Starting phenix.real_space_refine on Mon Aug 25 23:06:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0e_18790/08_2025/8r0e_18790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0e_18790/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r0e_18790/08_2025/8r0e_18790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0e_18790/08_2025/8r0e_18790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r0e_18790/08_2025/8r0e_18790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0e_18790/08_2025/8r0e_18790.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 10, 'ARG:plan': 17, 'ASP:plan': 16, 'GLU:plan': 17, 'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 318 Time building chain proxies: 6.84, per 1000 atoms: 0.21 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.28 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: 5.64 Time building geometry restraints manager: 3.51 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: 0.02 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.170 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG C 708 TYR 0.014 0.002 TYR D 244 PHE 0.030 0.003 PHE C 575 TRP 0.011 0.003 TRP B 454 HIS 0.009 0.002 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.01236 (32506) covalent geometry : angle 1.20445 (44118) hydrogen bonds : bond 0.17550 ( 1408) hydrogen bonds : angle 6.86657 ( 3990) *********************** 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 : 1.338 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: 0.8927 time to fit residues: 549.5546 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.219898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.194059 restraints weight = 32781.477| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.07 r_work: 0.3808 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32506 Z= 0.136 Angle : 0.627 6.860 44118 Z= 0.335 Chirality : 0.046 0.201 5114 Planarity : 0.005 0.047 5976 Dihedral : 5.202 24.066 4800 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.94 % Allowed : 11.56 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.12), residues: 4512 helix: -0.68 (0.11), residues: 1968 sheet: -0.11 (0.24), residues: 522 loop : -3.10 (0.12), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 256 TYR 0.011 0.001 TYR D 203 PHE 0.020 0.002 PHE D 265 TRP 0.006 0.001 TRP F 454 HIS 0.006 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00288 (32506) covalent geometry : angle 0.62730 (44118) hydrogen bonds : bond 0.05384 ( 1408) hydrogen bonds : angle 4.77344 ( 3990) *********************** 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 485 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 430 time to evaluate : 1.242 Fit side-chains REVERT: A 292 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 295 LYS cc_start: 0.6217 (mttp) cc_final: 0.5906 (mmtt) REVERT: A 742 PHE cc_start: 0.6949 (m-10) cc_final: 0.6167 (m-80) REVERT: A 753 ARG cc_start: 0.6445 (mtm110) cc_final: 0.6218 (mmp80) REVERT: B 256 ARG cc_start: 0.7683 (mpt-90) cc_final: 0.7432 (mpp80) REVERT: B 295 LYS cc_start: 0.6418 (mttp) cc_final: 0.6197 (mmtm) REVERT: B 324 ILE cc_start: 0.8216 (tt) cc_final: 0.7964 (tp) REVERT: B 340 HIS cc_start: 0.6587 (m90) cc_final: 0.6095 (m-70) REVERT: B 554 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: B 568 GLN cc_start: 0.7772 (mm110) cc_final: 0.7499 (mt0) REVERT: B 720 MET cc_start: 0.2808 (OUTLIER) cc_final: 0.2333 (mpm) REVERT: B 742 PHE cc_start: 0.6863 (m-10) cc_final: 0.6200 (m-80) REVERT: C 256 ARG cc_start: 0.7528 (mpt-90) cc_final: 0.7234 (mpt-90) REVERT: C 508 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7398 (ttt) REVERT: C 560 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7356 (ttm-80) REVERT: D 210 ARG cc_start: 0.5897 (tpm170) cc_final: 0.5499 (ttp-110) REVERT: D 256 ARG cc_start: 0.7572 (mpt-90) cc_final: 0.7302 (mpp80) REVERT: D 275 MET cc_start: 0.8606 (mmm) cc_final: 0.8386 (mmm) REVERT: D 295 LYS cc_start: 0.6384 (mttp) cc_final: 0.6126 (mmtt) REVERT: D 508 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7395 (ttt) REVERT: D 753 ARG cc_start: 0.6328 (mtm110) cc_final: 0.6044 (mmp80) REVERT: E 256 ARG cc_start: 0.7676 (mpt-90) cc_final: 0.7443 (mpp80) REVERT: E 295 LYS cc_start: 0.6443 (mttp) cc_final: 0.6232 (mmtm) REVERT: E 324 ILE cc_start: 0.8228 (tt) cc_final: 0.7979 (tp) REVERT: E 340 HIS cc_start: 0.6604 (m90) cc_final: 0.6122 (m-70) REVERT: E 554 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: E 568 GLN cc_start: 0.7786 (mm110) cc_final: 0.7514 (mt0) REVERT: E 720 MET cc_start: 0.2782 (OUTLIER) cc_final: 0.2316 (mpm) REVERT: E 742 PHE cc_start: 0.6891 (m-10) cc_final: 0.6222 (m-80) REVERT: F 256 ARG cc_start: 0.7556 (mpt-90) cc_final: 0.7212 (mpt-90) REVERT: F 508 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7365 (ttt) REVERT: F 560 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7391 (ttm-80) outliers start: 55 outliers final: 19 residues processed: 460 average time/residue: 0.8466 time to fit residues: 442.4668 Evaluate side-chains 386 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 359 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 741 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 741 ARG Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 351 optimal weight: 0.7980 chunk 80 optimal weight: 0.0040 chunk 100 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 188 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 155 optimal weight: 0.0020 chunk 90 optimal weight: 8.9990 chunk 395 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 chunk 327 optimal weight: 8.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 624 ASN F 327 GLN F 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.221721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.193664 restraints weight = 33052.178| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.10 r_work: 0.3850 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 32506 Z= 0.102 Angle : 0.530 5.686 44118 Z= 0.279 Chirality : 0.044 0.204 5114 Planarity : 0.003 0.040 5976 Dihedral : 4.351 20.043 4800 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.98 % Allowed : 13.40 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.13), residues: 4512 helix: 0.83 (0.12), residues: 1926 sheet: 0.44 (0.24), residues: 522 loop : -2.38 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.014 0.001 TYR D 203 PHE 0.017 0.001 PHE D 265 TRP 0.009 0.001 TRP A 454 HIS 0.003 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00219 (32506) covalent geometry : angle 0.52952 (44118) hydrogen bonds : bond 0.03756 ( 1408) hydrogen bonds : angle 4.15611 ( 3990) *********************** 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 486 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 430 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6481 (mmpt) REVERT: A 295 LYS cc_start: 0.6078 (mttp) cc_final: 0.5807 (mmtt) REVERT: A 427 MET cc_start: 0.5160 (mpm) cc_final: 0.4316 (mmm) REVERT: A 488 GLU cc_start: 0.7654 (tt0) cc_final: 0.7417 (tt0) REVERT: A 508 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7347 (ttt) REVERT: A 599 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7833 (ptm160) REVERT: A 742 PHE cc_start: 0.6956 (m-10) cc_final: 0.6124 (m-80) REVERT: B 340 HIS cc_start: 0.6632 (m90) cc_final: 0.6264 (m170) REVERT: B 568 GLN cc_start: 0.7628 (mm110) cc_final: 0.7379 (mt0) REVERT: B 611 MET cc_start: 0.7860 (ptt) cc_final: 0.7503 (ptp) REVERT: B 720 MET cc_start: 0.2588 (OUTLIER) cc_final: 0.2204 (mpm) REVERT: B 742 PHE cc_start: 0.6816 (m-10) cc_final: 0.6178 (m-80) REVERT: C 218 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: C 417 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: C 427 MET cc_start: 0.5042 (mmt) cc_final: 0.4316 (mmt) REVERT: C 508 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7231 (ttt) REVERT: C 560 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7465 (ttm-80) REVERT: D 210 ARG cc_start: 0.5917 (tpm170) cc_final: 0.5427 (ttp-110) REVERT: D 288 LYS cc_start: 0.7617 (mttp) cc_final: 0.7306 (mmmt) REVERT: D 295 LYS cc_start: 0.6217 (mttp) cc_final: 0.5991 (mmtm) REVERT: D 427 MET cc_start: 0.4888 (mpm) cc_final: 0.4360 (mmt) REVERT: D 453 ARG cc_start: 0.7341 (mmt90) cc_final: 0.7125 (tpp80) REVERT: D 665 PRO cc_start: 0.7626 (Cg_endo) cc_final: 0.7257 (Cg_exo) REVERT: D 678 MET cc_start: 0.6789 (mmp) cc_final: 0.6244 (mpm) REVERT: D 753 ARG cc_start: 0.6306 (mtm110) cc_final: 0.6013 (mmp80) REVERT: E 256 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7473 (mpp80) REVERT: E 340 HIS cc_start: 0.6655 (m90) cc_final: 0.6084 (m-70) REVERT: E 483 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6426 (tp30) REVERT: E 568 GLN cc_start: 0.7631 (mm110) cc_final: 0.7381 (mt0) REVERT: E 611 MET cc_start: 0.7869 (ptt) cc_final: 0.7499 (ptp) REVERT: E 720 MET cc_start: 0.2541 (OUTLIER) cc_final: 0.2185 (mpm) REVERT: E 742 PHE cc_start: 0.6835 (m-10) cc_final: 0.6184 (m-80) REVERT: F 218 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: F 417 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: F 427 MET cc_start: 0.5010 (mmt) cc_final: 0.4316 (mmt) REVERT: F 442 MET cc_start: 0.5028 (OUTLIER) cc_final: 0.4795 (mmp) REVERT: F 508 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7134 (ttt) REVERT: F 560 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7505 (ttm-80) outliers start: 56 outliers final: 12 residues processed: 461 average time/residue: 0.8180 time to fit residues: 430.4625 Evaluate side-chains 395 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 370 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 508 MET 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 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 417 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG 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 253 LEU Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 508 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 90 optimal weight: 50.0000 chunk 248 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 330 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 163 optimal weight: 50.0000 chunk 340 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 C 624 ASN D 327 GLN E 260 ASN E 285 ASN F 285 ASN F 327 GLN F 624 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.211093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180969 restraints weight = 32345.348| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.32 r_work: 0.3516 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 32506 Z= 0.225 Angle : 0.733 8.906 44118 Z= 0.387 Chirality : 0.051 0.194 5114 Planarity : 0.005 0.046 5976 Dihedral : 5.037 24.567 4800 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.32 % Allowed : 14.92 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.12), residues: 4512 helix: -0.00 (0.11), residues: 1980 sheet: 0.48 (0.24), residues: 522 loop : -2.66 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 362 TYR 0.022 0.003 TYR D 203 PHE 0.018 0.002 PHE C 265 TRP 0.007 0.002 TRP B 476 HIS 0.006 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00532 (32506) covalent geometry : angle 0.73264 (44118) hydrogen bonds : bond 0.07604 ( 1408) hydrogen bonds : angle 4.82979 ( 3990) *********************** 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 468 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 374 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6749 (mmpt) REVERT: A 295 LYS cc_start: 0.6616 (mttp) cc_final: 0.6149 (mmtt) REVERT: A 427 MET cc_start: 0.5456 (mpm) cc_final: 0.4305 (mmt) REVERT: A 599 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8305 (ptm160) REVERT: A 641 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: A 651 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7306 (mppt) REVERT: A 678 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5694 (mpm) REVERT: A 742 PHE cc_start: 0.7081 (m-80) cc_final: 0.6095 (m-80) REVERT: B 321 GLU cc_start: 0.7517 (mp0) cc_final: 0.7274 (mm-30) REVERT: B 456 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7409 (mt) REVERT: B 568 GLN cc_start: 0.7872 (mm110) cc_final: 0.7557 (mm110) REVERT: B 611 MET cc_start: 0.8092 (ptt) cc_final: 0.7735 (ptp) REVERT: B 641 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7183 (mt0) REVERT: B 720 MET cc_start: 0.2910 (OUTLIER) cc_final: 0.2246 (mpm) REVERT: B 742 PHE cc_start: 0.6931 (m-10) cc_final: 0.5944 (m-80) REVERT: B 744 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6914 (ttm170) REVERT: B 754 LYS cc_start: 0.7355 (mtmt) cc_final: 0.7109 (mtpp) REVERT: C 210 ARG cc_start: 0.6496 (mmm-85) cc_final: 0.6071 (tpm170) REVERT: C 218 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: C 417 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: C 560 ARG cc_start: 0.8361 (ttm170) cc_final: 0.8135 (ttp80) REVERT: D 211 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6535 (tptt) REVERT: D 295 LYS cc_start: 0.6692 (mttp) cc_final: 0.6230 (mmtt) REVERT: D 427 MET cc_start: 0.5356 (mpm) cc_final: 0.4279 (mmt) REVERT: D 641 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: D 678 MET cc_start: 0.6684 (mmp) cc_final: 0.5925 (mpm) REVERT: D 742 PHE cc_start: 0.7087 (m-80) cc_final: 0.6088 (m-80) REVERT: D 753 ARG cc_start: 0.6584 (mtm110) cc_final: 0.5755 (mmp80) REVERT: E 256 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7639 (mpp80) REVERT: E 456 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7398 (mt) REVERT: E 560 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8244 (ttm170) REVERT: E 568 GLN cc_start: 0.7885 (mm110) cc_final: 0.7577 (mm110) REVERT: E 611 MET cc_start: 0.8101 (ptt) cc_final: 0.7716 (ptp) REVERT: E 641 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: E 720 MET cc_start: 0.2931 (OUTLIER) cc_final: 0.2257 (mpm) REVERT: E 742 PHE cc_start: 0.6943 (m-10) cc_final: 0.5954 (m-80) REVERT: E 744 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6900 (ttm170) REVERT: E 754 LYS cc_start: 0.7387 (mtmt) cc_final: 0.7142 (mtpp) REVERT: F 218 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: F 417 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: F 560 ARG cc_start: 0.8355 (ttm170) cc_final: 0.8121 (ttp80) outliers start: 94 outliers final: 32 residues processed: 435 average time/residue: 0.8647 time to fit residues: 427.8470 Evaluate side-chains 408 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 356 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 479 ILE 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 678 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 456 LEU 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 744 ARG 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 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 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 641 GLN Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 641 GLN Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 744 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 443 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 405 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 420 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN C 327 GLN 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 = 0.4345 r_free = 0.4345 target = 0.213702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.182317 restraints weight = 32444.595| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.33 r_work: 0.3561 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32506 Z= 0.125 Angle : 0.562 6.667 44118 Z= 0.299 Chirality : 0.045 0.204 5114 Planarity : 0.004 0.043 5976 Dihedral : 4.449 19.408 4800 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.47 % Allowed : 15.74 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 4512 helix: 0.73 (0.12), residues: 1944 sheet: 0.66 (0.25), residues: 522 loop : -2.27 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 256 TYR 0.014 0.001 TYR D 203 PHE 0.017 0.001 PHE B 265 TRP 0.010 0.001 TRP B 454 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00281 (32506) covalent geometry : angle 0.56202 (44118) hydrogen bonds : bond 0.05057 ( 1408) hydrogen bonds : angle 4.37216 ( 3990) *********************** 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 481 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 383 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6547 (mmpt) REVERT: A 321 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6115 (mm-30) REVERT: A 427 MET cc_start: 0.5320 (mpm) cc_final: 0.4339 (mmt) REVERT: A 599 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8140 (ptm160) REVERT: A 651 LYS cc_start: 0.7500 (mmtt) cc_final: 0.7255 (mppt) REVERT: A 742 PHE cc_start: 0.7099 (m-80) cc_final: 0.6114 (m-80) REVERT: A 757 MET cc_start: 0.6823 (mtt) cc_final: 0.6183 (mmt) REVERT: B 211 LYS cc_start: 0.6922 (mtpt) cc_final: 0.6260 (tptm) REVERT: B 288 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7676 (mppt) REVERT: B 340 HIS cc_start: 0.6884 (m90) cc_final: 0.6303 (m-70) REVERT: B 508 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7318 (ttt) REVERT: B 554 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 568 GLN cc_start: 0.7622 (mm110) cc_final: 0.7202 (mt0) REVERT: B 611 MET cc_start: 0.8027 (ptt) cc_final: 0.7798 (ptp) REVERT: B 678 MET cc_start: 0.6715 (mmp) cc_final: 0.6430 (mmm) REVERT: B 720 MET cc_start: 0.2592 (OUTLIER) cc_final: 0.1942 (mpm) REVERT: B 742 PHE cc_start: 0.6804 (m-80) cc_final: 0.5785 (m-80) REVERT: C 210 ARG cc_start: 0.6314 (mmm-85) cc_final: 0.5932 (tpm170) REVERT: C 218 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: C 417 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: C 427 MET cc_start: 0.5431 (mmt) cc_final: 0.4361 (mmt) REVERT: C 442 MET cc_start: 0.5356 (pmt) cc_final: 0.3628 (mmp) REVERT: C 486 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7985 (tttt) REVERT: C 508 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7252 (ttt) REVERT: C 560 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7910 (ttm-80) REVERT: D 288 LYS cc_start: 0.8069 (mttt) cc_final: 0.7836 (mptp) REVERT: D 321 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6070 (mm-30) REVERT: D 427 MET cc_start: 0.5297 (mpm) cc_final: 0.4331 (mmt) REVERT: D 504 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7826 (tp) REVERT: D 651 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7269 (mppt) REVERT: D 678 MET cc_start: 0.6752 (mmp) cc_final: 0.6051 (mpm) REVERT: D 742 PHE cc_start: 0.7091 (m-80) cc_final: 0.6118 (m-80) REVERT: D 753 ARG cc_start: 0.6587 (mtm110) cc_final: 0.5883 (mtm-85) REVERT: D 756 GLU cc_start: 0.6801 (mm-30) cc_final: 0.5803 (mt-10) REVERT: D 757 MET cc_start: 0.6752 (mtt) cc_final: 0.6117 (mmt) REVERT: E 211 LYS cc_start: 0.6916 (mtpt) cc_final: 0.6253 (tptm) REVERT: E 256 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7566 (mpp80) REVERT: E 288 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7659 (mppt) REVERT: E 315 LYS cc_start: 0.5255 (mmmt) cc_final: 0.5049 (mmtt) REVERT: E 454 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6433 (t-100) REVERT: E 554 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7875 (mt-10) REVERT: E 560 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8140 (ttm170) REVERT: E 568 GLN cc_start: 0.7640 (mm110) cc_final: 0.7222 (mt0) REVERT: E 611 MET cc_start: 0.8018 (ptt) cc_final: 0.7781 (ptp) REVERT: E 678 MET cc_start: 0.6765 (mmp) cc_final: 0.6486 (mmm) REVERT: E 720 MET cc_start: 0.2548 (OUTLIER) cc_final: 0.1897 (mpm) REVERT: E 742 PHE cc_start: 0.6842 (m-80) cc_final: 0.5835 (m-80) REVERT: F 218 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: F 417 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: F 427 MET cc_start: 0.5438 (mmt) cc_final: 0.4389 (mmt) REVERT: F 486 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.8008 (tttt) REVERT: F 508 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7287 (ttt) REVERT: F 560 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7911 (ttm-80) outliers start: 98 outliers final: 37 residues processed: 445 average time/residue: 0.9288 time to fit residues: 470.6091 Evaluate side-chains 419 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 361 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 486 LYS Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 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 383 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 720 MET 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 403 THR Chi-restraints excluded: chain E residue 454 TRP Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 486 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 309 optimal weight: 30.0000 chunk 219 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 358 optimal weight: 3.9990 chunk 364 optimal weight: 0.7980 chunk 414 optimal weight: 9.9990 chunk 357 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 91 optimal weight: 50.0000 chunk 171 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN C 327 GLN D 327 GLN 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 = 0.4312 r_free = 0.4312 target = 0.210420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180245 restraints weight = 32473.135| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.28 r_work: 0.3529 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3457 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= 0.205 Angle : 0.701 7.904 44118 Z= 0.371 Chirality : 0.050 0.199 5114 Planarity : 0.005 0.046 5976 Dihedral : 4.917 25.077 4800 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.93 % Allowed : 16.44 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.12), residues: 4512 helix: 0.30 (0.11), residues: 1944 sheet: 1.35 (0.26), residues: 450 loop : -2.46 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 662 TYR 0.021 0.002 TYR D 203 PHE 0.020 0.002 PHE F 265 TRP 0.007 0.002 TRP B 454 HIS 0.004 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00483 (32506) covalent geometry : angle 0.70113 (44118) hydrogen bonds : bond 0.07280 ( 1408) hydrogen bonds : angle 4.74625 ( 3990) *********************** 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 482 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 371 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LYS cc_start: 0.6436 (mttp) cc_final: 0.6077 (mmtt) REVERT: A 321 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6476 (mm-30) REVERT: A 448 THR cc_start: 0.6985 (p) cc_final: 0.6651 (t) REVERT: A 599 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (ptm160) REVERT: A 641 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: A 742 PHE cc_start: 0.7125 (m-80) cc_final: 0.6147 (m-80) REVERT: B 211 LYS cc_start: 0.7119 (mtpt) cc_final: 0.6512 (tptt) REVERT: B 288 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7767 (mppt) REVERT: B 321 GLU cc_start: 0.7652 (mp0) cc_final: 0.7292 (mm-30) REVERT: B 560 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (ttm170) REVERT: B 568 GLN cc_start: 0.7932 (mm110) cc_final: 0.7606 (mm110) REVERT: B 611 MET cc_start: 0.8082 (ptt) cc_final: 0.7877 (ptp) REVERT: B 720 MET cc_start: 0.2832 (OUTLIER) cc_final: 0.2189 (mpm) REVERT: B 742 PHE cc_start: 0.6903 (m-80) cc_final: 0.5900 (m-80) REVERT: B 754 LYS cc_start: 0.7340 (mtmt) cc_final: 0.7065 (mtpp) REVERT: C 218 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: C 417 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: C 486 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7946 (tttt) REVERT: C 560 ARG cc_start: 0.8290 (ttm170) cc_final: 0.7943 (ttm-80) REVERT: C 611 MET cc_start: 0.8130 (ptt) cc_final: 0.7671 (ptm) REVERT: C 757 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6081 (mtt) REVERT: D 211 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6509 (tptt) REVERT: D 288 LYS cc_start: 0.8098 (mttt) cc_final: 0.7893 (mptp) REVERT: D 295 LYS cc_start: 0.6461 (mttp) cc_final: 0.6090 (mmtt) REVERT: D 321 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6415 (mm-30) REVERT: D 397 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: D 504 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7815 (tp) REVERT: D 641 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: D 658 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7992 (mtmt) REVERT: D 678 MET cc_start: 0.6699 (mmp) cc_final: 0.5993 (mpm) REVERT: D 742 PHE cc_start: 0.7129 (m-80) cc_final: 0.6256 (m-80) REVERT: D 753 ARG cc_start: 0.6616 (mtm110) cc_final: 0.6155 (mtm-85) REVERT: E 211 LYS cc_start: 0.7120 (mtpt) cc_final: 0.6511 (tptt) REVERT: E 256 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7530 (mpp80) REVERT: E 288 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7095 (mppt) REVERT: E 292 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: E 315 LYS cc_start: 0.5145 (mmmt) cc_final: 0.4902 (mmtt) REVERT: E 321 GLU cc_start: 0.7642 (mp0) cc_final: 0.7286 (mm-30) REVERT: E 534 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: E 560 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8218 (ttm170) REVERT: E 568 GLN cc_start: 0.7945 (mm110) cc_final: 0.7619 (mm110) REVERT: E 611 MET cc_start: 0.8077 (ptt) cc_final: 0.7870 (ptp) REVERT: E 720 MET cc_start: 0.2847 (OUTLIER) cc_final: 0.2191 (mpm) REVERT: E 742 PHE cc_start: 0.6910 (m-80) cc_final: 0.5904 (m-80) REVERT: E 754 LYS cc_start: 0.7327 (mtmt) cc_final: 0.7055 (mtpp) REVERT: F 218 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: F 417 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: F 486 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7927 (tttt) REVERT: F 560 ARG cc_start: 0.8293 (ttm170) cc_final: 0.8015 (ttm-80) REVERT: F 611 MET cc_start: 0.8120 (ptt) cc_final: 0.7657 (ptm) outliers start: 111 outliers final: 44 residues processed: 438 average time/residue: 0.9728 time to fit residues: 481.8530 Evaluate side-chains 428 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 359 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 383 ILE 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 705 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 560 ARG 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 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 486 LYS Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 741 ARG Chi-restraints excluded: chain C residue 757 MET 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 383 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 641 GLN Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 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 E residue 761 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 403 optimal weight: 8.9990 chunk 413 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 445 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN C 760 GLN D 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.214073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177545 restraints weight = 32835.496| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.54 r_work: 0.3495 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32506 Z= 0.111 Angle : 0.532 6.112 44118 Z= 0.283 Chirality : 0.045 0.202 5114 Planarity : 0.004 0.044 5976 Dihedral : 4.234 19.476 4800 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.76 % Allowed : 17.89 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.13), residues: 4512 helix: 1.03 (0.12), residues: 1944 sheet: 1.43 (0.26), residues: 456 loop : -2.15 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.012 0.001 TYR D 203 PHE 0.017 0.001 PHE B 265 TRP 0.014 0.001 TRP B 454 HIS 0.002 0.000 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00246 (32506) covalent geometry : angle 0.53225 (44118) hydrogen bonds : bond 0.04430 ( 1408) hydrogen bonds : angle 4.22998 ( 3990) *********************** 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 459 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 381 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6507 (mmpt) REVERT: A 321 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5903 (mm-30) REVERT: A 427 MET cc_start: 0.5805 (mmm) cc_final: 0.4829 (mmt) REVERT: A 508 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7361 (ttt) REVERT: A 599 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8035 (ptm160) REVERT: A 611 MET cc_start: 0.7797 (ptt) cc_final: 0.7427 (ptm) REVERT: A 742 PHE cc_start: 0.7018 (m-80) cc_final: 0.6212 (m-80) REVERT: A 756 GLU cc_start: 0.6683 (mm-30) cc_final: 0.5994 (mt-10) REVERT: A 757 MET cc_start: 0.6925 (mtt) cc_final: 0.6471 (mmt) REVERT: B 211 LYS cc_start: 0.6915 (mtpt) cc_final: 0.6404 (tptm) REVERT: B 340 HIS cc_start: 0.6904 (m90) cc_final: 0.6315 (m-70) REVERT: B 427 MET cc_start: 0.5505 (mmt) cc_final: 0.4587 (mmt) REVERT: B 534 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 568 GLN cc_start: 0.7470 (mm110) cc_final: 0.7118 (mt0) REVERT: B 678 MET cc_start: 0.6903 (mmp) cc_final: 0.6610 (mmm) REVERT: B 720 MET cc_start: 0.2482 (OUTLIER) cc_final: 0.1999 (mpm) REVERT: B 742 PHE cc_start: 0.6816 (m-80) cc_final: 0.5985 (m-80) REVERT: B 754 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7196 (mtpp) REVERT: C 218 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: C 417 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: C 427 MET cc_start: 0.5245 (mmt) cc_final: 0.4401 (mmt) REVERT: C 486 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7957 (tttt) REVERT: C 508 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7197 (ttt) REVERT: C 554 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 560 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7735 (ttm-80) REVERT: C 611 MET cc_start: 0.7917 (ptt) cc_final: 0.7595 (ptm) REVERT: C 760 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6160 (tt0) REVERT: D 321 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5909 (mm-30) REVERT: D 427 MET cc_start: 0.5731 (mmm) cc_final: 0.4683 (mmt) REVERT: D 504 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (tp) REVERT: D 611 MET cc_start: 0.7799 (ptt) cc_final: 0.7204 (ptm) REVERT: D 658 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8023 (mtmt) REVERT: D 678 MET cc_start: 0.6776 (mmp) cc_final: 0.6199 (mpm) REVERT: D 742 PHE cc_start: 0.7075 (m-80) cc_final: 0.6216 (m-80) REVERT: D 753 ARG cc_start: 0.6587 (mtm110) cc_final: 0.6112 (mtm-85) REVERT: D 756 GLU cc_start: 0.6704 (mm-30) cc_final: 0.5994 (mt-10) REVERT: D 757 MET cc_start: 0.6859 (mtt) cc_final: 0.6410 (mmt) REVERT: E 211 LYS cc_start: 0.6902 (mtpt) cc_final: 0.6404 (tptm) REVERT: E 288 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.6824 (mppt) REVERT: E 292 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: E 427 MET cc_start: 0.5493 (mmt) cc_final: 0.4575 (mmt) REVERT: E 560 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7899 (ttm170) REVERT: E 568 GLN cc_start: 0.7465 (mm110) cc_final: 0.7127 (mt0) REVERT: E 678 MET cc_start: 0.6875 (mmp) cc_final: 0.6577 (mmm) REVERT: E 720 MET cc_start: 0.2467 (OUTLIER) cc_final: 0.1983 (mpm) REVERT: E 742 PHE cc_start: 0.6826 (m-80) cc_final: 0.5985 (m-80) REVERT: E 754 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7198 (mtpp) REVERT: F 218 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: F 417 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: F 427 MET cc_start: 0.5251 (mmt) cc_final: 0.4404 (mmt) REVERT: F 486 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: F 508 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7174 (ttt) REVERT: F 554 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7775 (mt-10) REVERT: F 560 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7754 (ttm-80) REVERT: F 611 MET cc_start: 0.7919 (ptt) cc_final: 0.7595 (ptm) outliers start: 78 outliers final: 27 residues processed: 434 average time/residue: 0.8846 time to fit residues: 435.5646 Evaluate side-chains 414 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 MET 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 720 MET 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 534 GLU 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 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 486 LYS Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 760 GLN 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 327 GLN Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 560 ARG 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 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain F residue 508 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 166 optimal weight: 50.0000 chunk 233 optimal weight: 30.0000 chunk 232 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 158 optimal weight: 50.0000 chunk 32 optimal weight: 0.8980 chunk 304 optimal weight: 30.0000 chunk 284 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 C 760 GLN D 327 GLN D 760 GLN F 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.210308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180664 restraints weight = 32592.422| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.28 r_work: 0.3526 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3666 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= 0.207 Angle : 0.691 7.862 44118 Z= 0.365 Chirality : 0.050 0.193 5114 Planarity : 0.005 0.047 5976 Dihedral : 4.767 23.877 4800 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.29 % Allowed : 17.72 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4512 helix: 0.54 (0.11), residues: 1944 sheet: 1.39 (0.26), residues: 450 loop : -2.37 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 753 TYR 0.020 0.003 TYR D 203 PHE 0.024 0.002 PHE C 265 TRP 0.009 0.002 TRP E 454 HIS 0.004 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00493 (32506) covalent geometry : angle 0.69083 (44118) hydrogen bonds : bond 0.07065 ( 1408) hydrogen bonds : angle 4.66224 ( 3990) *********************** 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 462 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 369 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6465 (mm-30) REVERT: A 427 MET cc_start: 0.6003 (mmm) cc_final: 0.4767 (mmt) REVERT: A 534 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: A 599 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8288 (ptm160) REVERT: A 608 MET cc_start: 0.8951 (mtm) cc_final: 0.8750 (mtm) REVERT: A 611 MET cc_start: 0.8046 (ptt) cc_final: 0.7667 (ptm) REVERT: A 742 PHE cc_start: 0.7177 (m-80) cc_final: 0.6295 (m-80) REVERT: A 760 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.6196 (tt0) REVERT: B 211 LYS cc_start: 0.7102 (mtpt) cc_final: 0.6506 (tptt) REVERT: B 288 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7023 (mppt) REVERT: B 292 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: B 321 GLU cc_start: 0.7672 (mp0) cc_final: 0.7293 (mm-30) REVERT: B 534 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 560 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (ttm170) REVERT: B 568 GLN cc_start: 0.7961 (mm110) cc_final: 0.7641 (mm110) REVERT: B 720 MET cc_start: 0.2976 (OUTLIER) cc_final: 0.2314 (mpm) REVERT: B 742 PHE cc_start: 0.6876 (m-80) cc_final: 0.5884 (m-80) REVERT: B 754 LYS cc_start: 0.7377 (mtmt) cc_final: 0.7106 (mtpp) REVERT: C 218 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: C 417 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: C 427 MET cc_start: 0.5577 (mmt) cc_final: 0.4484 (mmt) REVERT: C 486 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7908 (tttt) REVERT: C 508 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7417 (ttt) REVERT: C 534 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: C 560 ARG cc_start: 0.8361 (ttm170) cc_final: 0.8015 (ttm-80) REVERT: C 611 MET cc_start: 0.8073 (ptt) cc_final: 0.7733 (ptm) REVERT: C 730 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7067 (tt0) REVERT: D 211 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6571 (tptt) REVERT: D 321 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: D 427 MET cc_start: 0.5984 (mmm) cc_final: 0.4858 (mmt) REVERT: D 504 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7777 (tp) REVERT: D 534 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: D 560 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8278 (ttm170) REVERT: D 611 MET cc_start: 0.7999 (ptt) cc_final: 0.7578 (ptm) REVERT: D 658 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8030 (mtmt) REVERT: D 678 MET cc_start: 0.6850 (mmp) cc_final: 0.6055 (mpm) REVERT: D 742 PHE cc_start: 0.7160 (m-80) cc_final: 0.6284 (m-80) REVERT: D 753 ARG cc_start: 0.6672 (mtm110) cc_final: 0.6223 (mtm-85) REVERT: D 760 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: E 211 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6521 (tptt) REVERT: E 288 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7020 (mppt) REVERT: E 292 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: E 321 GLU cc_start: 0.7666 (mp0) cc_final: 0.7286 (mm-30) REVERT: E 560 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8262 (ttm170) REVERT: E 568 GLN cc_start: 0.7957 (mm110) cc_final: 0.7640 (mm110) REVERT: E 720 MET cc_start: 0.2974 (OUTLIER) cc_final: 0.2299 (mpm) REVERT: E 742 PHE cc_start: 0.6904 (m-80) cc_final: 0.5913 (m-80) REVERT: E 754 LYS cc_start: 0.7364 (mtmt) cc_final: 0.7099 (mtpp) REVERT: F 218 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: F 417 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: F 427 MET cc_start: 0.5590 (mmt) cc_final: 0.4491 (mmt) REVERT: F 486 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7917 (tttt) REVERT: F 508 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7427 (ttt) REVERT: F 534 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: F 560 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8030 (ttm-80) REVERT: F 611 MET cc_start: 0.8088 (ptt) cc_final: 0.7735 (ptm) REVERT: F 757 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6194 (mtt) outliers start: 93 outliers final: 37 residues processed: 431 average time/residue: 0.8620 time to fit residues: 421.6924 Evaluate side-chains 425 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 760 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 403 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 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 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 486 LYS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 534 GLU 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 504 LEU Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 560 ARG 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 760 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 560 ARG 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 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 486 LYS Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 196 optimal weight: 7.9990 chunk 423 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 325 optimal weight: 3.9990 chunk 400 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 323 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.210417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180555 restraints weight = 32279.500| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.22 r_work: 0.3542 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32506 Z= 0.190 Angle : 0.670 7.712 44118 Z= 0.355 Chirality : 0.049 0.200 5114 Planarity : 0.005 0.047 5976 Dihedral : 4.779 23.289 4800 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.71 % Allowed : 17.47 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.12), residues: 4512 helix: 0.49 (0.11), residues: 1944 sheet: 1.35 (0.26), residues: 450 loop : -2.38 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 753 TYR 0.020 0.002 TYR D 203 PHE 0.024 0.002 PHE C 265 TRP 0.009 0.002 TRP F 454 HIS 0.003 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00449 (32506) covalent geometry : angle 0.67038 (44118) hydrogen bonds : bond 0.06679 ( 1408) hydrogen bonds : angle 4.62293 ( 3990) *********************** 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 474 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 369 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6083 (mm-30) REVERT: A 348 ASN cc_start: 0.8233 (t0) cc_final: 0.7944 (m-40) REVERT: A 534 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: A 599 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8128 (ptm160) REVERT: A 608 MET cc_start: 0.8762 (mtm) cc_final: 0.8498 (mtm) REVERT: A 611 MET cc_start: 0.7853 (ptt) cc_final: 0.7560 (ptm) REVERT: A 742 PHE cc_start: 0.7083 (m-80) cc_final: 0.6347 (m-80) REVERT: A 757 MET cc_start: 0.6815 (mtt) cc_final: 0.6373 (mmt) REVERT: B 211 LYS cc_start: 0.6979 (mtpt) cc_final: 0.6568 (tptt) REVERT: B 321 GLU cc_start: 0.7420 (mp0) cc_final: 0.7070 (mm-30) REVERT: B 454 TRP cc_start: 0.7693 (OUTLIER) cc_final: 0.6701 (t-100) REVERT: B 456 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7400 (mt) REVERT: B 534 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: B 560 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7944 (ttm170) REVERT: B 568 GLN cc_start: 0.7614 (mm110) cc_final: 0.7337 (mm110) REVERT: B 678 MET cc_start: 0.6778 (mmp) cc_final: 0.6517 (mmm) REVERT: B 720 MET cc_start: 0.2623 (OUTLIER) cc_final: 0.2163 (mpm) REVERT: B 742 PHE cc_start: 0.6891 (m-80) cc_final: 0.6066 (m-80) REVERT: C 218 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: C 417 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7072 (tp30) REVERT: C 427 MET cc_start: 0.5280 (mmt) cc_final: 0.4218 (mmt) REVERT: C 486 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7864 (tttt) REVERT: C 508 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7256 (ttt) REVERT: C 534 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: C 560 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7786 (ttm-80) REVERT: C 611 MET cc_start: 0.7948 (ptt) cc_final: 0.7686 (ptm) REVERT: D 211 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6641 (tptt) REVERT: D 295 LYS cc_start: 0.6423 (mttm) cc_final: 0.6167 (mmtt) REVERT: D 321 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6096 (mm-30) REVERT: D 427 MET cc_start: 0.5772 (mmm) cc_final: 0.4635 (mmt) REVERT: D 504 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7772 (tp) REVERT: D 534 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: D 611 MET cc_start: 0.7824 (ptt) cc_final: 0.7262 (ptm) REVERT: D 641 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6991 (mt0) REVERT: D 658 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7910 (mtmt) REVERT: D 678 MET cc_start: 0.6803 (mmp) cc_final: 0.6248 (mpm) REVERT: D 742 PHE cc_start: 0.7043 (m-80) cc_final: 0.6307 (m-80) REVERT: D 753 ARG cc_start: 0.6553 (mtm110) cc_final: 0.6089 (mtm-85) REVERT: D 757 MET cc_start: 0.6802 (mtt) cc_final: 0.6363 (mmt) REVERT: E 211 LYS cc_start: 0.6968 (mtpt) cc_final: 0.6557 (tptt) REVERT: E 288 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.6876 (mppt) REVERT: E 292 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: E 454 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.6693 (t-100) REVERT: E 534 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: E 560 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7954 (ttm170) REVERT: E 568 GLN cc_start: 0.7621 (mm110) cc_final: 0.7349 (mm110) REVERT: E 720 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.2156 (mpm) REVERT: E 742 PHE cc_start: 0.6910 (m-80) cc_final: 0.6072 (m-80) REVERT: F 218 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: F 417 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: F 427 MET cc_start: 0.5287 (mmt) cc_final: 0.4221 (mmt) REVERT: F 486 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7869 (tttt) REVERT: F 508 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7191 (ttt) REVERT: F 534 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: F 560 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7793 (ttm-80) REVERT: F 611 MET cc_start: 0.7942 (ptt) cc_final: 0.7679 (ptm) REVERT: F 757 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5930 (mtt) outliers start: 105 outliers final: 46 residues processed: 436 average time/residue: 0.9529 time to fit residues: 470.2305 Evaluate side-chains 441 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 364 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 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 454 TRP Chi-restraints excluded: chain B residue 456 LEU 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 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 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 486 LYS Chi-restraints excluded: chain C residue 504 LEU 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 504 LEU Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 641 GLN 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 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 454 TRP 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 720 MET Chi-restraints excluded: chain E residue 760 GLN 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 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 486 LYS Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 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 407 optimal weight: 3.9990 chunk 367 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 380 optimal weight: 0.5980 chunk 83 optimal weight: 50.0000 chunk 387 optimal weight: 30.0000 chunk 315 optimal weight: 20.0000 chunk 173 optimal weight: 0.0970 chunk 244 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 375 optimal weight: 50.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN C 760 GLN D 327 GLN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN F 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.210700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180187 restraints weight = 32626.521| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.26 r_work: 0.3533 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 32506 Z= 0.161 Angle : 0.749 59.187 44118 Z= 0.410 Chirality : 0.047 0.520 5114 Planarity : 0.005 0.054 5976 Dihedral : 4.741 23.097 4800 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.25 % Allowed : 18.46 % Favored : 78.29 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.12), residues: 4512 helix: 0.54 (0.11), residues: 1944 sheet: 1.36 (0.26), residues: 450 loop : -2.37 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 753 TYR 0.017 0.002 TYR D 203 PHE 0.023 0.002 PHE C 265 TRP 0.009 0.001 TRP E 454 HIS 0.002 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00354 (32506) covalent geometry : angle 0.74875 (44118) hydrogen bonds : bond 0.06400 ( 1408) hydrogen bonds : angle 4.61042 ( 3990) ********************** 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 456 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 364 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6602 (mmpt) REVERT: A 321 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6361 (mm-30) REVERT: A 348 ASN cc_start: 0.8458 (t0) cc_final: 0.8125 (m-40) REVERT: A 427 MET cc_start: 0.5658 (mmm) cc_final: 0.4806 (mmt) REVERT: A 534 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: A 599 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8219 (ptm160) REVERT: A 608 MET cc_start: 0.8923 (mtm) cc_final: 0.8690 (mtm) REVERT: A 611 MET cc_start: 0.8020 (ptt) cc_final: 0.7686 (ptm) REVERT: A 742 PHE cc_start: 0.7144 (m-80) cc_final: 0.6293 (m-80) REVERT: A 757 MET cc_start: 0.6852 (mtt) cc_final: 0.6153 (mmt) REVERT: B 211 LYS cc_start: 0.7011 (mtpt) cc_final: 0.6436 (tptt) REVERT: B 454 TRP cc_start: 0.7655 (OUTLIER) cc_final: 0.6595 (t-100) REVERT: B 456 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7407 (mt) REVERT: B 534 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 560 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8249 (ttm170) REVERT: B 568 GLN cc_start: 0.7878 (mm110) cc_final: 0.7555 (mm110) REVERT: B 678 MET cc_start: 0.6712 (mmp) cc_final: 0.6403 (mmm) REVERT: B 720 MET cc_start: 0.2724 (OUTLIER) cc_final: 0.2168 (mpm) REVERT: B 742 PHE cc_start: 0.6876 (m-80) cc_final: 0.5897 (m-80) REVERT: C 218 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: C 417 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: C 427 MET cc_start: 0.5459 (mmt) cc_final: 0.4269 (mmt) REVERT: C 486 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (tttt) REVERT: C 508 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7333 (ttt) REVERT: C 534 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: C 560 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8027 (ttm-80) REVERT: C 611 MET cc_start: 0.8063 (ptt) cc_final: 0.7759 (ptm) REVERT: D 211 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6504 (tptt) REVERT: D 295 LYS cc_start: 0.6508 (mttm) cc_final: 0.6220 (mmtt) REVERT: D 321 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: D 427 MET cc_start: 0.5968 (mmm) cc_final: 0.4821 (mmt) REVERT: D 504 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7757 (tp) REVERT: D 534 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: D 611 MET cc_start: 0.7943 (ptt) cc_final: 0.7349 (ptm) REVERT: D 641 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: D 658 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7989 (mtmt) REVERT: D 678 MET cc_start: 0.6861 (mmp) cc_final: 0.6084 (mpm) REVERT: D 742 PHE cc_start: 0.7110 (m-80) cc_final: 0.6200 (m-80) REVERT: D 753 ARG cc_start: 0.6575 (mtm110) cc_final: 0.5891 (mtm-85) REVERT: D 757 MET cc_start: 0.6819 (mtt) cc_final: 0.6126 (mmt) REVERT: E 211 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6413 (tptt) REVERT: E 288 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7037 (mppt) REVERT: E 292 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: E 454 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.6583 (t-100) REVERT: E 534 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 560 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8236 (ttm170) REVERT: E 568 GLN cc_start: 0.7874 (mm110) cc_final: 0.7557 (mm110) REVERT: E 720 MET cc_start: 0.2735 (OUTLIER) cc_final: 0.2166 (mpm) REVERT: E 742 PHE cc_start: 0.6963 (m-80) cc_final: 0.5911 (m-80) REVERT: F 218 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: F 417 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: F 427 MET cc_start: 0.5482 (mmt) cc_final: 0.4295 (mmt) REVERT: F 486 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7925 (tttt) REVERT: F 508 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7328 (ttt) REVERT: F 534 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: F 560 ARG cc_start: 0.8323 (ttm170) cc_final: 0.8038 (ttm-80) REVERT: F 611 MET cc_start: 0.8062 (ptt) cc_final: 0.7752 (ptm) REVERT: F 757 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6110 (mtt) outliers start: 92 outliers final: 47 residues processed: 420 average time/residue: 0.8629 time to fit residues: 411.3282 Evaluate side-chains 442 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 363 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 218 GLU 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 454 TRP Chi-restraints excluded: chain B residue 456 LEU 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 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 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 486 LYS Chi-restraints excluded: chain C residue 504 LEU 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 327 GLN Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 641 GLN 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 288 LYS Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 454 TRP 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 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 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 486 LYS Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 741 ARG Chi-restraints excluded: chain F residue 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 287 optimal weight: 6.9990 chunk 370 optimal weight: 7.9990 chunk 183 optimal weight: 0.2980 chunk 84 optimal weight: 30.0000 chunk 391 optimal weight: 20.0000 chunk 344 optimal weight: 5.9990 chunk 184 optimal weight: 0.0040 chunk 283 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 chunk 229 optimal weight: 50.0000 chunk 117 optimal weight: 3.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 327 GLN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.181256 restraints weight = 32560.666| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.23 r_work: 0.3540 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 32506 Z= 0.187 Angle : 0.816 59.182 44118 Z= 0.464 Chirality : 0.048 0.752 5114 Planarity : 0.005 0.057 5976 Dihedral : 4.734 23.057 4800 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.18 % Allowed : 18.49 % Favored : 78.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4512 helix: 0.55 (0.11), residues: 1944 sheet: 1.36 (0.26), residues: 450 loop : -2.37 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 732 TYR 0.016 0.001 TYR D 203 PHE 0.022 0.002 PHE C 265 TRP 0.009 0.001 TRP E 454 HIS 0.002 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00386 (32506) covalent geometry : angle 0.81569 (44118) hydrogen bonds : bond 0.06349 ( 1408) hydrogen bonds : angle 4.60713 ( 3990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12103.81 seconds wall clock time: 205 minutes 46.80 seconds (12346.80 seconds total)