptp) REVERT: C 295 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.6008 (mmpt) REVERT: C 417 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: C 427 MET cc_start: 0.5372 (mmt) cc_final: 0.4361 (mmt) REVERT: C 508 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7293 (ttt) REVERT: C 560 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7832 (ttm-80) REVERT: C 611 MET cc_start: 0.7995 (ptt) cc_final: 0.7691 (ptm) REVERT: C 678 MET cc_start: 0.6911 (mmp) cc_final: 0.6474 (mmm) REVERT: D 211 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6378 (tptt) REVERT: D 427 MET cc_start: 0.5995 (mmm) cc_final: 0.4942 (mmt) REVERT: D 611 MET cc_start: 0.7882 (ptt) cc_final: 0.7315 (ptm) REVERT: D 658 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8126 (mtmt) REVERT: D 674 PHE cc_start: 0.7153 (t80) cc_final: 0.6744 (t80) REVERT: D 678 MET cc_start: 0.6896 (mmp) cc_final: 0.6083 (mpm) REVERT: D 742 PHE cc_start: 0.6988 (m-80) cc_final: 0.6119 (m-80) REVERT: D 753 ARG cc_start: 0.6592 (mtm110) cc_final: 0.5918 (mtm-85) REVERT: D 756 GLU cc_start: 0.6926 (mm-30) cc_final: 0.5856 (mt-10) REVERT: D 757 MET cc_start: 0.6913 (mtt) cc_final: 0.6238 (mmt) REVERT: D 760 GLN cc_start: 0.6365 (OUTLIER) cc_final: 0.5963 (pp30) REVERT: E 211 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6263 (tptm) REVERT: E 315 LYS cc_start: 0.5155 (mmmt) cc_final: 0.4921 (mmtt) REVERT: E 348 ASN cc_start: 0.8538 (t0) cc_final: 0.8334 (t0) REVERT: E 359 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7020 (ttm170) REVERT: E 427 MET cc_start: 0.5581 (mmt) cc_final: 0.4684 (mmt) REVERT: E 534 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: E 560 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8149 (ttm170) REVERT: E 568 GLN cc_start: 0.7626 (mm110) cc_final: 0.7168 (mt0) REVERT: E 678 MET cc_start: 0.6892 (mmp) cc_final: 0.6569 (mmm) REVERT: E 720 MET cc_start: 0.2571 (OUTLIER) cc_final: 0.1963 (mpm) REVERT: E 742 PHE cc_start: 0.6844 (m-80) cc_final: 0.5777 (m-80) REVERT: E 754 LYS cc_start: 0.7238 (mtmt) cc_final: 0.6983 (mtpp) REVERT: F 218 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: F 283 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6604 (mm-30) REVERT: F 288 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7198 (mptp) REVERT: F 417 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: F 427 MET cc_start: 0.5385 (mmt) cc_final: 0.4370 (mmt) REVERT: F 508 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7270 (ttt) REVERT: F 554 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7842 (mt-10) REVERT: F 560 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7847 (ttm-80) REVERT: F 611 MET cc_start: 0.8000 (ptt) cc_final: 0.7693 (ptm) REVERT: F 678 MET cc_start: 0.6903 (mmp) cc_final: 0.6469 (mmm) outliers start: 78 outliers final: 31 residues processed: 429 average time/residue: 1.7300 time to fit residues: 850.9816 Evaluate side-chains 414 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 361 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 760 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 274 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 345 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 120 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN D 327 GLN D 760 GLN E 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.210685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.180801 restraints weight = 32526.698| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.26 r_work: 0.3526 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 32506 Z= 0.221 Angle : 0.711 5.920 44118 Z= 0.377 Chirality : 0.050 0.194 5114 Planarity : 0.005 0.048 5976 Dihedral : 4.789 24.120 4800 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.86 % Allowed : 18.64 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.93 (0.12), residues: 4512 helix: 0.55 (0.11), residues: 1944 sheet: 1.42 (0.26), residues: 450 loop : -2.31 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 454 HIS 0.003 0.001 HIS E 317 PHE 0.022 0.002 PHE E 265 TYR 0.021 0.003 TYR D 203 ARG 0.007 0.001 ARG C 753 Details of bonding type rmsd hydrogen bonds : bond 0.07321 ( 1408) hydrogen bonds : angle 4.66220 ( 3990) covalent geometry : bond 0.00528 (32506) covalent geometry : angle 0.71145 (44118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6559 (mmm-85) cc_final: 0.6162 (tpm170) REVERT: A 211 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6671 (mmpt) REVERT: A 321 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6470 (mm-30) REVERT: A 348 ASN cc_start: 0.8454 (t0) cc_final: 0.8091 (m-40) REVERT: A 359 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7277 (ttm-80) REVERT: A 427 MET cc_start: 0.6038 (mmm) cc_final: 0.5774 (mmm) REVERT: A 534 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: A 599 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8304 (ptm160) REVERT: A 678 MET cc_start: 0.6678 (mmp) cc_final: 0.6020 (mpm) REVERT: A 742 PHE cc_start: 0.7197 (m-80) cc_final: 0.6294 (m-80) REVERT: B 315 LYS cc_start: 0.5265 (mmmt) cc_final: 0.5016 (mmpt) REVERT: B 321 GLU cc_start: 0.7693 (mp0) cc_final: 0.7309 (mm-30) REVERT: B 534 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: B 560 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8309 (ttm170) REVERT: B 568 GLN cc_start: 0.7971 (mm110) cc_final: 0.7652 (mm110) REVERT: B 742 PHE cc_start: 0.6876 (m-80) cc_final: 0.5909 (m-80) REVERT: B 754 LYS cc_start: 0.7401 (mtmt) cc_final: 0.7149 (mtpp) REVERT: C 218 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: C 283 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6974 (mm-30) REVERT: C 288 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7469 (mptp) REVERT: C 295 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6206 (mmpt) REVERT: C 417 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: C 560 ARG cc_start: 0.8291 (ttm170) cc_final: 0.8022 (ttm-80) REVERT: C 611 MET cc_start: 0.8033 (ptt) cc_final: 0.7693 (ptm) REVERT: D 211 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6591 (tptp) REVERT: D 427 MET cc_start: 0.6048 (mmm) cc_final: 0.4826 (mmt) REVERT: D 448 THR cc_start: 0.7008 (p) cc_final: 0.6668 (t) REVERT: D 534 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: D 611 MET cc_start: 0.8063 (ptt) cc_final: 0.7704 (ptm) REVERT: D 658 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7986 (mtmt) REVERT: D 678 MET cc_start: 0.6891 (mmp) cc_final: 0.6118 (mpm) REVERT: D 742 PHE cc_start: 0.7171 (m-80) cc_final: 0.6251 (m-80) REVERT: D 753 ARG cc_start: 0.6636 (mtm110) cc_final: 0.6181 (mtm-85) REVERT: D 760 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5918 (tt0) REVERT: E 211 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6561 (tptt) REVERT: E 292 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: E 315 LYS cc_start: 0.5254 (mmmt) cc_final: 0.5017 (mmpt) REVERT: E 321 GLU cc_start: 0.7694 (mp0) cc_final: 0.7300 (mm-30) REVERT: E 359 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7310 (ttm170) REVERT: E 534 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: E 560 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8276 (ttm170) REVERT: E 568 GLN cc_start: 0.7958 (mm110) cc_final: 0.7643 (mm110) REVERT: E 742 PHE cc_start: 0.6975 (m-80) cc_final: 0.5938 (m-80) REVERT: E 754 LYS cc_start: 0.7377 (mtmt) cc_final: 0.7095 (mtpp) REVERT: F 218 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: F 283 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6992 (mm-30) REVERT: F 288 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7459 (mptp) REVERT: F 417 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: F 560 ARG cc_start: 0.8319 (ttm170) cc_final: 0.8054 (ttm-80) REVERT: F 611 MET cc_start: 0.8046 (ptt) cc_final: 0.7697 (ptm) outliers start: 81 outliers final: 32 residues processed: 424 average time/residue: 1.8222 time to fit residues: 892.3007 Evaluate side-chains 416 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 760 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 741 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 1 optimal weight: 50.0000 chunk 123 optimal weight: 3.9990 chunk 300 optimal weight: 50.0000 chunk 285 optimal weight: 7.9990 chunk 407 optimal weight: 0.9990 chunk 329 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN D 327 GLN D 760 GLN E 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.211148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.181125 restraints weight = 32360.166| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.24 r_work: 0.3533 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32506 Z= 0.188 Angle : 0.666 6.148 44118 Z= 0.354 Chirality : 0.049 0.200 5114 Planarity : 0.005 0.048 5976 Dihedral : 4.763 23.180 4800 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.79 % Allowed : 19.06 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.99 (0.12), residues: 4512 helix: 0.49 (0.11), residues: 1944 sheet: 1.35 (0.26), residues: 450 loop : -2.32 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 454 HIS 0.002 0.001 HIS A 404 PHE 0.021 0.002 PHE C 265 TYR 0.021 0.002 TYR D 203 ARG 0.006 0.001 ARG C 753 Details of bonding type rmsd hydrogen bonds : bond 0.06648 ( 1408) hydrogen bonds : angle 4.58495 ( 3990) covalent geometry : bond 0.00443 (32506) covalent geometry : angle 0.66604 (44118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24841.63 seconds wall clock time: 426 minutes 43.89 seconds (25603.89 seconds total)