Starting phenix.real_space_refine on Fri Jun 27 05:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0e_18790/06_2025/8r0e_18790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0e_18790/06_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_18790/06_2025/8r0e_18790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0e_18790/06_2025/8r0e_18790.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0e_18790/06_2025/8r0e_18790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0e_18790/06_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-5710/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: 18.49, per 1000 atoms: 0.58 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: 8.19 Conformation dependent library (CDL) restraints added in 4.7 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: 4.09 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: 11.01 Time building geometry restraints manager: 9.60 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: 0.18 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 70.890 Find NCS groups from input model: 1.440 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:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.880 ------------------------------------------------------------------------------- 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 : 3.225 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: 1.9078 time to fit residues: 1182.0096 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 : 3.721 ------------------------------------------------------------------------------- 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: 0.3768 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 7.179 Fit side-chains REVERT: A 211 LYS cc_start: 0.6866 (mtpt) cc_final: 0.6547 (mmpt) REVERT: A 295 LYS cc_start: 0.6379 (mttp) cc_final: 0.5987 (mmtt) REVERT: A 442 MET cc_start: 0.4773 (ptp) cc_final: 0.3675 (tmm) REVERT: A 678 MET cc_start: 0.6454 (mmp) cc_final: 0.5842 (mpm) REVERT: A 733 ARG cc_start: 0.6920 (mtp85) cc_final: 0.6642 (mtp180) REVERT: A 742 PHE cc_start: 0.6919 (m-10) cc_final: 0.5933 (m-80) REVERT: A 753 ARG cc_start: 0.6390 (mtm110) cc_final: 0.5722 (mmp80) REVERT: B 210 ARG cc_start: 0.5580 (tpm170) cc_final: 0.5365 (tpm170) REVERT: B 256 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.7379 (mpp80) REVERT: B 295 LYS cc_start: 0.6519 (mttp) cc_final: 0.6235 (mmtm) REVERT: B 324 ILE cc_start: 0.8203 (tt) cc_final: 0.7948 (tp) REVERT: B 340 HIS cc_start: 0.6668 (m90) cc_final: 0.6142 (m-70) REVERT: B 554 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: B 568 GLN cc_start: 0.7786 (mm110) cc_final: 0.7369 (mt0) REVERT: B 720 MET cc_start: 0.2718 (OUTLIER) cc_final: 0.2168 (mpm) REVERT: B 742 PHE cc_start: 0.6853 (m-10) cc_final: 0.5932 (m-80) REVERT: B 753 ARG cc_start: 0.6208 (mtm110) cc_final: 0.5620 (mmp80) REVERT: C 256 ARG cc_start: 0.7572 (mpt-90) cc_final: 0.7252 (mpt-90) REVERT: C 295 LYS cc_start: 0.6560 (mttp) cc_final: 0.6209 (mmpt) REVERT: C 508 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7290 (ttt) REVERT: C 560 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7498 (ttm-80) REVERT: C 753 ARG cc_start: 0.6143 (mtm110) cc_final: 0.5703 (mmp80) REVERT: D 210 ARG cc_start: 0.5723 (tpm170) cc_final: 0.5143 (ttp-110) REVERT: D 256 ARG cc_start: 0.7608 (mpt-90) cc_final: 0.7255 (mpp80) REVERT: D 288 LYS cc_start: 0.7776 (mttt) cc_final: 0.7230 (mmmt) REVERT: D 295 LYS cc_start: 0.6529 (mttp) cc_final: 0.6179 (mmtt) REVERT: D 324 ILE cc_start: 0.8202 (tt) cc_final: 0.8000 (tp) REVERT: D 442 MET cc_start: 0.4720 (ptp) cc_final: 0.3639 (tmm) REVERT: D 508 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7307 (ttt) REVERT: D 753 ARG cc_start: 0.6255 (mtm110) cc_final: 0.5541 (mmp80) REVERT: E 210 ARG cc_start: 0.5581 (tpm170) cc_final: 0.5366 (tpm170) REVERT: E 256 ARG cc_start: 0.7693 (mpt-90) cc_final: 0.7367 (mpp80) REVERT: E 295 LYS cc_start: 0.6521 (mttp) cc_final: 0.6242 (mmtm) REVERT: E 324 ILE cc_start: 0.8210 (tt) cc_final: 0.7965 (tp) REVERT: E 340 HIS cc_start: 0.6693 (m90) cc_final: 0.6170 (m-70) REVERT: E 560 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7532 (ttm170) REVERT: E 568 GLN cc_start: 0.7816 (mm110) cc_final: 0.7378 (mt0) REVERT: E 720 MET cc_start: 0.2697 (OUTLIER) cc_final: 0.2127 (mpm) REVERT: E 742 PHE cc_start: 0.6839 (m-10) cc_final: 0.5936 (m-80) REVERT: E 753 ARG cc_start: 0.6235 (mtm110) cc_final: 0.5638 (mmp80) REVERT: F 219 MET cc_start: 0.7841 (mtt) cc_final: 0.7530 (mtm) REVERT: F 256 ARG cc_start: 0.7650 (mpt-90) cc_final: 0.7351 (mpt-90) REVERT: F 295 LYS cc_start: 0.6517 (mttp) cc_final: 0.6279 (mmtm) REVERT: F 508 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7271 (ttt) REVERT: F 560 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7520 (ttm-80) REVERT: F 753 ARG cc_start: 0.6129 (mtm110) cc_final: 0.5687 (mmp80) outliers start: 55 outliers final: 19 residues processed: 458 average time/residue: 2.2009 time to fit residues: 1153.8180 Evaluate side-chains 393 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 3.456 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 34 optimal weight: 10.0000 chunk 386 optimal weight: 40.0000 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: 0.8980 chunk 259 optimal weight: 9.9990 chunk 227 optimal weight: 30.0000 chunk 315 optimal weight: 4.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.212868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.188282 restraints weight = 32492.387| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.09 r_work: 0.3778 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32506 Z= 0.194 Angle : 0.706 8.253 44118 Z= 0.374 Chirality : 0.049 0.200 5114 Planarity : 0.005 0.042 5976 Dihedral : 5.155 23.357 4800 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.83 % Allowed : 12.87 % Favored : 84.30 % 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: -1.93 (0.12), residues: 4512 helix: -0.24 (0.11), residues: 2016 sheet: 0.25 (0.24), residues: 522 loop : -2.90 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 476 HIS 0.005 0.001 HIS E 317 PHE 0.023 0.002 PHE D 265 TYR 0.020 0.002 TYR D 203 ARG 0.004 0.001 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.07179 ( 1408) hydrogen bonds : angle 4.84672 ( 3990) covalent geometry : bond 0.00450 (32506) covalent geometry : angle 0.70590 (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: 80 poor density : 387 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LYS cc_start: 0.6336 (mttp) cc_final: 0.6014 (mmtt) REVERT: A 427 MET cc_start: 0.5193 (mpm) cc_final: 0.4546 (mmt) REVERT: A 442 MET cc_start: 0.5071 (ptp) cc_final: 0.4365 (tmm) REVERT: A 599 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8119 (ptm160) REVERT: A 641 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: A 678 MET cc_start: 0.6535 (mmp) cc_final: 0.6274 (mpm) REVERT: A 742 PHE cc_start: 0.7095 (m-10) cc_final: 0.6318 (m-80) REVERT: B 256 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7644 (mpp80) REVERT: B 340 HIS cc_start: 0.6622 (m90) cc_final: 0.6102 (m-70) REVERT: B 554 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: B 611 MET cc_start: 0.7941 (ptt) cc_final: 0.7587 (ptp) REVERT: B 641 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: B 720 MET cc_start: 0.2987 (OUTLIER) cc_final: 0.2373 (mpm) REVERT: B 742 PHE cc_start: 0.6905 (m-10) cc_final: 0.6250 (m-80) REVERT: C 218 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: C 256 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7352 (mpt-90) REVERT: C 417 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: C 442 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4785 (mmm) REVERT: C 508 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7327 (ttt) REVERT: C 560 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7802 (ttp80) REVERT: D 256 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7455 (mpp80) REVERT: D 295 LYS cc_start: 0.6446 (mttp) cc_final: 0.6106 (mmtt) REVERT: D 427 MET cc_start: 0.4975 (mpm) cc_final: 0.4676 (mmt) REVERT: D 442 MET cc_start: 0.4941 (ptp) cc_final: 0.4442 (tmm) REVERT: D 641 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7040 (mt0) REVERT: D 678 MET cc_start: 0.6742 (mmp) cc_final: 0.6362 (mpm) REVERT: D 742 PHE cc_start: 0.7069 (m-10) cc_final: 0.6371 (m-80) REVERT: D 751 ASP cc_start: 0.6945 (m-30) cc_final: 0.6727 (m-30) REVERT: D 753 ARG cc_start: 0.6466 (mtm110) cc_final: 0.6193 (mmp80) REVERT: E 256 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7630 (mpp80) REVERT: E 340 HIS cc_start: 0.6604 (m90) cc_final: 0.6083 (m-70) REVERT: E 611 MET cc_start: 0.7923 (ptt) cc_final: 0.7566 (ptp) REVERT: E 641 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6947 (mt0) REVERT: E 720 MET cc_start: 0.3021 (OUTLIER) cc_final: 0.2399 (mpm) REVERT: E 742 PHE cc_start: 0.6930 (m-10) cc_final: 0.6274 (m-80) REVERT: F 218 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: F 256 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7364 (mpt-90) REVERT: F 417 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: F 508 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7264 (ttt) REVERT: F 560 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7806 (ttp80) outliers start: 80 outliers final: 25 residues processed: 435 average time/residue: 1.8130 time to fit residues: 901.2153 Evaluate side-chains 402 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 3.341 ------------------------------------------------------------------------------- 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 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 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 256 ARG Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 442 MET 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 641 GLN 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 253 LEU 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 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: 0.6980 chunk 147 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 444 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN C 624 ASN D 327 GLN D 624 ASN F 327 GLN F 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.214726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184259 restraints weight = 32772.833| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.34 r_work: 0.3574 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32506 Z= 0.119 Angle : 0.556 6.192 44118 Z= 0.295 Chirality : 0.045 0.209 5114 Planarity : 0.004 0.043 5976 Dihedral : 4.478 19.172 4800 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.11 % Allowed : 14.99 % 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: -0.97 (0.13), residues: 4512 helix: 0.68 (0.12), residues: 1938 sheet: 0.70 (0.25), residues: 516 loop : -2.40 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 454 HIS 0.002 0.001 HIS E 317 PHE 0.021 0.001 PHE D 265 TYR 0.013 0.001 TYR D 203 ARG 0.004 0.000 ARG C 256 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 1408) hydrogen bonds : angle 4.35225 ( 3990) covalent geometry : bond 0.00265 (32506) covalent geometry : angle 0.55620 (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: 88 poor density : 382 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.5154 (mpm) cc_final: 0.4271 (mmt) REVERT: A 599 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7994 (ptm160) REVERT: A 674 PHE cc_start: 0.7237 (t80) cc_final: 0.6914 (t80) REVERT: A 678 MET cc_start: 0.6535 (mmp) cc_final: 0.6010 (mpm) REVERT: A 742 PHE cc_start: 0.7075 (m-80) cc_final: 0.6191 (m-80) REVERT: A 756 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6013 (mt-10) REVERT: A 757 MET cc_start: 0.6754 (mtt) cc_final: 0.6403 (mmt) REVERT: B 211 LYS cc_start: 0.6820 (mtpt) cc_final: 0.6283 (tptm) REVERT: B 256 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7470 (mpp80) REVERT: B 340 HIS cc_start: 0.6753 (m90) cc_final: 0.6187 (m-70) REVERT: B 554 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: B 611 MET cc_start: 0.7949 (ptt) cc_final: 0.7601 (ptp) REVERT: B 720 MET cc_start: 0.2624 (OUTLIER) cc_final: 0.2103 (mpm) REVERT: B 742 PHE cc_start: 0.6832 (m-10) cc_final: 0.6010 (m-80) REVERT: B 756 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6034 (mt-10) REVERT: B 772 ARG cc_start: 0.6657 (mmm160) cc_final: 0.6445 (mmt180) REVERT: C 218 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: C 364 ASP cc_start: 0.7668 (p0) cc_final: 0.7385 (p0) REVERT: C 417 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: C 427 MET cc_start: 0.5170 (mmt) cc_final: 0.4232 (mmt) REVERT: C 508 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7162 (ttt) REVERT: C 560 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7604 (ttm-80) REVERT: D 211 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6486 (tptm) REVERT: D 295 LYS cc_start: 0.6293 (mttp) cc_final: 0.5962 (mmtt) REVERT: D 427 MET cc_start: 0.5203 (mpm) cc_final: 0.4340 (mmt) REVERT: D 678 MET cc_start: 0.6758 (mmp) cc_final: 0.6221 (mpm) REVERT: D 742 PHE cc_start: 0.7127 (m-80) cc_final: 0.6307 (m-80) REVERT: D 753 ARG cc_start: 0.6507 (mtm110) cc_final: 0.6053 (mtm-85) REVERT: D 756 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6005 (mt-10) REVERT: D 757 MET cc_start: 0.6708 (mtt) cc_final: 0.6380 (mmt) REVERT: E 211 LYS cc_start: 0.6815 (mtpt) cc_final: 0.6274 (tptm) REVERT: E 256 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7498 (mpp80) REVERT: E 340 HIS cc_start: 0.6748 (m90) cc_final: 0.6182 (m-70) REVERT: E 611 MET cc_start: 0.7944 (ptt) cc_final: 0.7603 (ptp) REVERT: E 720 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.2101 (mpm) REVERT: E 742 PHE cc_start: 0.6844 (m-10) cc_final: 0.6014 (m-80) REVERT: E 756 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6029 (mt-10) REVERT: F 218 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: F 364 ASP cc_start: 0.7663 (p0) cc_final: 0.7374 (p0) REVERT: F 417 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7101 (tp30) REVERT: F 427 MET cc_start: 0.5170 (mmt) cc_final: 0.4242 (mmt) REVERT: F 508 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7135 (ttt) REVERT: F 560 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7614 (ttm-80) outliers start: 88 outliers final: 30 residues processed: 430 average time/residue: 1.8326 time to fit residues: 901.4601 Evaluate side-chains 409 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 366 time to evaluate : 3.425 ------------------------------------------------------------------------------- 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 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 720 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 256 ARG 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 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 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 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 383 ILE 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 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: 8.9990 chunk 446 optimal weight: 5.9990 chunk 154 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 chunk 320 optimal weight: 9.9990 chunk 228 optimal weight: 50.0000 chunk 243 optimal weight: 0.0670 chunk 221 optimal weight: 0.9990 chunk 277 optimal weight: 0.0020 chunk 44 optimal weight: 0.0980 overall best weight: 1.0330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN D 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.216516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185286 restraints weight = 32756.648| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.36 r_work: 0.3590 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32506 Z= 0.103 Angle : 0.506 7.840 44118 Z= 0.268 Chirality : 0.044 0.201 5114 Planarity : 0.003 0.044 5976 Dihedral : 4.035 19.765 4800 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.72 % Allowed : 15.81 % Favored : 81.47 % 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: -0.35 (0.13), residues: 4512 helix: 1.23 (0.12), residues: 1974 sheet: 0.80 (0.25), residues: 522 loop : -2.12 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 454 HIS 0.001 0.000 HIS E 317 PHE 0.018 0.001 PHE C 265 TYR 0.010 0.001 TYR D 203 ARG 0.004 0.000 ARG E 256 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1408) hydrogen bonds : angle 4.07517 ( 3990) covalent geometry : bond 0.00225 (32506) covalent geometry : angle 0.50584 (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 482 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 405 time to evaluate : 3.336 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7957 (mttt) cc_final: 0.7500 (mmmt) REVERT: A 427 MET cc_start: 0.5552 (mpm) cc_final: 0.4690 (mmt) REVERT: A 488 GLU cc_start: 0.7804 (tt0) cc_final: 0.7434 (tt0) REVERT: A 599 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8120 (ptm160) REVERT: A 678 MET cc_start: 0.6519 (mmp) cc_final: 0.5812 (mpm) REVERT: A 742 PHE cc_start: 0.7083 (m-80) cc_final: 0.6093 (m-80) REVERT: A 757 MET cc_start: 0.6758 (mtt) cc_final: 0.6146 (mmt) REVERT: B 211 LYS cc_start: 0.6853 (mtpt) cc_final: 0.6286 (tptm) REVERT: B 256 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7630 (mpp80) REVERT: B 340 HIS cc_start: 0.6789 (m90) cc_final: 0.6179 (m-70) REVERT: B 427 MET cc_start: 0.5488 (mmt) cc_final: 0.4612 (mmt) REVERT: B 534 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: B 720 MET cc_start: 0.2628 (OUTLIER) cc_final: 0.1957 (mpm) REVERT: B 742 PHE cc_start: 0.6757 (m-80) cc_final: 0.5822 (m-80) REVERT: B 754 LYS cc_start: 0.7326 (mtmt) cc_final: 0.7062 (mtpp) REVERT: C 218 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: C 288 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7314 (mptp) REVERT: C 417 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: C 427 MET cc_start: 0.5177 (mmt) cc_final: 0.4137 (mmt) REVERT: C 508 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7330 (ttt) REVERT: C 554 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 560 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7834 (ttm-80) REVERT: C 611 MET cc_start: 0.7890 (ptt) cc_final: 0.7531 (ptm) REVERT: D 211 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6300 (tptm) REVERT: D 427 MET cc_start: 0.5600 (mpm) cc_final: 0.4757 (mmt) REVERT: D 508 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7388 (ttt) REVERT: D 674 PHE cc_start: 0.7139 (t80) cc_final: 0.6743 (t80) REVERT: D 678 MET cc_start: 0.6778 (mmp) cc_final: 0.5993 (mpm) REVERT: D 742 PHE cc_start: 0.7113 (m-80) cc_final: 0.6202 (m-80) REVERT: D 753 ARG cc_start: 0.6687 (mtm110) cc_final: 0.5668 (mmp80) REVERT: D 757 MET cc_start: 0.6652 (mtt) cc_final: 0.6071 (mmt) REVERT: E 211 LYS cc_start: 0.6865 (mtpt) cc_final: 0.6282 (tptm) REVERT: E 256 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7638 (mpp80) REVERT: E 340 HIS cc_start: 0.6798 (m90) cc_final: 0.6229 (m-70) REVERT: E 427 MET cc_start: 0.5456 (mmt) cc_final: 0.4574 (mmt) REVERT: E 560 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: E 611 MET cc_start: 0.8097 (ptt) cc_final: 0.7895 (ptp) REVERT: E 720 MET cc_start: 0.2597 (OUTLIER) cc_final: 0.1959 (mpm) REVERT: E 742 PHE cc_start: 0.6757 (m-80) cc_final: 0.5809 (m-80) REVERT: E 754 LYS cc_start: 0.7351 (mtmt) cc_final: 0.7090 (mtpp) REVERT: F 218 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: F 288 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7334 (mptp) REVERT: F 417 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: F 427 MET cc_start: 0.5182 (mmt) cc_final: 0.4139 (mmt) REVERT: F 508 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7338 (ttt) REVERT: F 560 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7868 (ttm-80) REVERT: F 611 MET cc_start: 0.7873 (ptt) cc_final: 0.7516 (ptm) outliers start: 77 outliers final: 25 residues processed: 447 average time/residue: 1.7411 time to fit residues: 895.0274 Evaluate side-chains 409 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 3.307 ------------------------------------------------------------------------------- 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 383 ILE 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 720 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 383 ILE 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 383 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 VAL 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 383 ILE Chi-restraints excluded: chain D residue 479 ILE 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 256 ARG 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 Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 315 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 75 optimal weight: 50.0000 chunk 283 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 234 optimal weight: 30.0000 chunk 329 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 chunk 392 optimal weight: 30.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN C 327 GLN D 327 GLN E 260 ASN E 327 GLN F 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.212962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183812 restraints weight = 32559.498| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.28 r_work: 0.3559 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32506 Z= 0.157 Angle : 0.602 6.699 44118 Z= 0.319 Chirality : 0.047 0.201 5114 Planarity : 0.004 0.048 5976 Dihedral : 4.408 21.084 4800 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.61 % Allowed : 16.44 % Favored : 79.95 % 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: -0.62 (0.13), residues: 4512 helix: 0.87 (0.12), residues: 1944 sheet: 1.64 (0.26), residues: 444 loop : -2.22 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 454 HIS 0.003 0.001 HIS E 317 PHE 0.019 0.002 PHE B 265 TYR 0.015 0.002 TYR D 203 ARG 0.004 0.001 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 1408) hydrogen bonds : angle 4.41567 ( 3990) covalent geometry : bond 0.00362 (32506) covalent geometry : angle 0.60159 (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 472 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 370 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8038 (mttt) cc_final: 0.7782 (mptp) REVERT: A 319 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6710 (mm-30) REVERT: A 427 MET cc_start: 0.5529 (mpm) cc_final: 0.4658 (mmt) REVERT: A 599 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (ptm160) REVERT: A 651 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7330 (mppt) REVERT: A 678 MET cc_start: 0.6574 (mmp) cc_final: 0.5886 (mpm) REVERT: A 742 PHE cc_start: 0.7038 (m-80) cc_final: 0.6151 (m-80) REVERT: A 756 GLU cc_start: 0.6867 (mm-30) cc_final: 0.5950 (mt-10) REVERT: B 211 LYS cc_start: 0.7048 (mtpt) cc_final: 0.6407 (tptm) REVERT: B 256 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7534 (mpp80) REVERT: B 288 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7668 (mppt) REVERT: B 340 HIS cc_start: 0.6798 (m90) cc_final: 0.6275 (m-70) REVERT: B 534 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 720 MET cc_start: 0.2782 (OUTLIER) cc_final: 0.2194 (mpm) REVERT: B 742 PHE cc_start: 0.6900 (m-80) cc_final: 0.5933 (m-80) REVERT: B 754 LYS cc_start: 0.7396 (mtmt) cc_final: 0.7155 (mtpp) REVERT: C 218 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: C 288 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7473 (mptp) REVERT: C 417 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: C 427 MET cc_start: 0.5512 (mmt) cc_final: 0.4296 (mmt) REVERT: C 508 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7360 (ttt) REVERT: C 534 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: C 560 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7973 (ttm-80) REVERT: C 611 MET cc_start: 0.8033 (ptt) cc_final: 0.7652 (ptm) REVERT: D 211 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6529 (tptt) REVERT: D 295 LYS cc_start: 0.6355 (mttp) cc_final: 0.5976 (mmtt) REVERT: D 427 MET cc_start: 0.5467 (mpm) cc_final: 0.4595 (mmt) REVERT: D 678 MET cc_start: 0.6838 (mmp) cc_final: 0.6026 (mpm) REVERT: D 742 PHE cc_start: 0.7167 (m-80) cc_final: 0.6218 (m-80) REVERT: D 753 ARG cc_start: 0.6706 (mtm110) cc_final: 0.6161 (mtm-85) REVERT: D 756 GLU cc_start: 0.6825 (mm-30) cc_final: 0.5895 (mt-10) REVERT: E 211 LYS cc_start: 0.7060 (mtpt) cc_final: 0.6410 (tptm) REVERT: E 256 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7563 (mpp80) REVERT: E 288 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7646 (mppt) REVERT: E 340 HIS cc_start: 0.6789 (m90) cc_final: 0.6257 (m-70) REVERT: E 534 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: E 560 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (ttm170) REVERT: E 720 MET cc_start: 0.2783 (OUTLIER) cc_final: 0.2078 (mpm) REVERT: E 742 PHE cc_start: 0.6919 (m-80) cc_final: 0.5949 (m-80) REVERT: E 754 LYS cc_start: 0.7397 (mtmt) cc_final: 0.7158 (mtpp) REVERT: F 218 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: F 288 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7465 (mptp) REVERT: F 417 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: F 427 MET cc_start: 0.5511 (mmt) cc_final: 0.4296 (mmt) REVERT: F 508 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7369 (ttt) REVERT: F 534 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: F 560 ARG cc_start: 0.8297 (ttm170) cc_final: 0.8032 (ttm-80) REVERT: F 611 MET cc_start: 0.8025 (ptt) cc_final: 0.7638 (ptm) outliers start: 102 outliers final: 35 residues processed: 433 average time/residue: 1.8277 time to fit residues: 908.0993 Evaluate side-chains 421 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 365 time to evaluate : 3.223 ------------------------------------------------------------------------------- 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 383 ILE 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 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 456 LEU 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 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 534 GLU 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 292 GLU Chi-restraints excluded: chain D residue 383 ILE 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 456 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 385 optimal weight: 50.0000 chunk 180 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 381 optimal weight: 7.9990 chunk 162 optimal weight: 50.0000 chunk 445 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 269 optimal weight: 0.1980 chunk 362 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- 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 B 760 GLN C 327 GLN D 327 GLN E 760 GLN F 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.211133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.182528 restraints weight = 32598.483| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.24 r_work: 0.3561 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32506 Z= 0.191 Angle : 0.669 7.143 44118 Z= 0.355 Chirality : 0.049 0.198 5114 Planarity : 0.005 0.048 5976 Dihedral : 4.811 24.163 4800 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.82 % Allowed : 16.62 % 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: -1.05 (0.12), residues: 4512 helix: 0.44 (0.11), residues: 1980 sheet: 1.47 (0.26), residues: 450 loop : -2.44 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 454 HIS 0.003 0.001 HIS E 317 PHE 0.019 0.002 PHE C 265 TYR 0.020 0.002 TYR A 203 ARG 0.005 0.001 ARG B 662 Details of bonding type rmsd hydrogen bonds : bond 0.06856 ( 1408) hydrogen bonds : angle 4.64333 ( 3990) covalent geometry : bond 0.00449 (32506) covalent geometry : angle 0.66875 (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 482 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 374 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ASN cc_start: 0.8440 (t0) cc_final: 0.8122 (m-40) REVERT: A 599 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8200 (ptm160) REVERT: A 678 MET cc_start: 0.6659 (mmp) cc_final: 0.6061 (mpm) REVERT: A 742 PHE cc_start: 0.7217 (m-80) cc_final: 0.6405 (m-80) REVERT: A 757 MET cc_start: 0.6979 (mtt) cc_final: 0.6467 (mmt) REVERT: A 760 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.6211 (tt0) REVERT: B 211 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6667 (tptt) REVERT: B 256 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7581 (mpp80) REVERT: B 288 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7876 (mppt) REVERT: B 321 GLU cc_start: 0.7588 (mp0) cc_final: 0.7237 (mm-30) REVERT: B 534 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: B 678 MET cc_start: 0.6899 (mmp) cc_final: 0.6650 (mmm) REVERT: B 742 PHE cc_start: 0.6987 (m-80) cc_final: 0.6099 (m-80) REVERT: B 754 LYS cc_start: 0.7493 (mtmt) cc_final: 0.7290 (mtpp) REVERT: C 218 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: C 288 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7597 (mptp) REVERT: C 417 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7502 (tp30) REVERT: C 442 MET cc_start: 0.5834 (ptm) cc_final: 0.4489 (mmm) REVERT: C 508 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: C 534 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: C 560 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7988 (ttm-80) REVERT: C 611 MET cc_start: 0.8076 (ptt) cc_final: 0.7697 (ptm) REVERT: C 663 LYS cc_start: 0.7284 (ttmm) cc_final: 0.7060 (mtmm) REVERT: D 211 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6762 (tptt) REVERT: D 295 LYS cc_start: 0.6380 (mttp) cc_final: 0.6029 (mmtt) REVERT: D 658 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8080 (mtmt) REVERT: D 678 MET cc_start: 0.6939 (mmp) cc_final: 0.6268 (mpm) REVERT: D 742 PHE cc_start: 0.7231 (m-80) cc_final: 0.6400 (m-80) REVERT: D 753 ARG cc_start: 0.6760 (mtm110) cc_final: 0.6246 (mtm-85) REVERT: D 757 MET cc_start: 0.6966 (mtt) cc_final: 0.6442 (mmt) REVERT: E 211 LYS cc_start: 0.7199 (mtpt) cc_final: 0.6666 (tptt) REVERT: E 256 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7599 (mpp80) REVERT: E 288 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7853 (mppt) REVERT: E 321 GLU cc_start: 0.7584 (mp0) cc_final: 0.7237 (mm-30) REVERT: E 534 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: E 560 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8199 (ttm170) REVERT: E 678 MET cc_start: 0.6898 (mmp) cc_final: 0.6653 (mmm) REVERT: E 742 PHE cc_start: 0.7004 (m-80) cc_final: 0.6109 (m-80) REVERT: E 754 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7298 (mtpp) REVERT: F 218 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: F 288 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7600 (mptp) REVERT: F 364 ASP cc_start: 0.7810 (p0) cc_final: 0.7513 (p0) REVERT: F 417 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: F 508 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: F 534 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: F 560 ARG cc_start: 0.8316 (ttm170) cc_final: 0.8036 (ttm-80) REVERT: F 611 MET cc_start: 0.8076 (ptt) cc_final: 0.7694 (ptm) REVERT: F 663 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7075 (mtmm) outliers start: 108 outliers final: 45 residues processed: 435 average time/residue: 2.5085 time to fit residues: 1245.6535 Evaluate side-chains 420 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 3.586 ------------------------------------------------------------------------------- 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 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 705 SER 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 256 ARG 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 364 ASP 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 456 LEU Chi-restraints excluded: chain B residue 534 GLU 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 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 479 ILE Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 705 SER 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 364 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 456 LEU 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 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 663 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 130 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 428 optimal weight: 0.9980 chunk 364 optimal weight: 0.2980 chunk 275 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 430 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.214189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183612 restraints weight = 32802.194| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.26 r_work: 0.3568 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32506 Z= 0.115 Angle : 0.534 6.056 44118 Z= 0.284 Chirality : 0.045 0.204 5114 Planarity : 0.004 0.046 5976 Dihedral : 4.202 19.699 4800 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.04 % Allowed : 17.68 % Favored : 79.28 % 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: -0.38 (0.13), residues: 4512 helix: 1.09 (0.12), residues: 1950 sheet: 1.55 (0.26), residues: 450 loop : -2.08 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 454 HIS 0.001 0.000 HIS A 404 PHE 0.018 0.001 PHE F 265 TYR 0.013 0.001 TYR D 203 ARG 0.004 0.000 ARG E 256 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 1408) hydrogen bonds : angle 4.22511 ( 3990) covalent geometry : bond 0.00253 (32506) covalent geometry : angle 0.53398 (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 452 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 366 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8041 (mttt) cc_final: 0.7747 (mptp) REVERT: A 348 ASN cc_start: 0.8500 (t0) cc_final: 0.8171 (m-40) REVERT: A 397 GLU cc_start: 0.7557 (tt0) cc_final: 0.7303 (tp30) REVERT: A 427 MET cc_start: 0.6001 (mmm) cc_final: 0.5205 (mmt) REVERT: A 504 LEU cc_start: 0.7793 (mt) cc_final: 0.7521 (mm) REVERT: A 599 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8150 (ptm160) REVERT: A 611 MET cc_start: 0.7876 (ptt) cc_final: 0.7419 (ptm) REVERT: A 651 LYS cc_start: 0.7537 (mmtt) cc_final: 0.7232 (mppt) REVERT: A 674 PHE cc_start: 0.7086 (t80) cc_final: 0.6694 (t80) REVERT: A 678 MET cc_start: 0.6493 (mmp) cc_final: 0.5898 (mpm) REVERT: A 742 PHE cc_start: 0.6958 (m-80) cc_final: 0.6136 (m-80) REVERT: A 756 GLU cc_start: 0.6698 (mm-30) cc_final: 0.5677 (mt-10) REVERT: A 757 MET cc_start: 0.6759 (mtt) cc_final: 0.6052 (mmt) REVERT: B 211 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6231 (tptm) REVERT: B 340 HIS cc_start: 0.6915 (m90) cc_final: 0.6326 (m-70) REVERT: B 508 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7323 (ttt) REVERT: B 534 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: B 678 MET cc_start: 0.6746 (mmp) cc_final: 0.6415 (mmm) REVERT: B 742 PHE cc_start: 0.6704 (m-80) cc_final: 0.5749 (m-80) REVERT: B 754 LYS cc_start: 0.7336 (mtmt) cc_final: 0.7080 (mtpp) REVERT: B 756 GLU cc_start: 0.6654 (mm-30) cc_final: 0.5996 (mt-10) REVERT: C 218 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: C 417 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: C 427 MET cc_start: 0.5530 (mmt) cc_final: 0.4396 (mmt) REVERT: C 442 MET cc_start: 0.5093 (ptm) cc_final: 0.3860 (mmm) REVERT: C 508 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7302 (ttt) REVERT: C 534 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: C 560 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7828 (ttm-80) REVERT: C 611 MET cc_start: 0.7967 (ptt) cc_final: 0.7630 (ptm) REVERT: C 663 LYS cc_start: 0.7230 (ttmm) cc_final: 0.6960 (mtmm) REVERT: C 678 MET cc_start: 0.6982 (mmp) cc_final: 0.6547 (mmm) REVERT: D 211 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6389 (tptt) REVERT: D 321 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6089 (mm-30) REVERT: D 427 MET cc_start: 0.6016 (mmm) cc_final: 0.5039 (mmt) REVERT: D 611 MET cc_start: 0.7865 (ptt) cc_final: 0.7444 (ptm) REVERT: D 658 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8080 (mtmt) REVERT: D 678 MET cc_start: 0.6752 (mmp) cc_final: 0.5987 (mpm) REVERT: D 742 PHE cc_start: 0.6946 (m-80) cc_final: 0.6121 (m-80) REVERT: D 753 ARG cc_start: 0.6549 (mtm110) cc_final: 0.5828 (mtm-85) REVERT: D 756 GLU cc_start: 0.6691 (mm-30) cc_final: 0.5709 (mt-10) REVERT: D 757 MET cc_start: 0.6742 (mtt) cc_final: 0.6068 (mmt) REVERT: E 211 LYS cc_start: 0.6876 (mtpt) cc_final: 0.6277 (tptm) REVERT: E 340 HIS cc_start: 0.6906 (m90) cc_final: 0.6308 (m-70) REVERT: E 348 ASN cc_start: 0.8550 (t0) cc_final: 0.8193 (m110) REVERT: E 508 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7363 (ttt) REVERT: E 534 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: E 560 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8164 (ttm170) REVERT: E 678 MET cc_start: 0.6695 (mmp) cc_final: 0.6368 (mmm) REVERT: E 742 PHE cc_start: 0.6772 (m-80) cc_final: 0.5813 (m-80) REVERT: E 754 LYS cc_start: 0.7343 (mtmt) cc_final: 0.7091 (mtpp) REVERT: E 756 GLU cc_start: 0.6618 (mm-30) cc_final: 0.5948 (mt-10) REVERT: F 218 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: F 417 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: F 427 MET cc_start: 0.5528 (mmt) cc_final: 0.4429 (mmt) REVERT: F 508 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7284 (ttt) REVERT: F 534 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: F 560 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7877 (ttm-80) REVERT: F 611 MET cc_start: 0.7957 (ptt) cc_final: 0.7617 (ptm) REVERT: F 651 LYS cc_start: 0.7191 (mppt) cc_final: 0.6946 (mptt) REVERT: F 663 LYS cc_start: 0.7273 (ttmm) cc_final: 0.6983 (mtmm) REVERT: F 678 MET cc_start: 0.6935 (mmp) cc_final: 0.6491 (mmm) REVERT: F 772 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.5740 (mmt-90) outliers start: 86 outliers final: 41 residues processed: 423 average time/residue: 1.7963 time to fit residues: 872.5967 Evaluate side-chains 419 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 3.416 ------------------------------------------------------------------------------- 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 479 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 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 388 MET Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 GLU 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 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 321 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 761 THR 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 364 ASP 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 508 MET 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 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 Chi-restraints excluded: chain F residue 772 ARG 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: 9.9990 chunk 139 optimal weight: 0.0970 chunk 322 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 265 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 331 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN C 401 ASN D 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.212500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.181779 restraints weight = 32604.701| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.29 r_work: 0.3541 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32506 Z= 0.146 Angle : 0.588 5.846 44118 Z= 0.312 Chirality : 0.046 0.200 5114 Planarity : 0.004 0.048 5976 Dihedral : 4.345 20.830 4800 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.79 % Allowed : 18.18 % 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: -0.47 (0.13), residues: 4512 helix: 0.99 (0.12), residues: 1938 sheet: 1.55 (0.26), residues: 450 loop : -2.09 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 454 HIS 0.002 0.001 HIS D 406 PHE 0.019 0.002 PHE B 265 TYR 0.016 0.002 TYR D 203 ARG 0.004 0.000 ARG F 753 Details of bonding type rmsd hydrogen bonds : bond 0.05636 ( 1408) hydrogen bonds : angle 4.35516 ( 3990) covalent geometry : bond 0.00337 (32506) covalent geometry : angle 0.58800 (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 441 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 362 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ASN cc_start: 0.8199 (t0) cc_final: 0.7912 (m-40) REVERT: A 427 MET cc_start: 0.5787 (mmm) cc_final: 0.4785 (mmt) REVERT: A 599 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8094 (ptm160) REVERT: A 611 MET cc_start: 0.7800 (ptt) cc_final: 0.7490 (ptm) REVERT: A 678 MET cc_start: 0.6585 (mmp) cc_final: 0.6146 (mpm) REVERT: A 742 PHE cc_start: 0.7016 (m-80) cc_final: 0.6263 (m-80) REVERT: A 756 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6097 (mt-10) REVERT: B 211 LYS cc_start: 0.6945 (mtpt) cc_final: 0.6542 (tptt) REVERT: B 534 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: B 560 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: B 678 MET cc_start: 0.6776 (mmp) cc_final: 0.6518 (mmm) REVERT: B 742 PHE cc_start: 0.6852 (m-80) cc_final: 0.6031 (m-80) REVERT: B 754 LYS cc_start: 0.7412 (mtmt) cc_final: 0.7207 (mtpp) REVERT: B 756 GLU cc_start: 0.6575 (mm-30) cc_final: 0.5961 (mt-10) REVERT: C 218 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: C 417 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7089 (tp30) REVERT: C 427 MET cc_start: 0.5299 (mmt) cc_final: 0.4364 (mmt) REVERT: C 442 MET cc_start: 0.5408 (ptm) cc_final: 0.4220 (mmm) REVERT: C 508 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7146 (ttt) REVERT: C 534 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: C 560 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7689 (ttm-80) REVERT: C 611 MET cc_start: 0.7882 (ptt) cc_final: 0.7616 (ptm) REVERT: D 211 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6665 (tptt) REVERT: D 321 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.5971 (mm-30) REVERT: D 427 MET cc_start: 0.5717 (mmm) cc_final: 0.4715 (mmt) REVERT: D 534 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: D 611 MET cc_start: 0.7841 (ptt) cc_final: 0.7562 (ptm) REVERT: D 658 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: D 678 MET cc_start: 0.6828 (mmp) cc_final: 0.6242 (mpm) REVERT: D 742 PHE cc_start: 0.7038 (m-80) cc_final: 0.6276 (m-80) REVERT: D 753 ARG cc_start: 0.6579 (mtm110) cc_final: 0.5997 (mmp80) REVERT: E 211 LYS cc_start: 0.6963 (mtpt) cc_final: 0.6550 (tptt) REVERT: E 348 ASN cc_start: 0.8263 (t0) cc_final: 0.7942 (m110) REVERT: E 534 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: E 560 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7934 (ttm170) REVERT: E 678 MET cc_start: 0.6802 (mmp) cc_final: 0.6544 (mmm) REVERT: E 742 PHE cc_start: 0.6892 (m-80) cc_final: 0.6058 (m-80) REVERT: E 754 LYS cc_start: 0.7420 (mtmt) cc_final: 0.7214 (mtpp) REVERT: E 756 GLU cc_start: 0.6551 (mm-30) cc_final: 0.5936 (mt-10) REVERT: F 218 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: F 417 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7083 (tp30) REVERT: F 427 MET cc_start: 0.5317 (mmt) cc_final: 0.4380 (mmt) REVERT: F 508 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7119 (ttt) REVERT: F 534 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: F 560 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7714 (ttm-80) REVERT: F 611 MET cc_start: 0.7875 (ptt) cc_final: 0.7611 (ptm) REVERT: F 663 LYS cc_start: 0.6988 (ttmm) cc_final: 0.6785 (mtmm) outliers start: 79 outliers final: 45 residues processed: 417 average time/residue: 1.8340 time to fit residues: 875.0449 Evaluate side-chains 420 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 358 time to evaluate : 3.469 ------------------------------------------------------------------------------- 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 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 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 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 560 ARG 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 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 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 321 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 761 THR 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 364 ASP 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 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 383 ILE 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 650 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 274 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 360 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 173 optimal weight: 0.0870 chunk 345 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 372 optimal weight: 0.0000 chunk 31 optimal weight: 7.9990 overall best weight: 3.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN C 327 GLN D 327 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.211292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180545 restraints weight = 32561.364| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.24 r_work: 0.3535 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32506 Z= 0.177 Angle : 0.647 5.511 44118 Z= 0.345 Chirality : 0.048 0.200 5114 Planarity : 0.005 0.048 5976 Dihedral : 4.653 22.937 4800 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.55 % Allowed : 18.67 % Favored : 78.78 % 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: -0.74 (0.12), residues: 4512 helix: 0.72 (0.12), residues: 1938 sheet: 1.46 (0.26), residues: 450 loop : -2.19 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 454 HIS 0.003 0.001 HIS E 317 PHE 0.021 0.002 PHE F 265 TYR 0.021 0.002 TYR D 203 ARG 0.006 0.001 ARG F 753 Details of bonding type rmsd hydrogen bonds : bond 0.06543 ( 1408) hydrogen bonds : angle 4.54512 ( 3990) covalent geometry : bond 0.00414 (32506) covalent geometry : angle 0.64740 (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 439 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 367 time to evaluate : 3.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ASN cc_start: 0.8496 (t0) cc_final: 0.8159 (m-40) REVERT: A 427 MET cc_start: 0.6090 (mmm) cc_final: 0.4955 (mmt) REVERT: A 599 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8259 (ptm160) REVERT: A 611 MET cc_start: 0.7983 (ptt) cc_final: 0.7646 (ptm) REVERT: A 678 MET cc_start: 0.6669 (mmp) cc_final: 0.5978 (mpm) REVERT: A 742 PHE cc_start: 0.7104 (m-80) cc_final: 0.6225 (m-80) REVERT: A 757 MET cc_start: 0.6835 (mtt) cc_final: 0.6087 (mmt) REVERT: B 211 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6358 (tptt) REVERT: B 321 GLU cc_start: 0.7636 (mp0) cc_final: 0.7258 (mm-30) REVERT: B 534 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: B 560 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8210 (ttm170) REVERT: B 678 MET cc_start: 0.6734 (mmp) cc_final: 0.6459 (mmm) REVERT: B 742 PHE cc_start: 0.6808 (m-80) cc_final: 0.5831 (m-80) REVERT: B 754 LYS cc_start: 0.7337 (mtmt) cc_final: 0.7083 (mtpp) REVERT: C 218 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: C 417 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: C 427 MET cc_start: 0.5496 (mmt) cc_final: 0.4353 (mmt) REVERT: C 508 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7340 (ttt) REVERT: C 534 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: C 560 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7947 (ttm-80) REVERT: C 611 MET cc_start: 0.8006 (ptt) cc_final: 0.7687 (ptm) REVERT: D 211 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6470 (tptt) REVERT: D 321 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6354 (mm-30) REVERT: D 427 MET cc_start: 0.6068 (mmm) cc_final: 0.4960 (mmt) REVERT: D 534 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: D 611 MET cc_start: 0.7979 (ptt) cc_final: 0.7650 (ptm) REVERT: D 658 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7983 (mtmt) REVERT: D 678 MET cc_start: 0.6792 (mmp) cc_final: 0.5978 (mpm) REVERT: D 742 PHE cc_start: 0.7072 (m-80) cc_final: 0.6175 (m-80) REVERT: D 753 ARG cc_start: 0.6543 (mtm110) cc_final: 0.5512 (mmp80) REVERT: D 757 MET cc_start: 0.6774 (mtt) cc_final: 0.6078 (mmt) REVERT: E 211 LYS cc_start: 0.6967 (mtpt) cc_final: 0.6353 (tptt) REVERT: E 321 GLU cc_start: 0.7648 (mp0) cc_final: 0.7255 (mm-30) REVERT: E 348 ASN cc_start: 0.8548 (t0) cc_final: 0.8324 (t0) REVERT: E 534 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: E 560 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (ttm170) REVERT: E 742 PHE cc_start: 0.6828 (m-80) cc_final: 0.5847 (m-80) REVERT: E 754 LYS cc_start: 0.7341 (mtmt) cc_final: 0.7089 (mtpp) REVERT: F 218 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: F 417 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: F 427 MET cc_start: 0.5489 (mmt) cc_final: 0.4337 (mmt) REVERT: F 508 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7320 (ttt) REVERT: F 534 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: F 560 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7990 (ttm-80) REVERT: F 611 MET cc_start: 0.7978 (ptt) cc_final: 0.7670 (ptm) REVERT: F 757 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6004 (mtt) outliers start: 72 outliers final: 41 residues processed: 412 average time/residue: 1.8455 time to fit residues: 876.4742 Evaluate side-chains 421 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 3.846 ------------------------------------------------------------------------------- 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 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 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 560 ARG 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 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 321 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 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 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 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 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 650 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 1 optimal weight: 50.0000 chunk 123 optimal weight: 0.7980 chunk 300 optimal weight: 50.0000 chunk 285 optimal weight: 5.9990 chunk 407 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN D 327 GLN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.209946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.179002 restraints weight = 32347.779| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.25 r_work: 0.3513 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 32506 Z= 0.228 Angle : 0.734 6.114 44118 Z= 0.391 Chirality : 0.051 0.194 5114 Planarity : 0.005 0.049 5976 Dihedral : 5.050 25.340 4800 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.48 % Allowed : 19.06 % Favored : 78.47 % 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: -1.14 (0.12), residues: 4512 helix: 0.29 (0.11), residues: 1980 sheet: 1.19 (0.26), residues: 456 loop : -2.35 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 454 HIS 0.003 0.001 HIS D 404 PHE 0.021 0.002 PHE F 265 TYR 0.028 0.003 TYR D 203 ARG 0.008 0.001 ARG F 753 Details of bonding type rmsd hydrogen bonds : bond 0.07590 ( 1408) hydrogen bonds : angle 4.76193 ( 3990) covalent geometry : bond 0.00542 (32506) covalent geometry : angle 0.73366 (44118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27262.81 seconds wall clock time: 473 minutes 10.14 seconds (28390.14 seconds total)