Starting phenix.real_space_refine on Mon Jun 16 09:07:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eax_27989/06_2025/8eax_27989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eax_27989/06_2025/8eax_27989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eax_27989/06_2025/8eax_27989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eax_27989/06_2025/8eax_27989.map" model { file = "/net/cci-nas-00/data/ceres_data/8eax_27989/06_2025/8eax_27989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eax_27989/06_2025/8eax_27989.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 120 5.16 5 C 11738 2.51 5 N 3174 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2333 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2293 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 2329 Chain: "C" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2329 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2274 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 289, 2272 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2310 Restraints were copied for chains: G, H, E, F Time building chain proxies: 15.57, per 1000 atoms: 0.84 Number of scatterers: 18458 At special positions: 0 Unit cell: (141.93, 138.61, 87.98, 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 120 16.00 O 3426 8.00 N 3174 7.00 C 11738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 3.5 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 414 through 423 removed outlier: 3.899A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.669A pdb=" N TYR A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.553A pdb=" N ALA A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.595A pdb=" N VAL A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.622A pdb=" N PHE A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.719A pdb=" N THR A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.551A pdb=" N GLN A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.576A pdb=" N TYR A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.020A pdb=" N PHE A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.674A pdb=" N LEU A 593 " --> pdb=" O CYS A 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.600A pdb=" N SER A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 removed outlier: 3.904A pdb=" N PHE A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 701 removed outlier: 4.377A pdb=" N ASP A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 689 " --> pdb=" O MET A 685 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 718 removed outlier: 3.999A pdb=" N ARG A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'B' and resid 415 through 423 removed outlier: 3.630A pdb=" N VAL B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.526A pdb=" N ASP B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.687A pdb=" N ILE B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 477 removed outlier: 4.249A pdb=" N LYS B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.518A pdb=" N ILE B 492 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 514 removed outlier: 3.924A pdb=" N TYR B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 545 removed outlier: 3.605A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.411A pdb=" N ARG B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 4.124A pdb=" N PHE B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 568 " --> pdb=" O GLN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 611 removed outlier: 3.614A pdb=" N GLN B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.545A pdb=" N HIS B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.910A pdb=" N ASN B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 676 removed outlier: 3.645A pdb=" N LEU B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 693 removed outlier: 3.614A pdb=" N THR B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 703 removed outlier: 3.622A pdb=" N ILE B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 4.299A pdb=" N LEU B 714 " --> pdb=" O MET B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 429 removed outlier: 3.709A pdb=" N ILE C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 removed outlier: 4.512A pdb=" N ASP C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 478 removed outlier: 3.602A pdb=" N VAL C 456 " --> pdb=" O PRO C 452 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 3.952A pdb=" N ILE C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.607A pdb=" N THR C 498 " --> pdb=" O GLY C 494 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 499 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.935A pdb=" N GLU C 524 " --> pdb=" O SER C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 546 removed outlier: 3.680A pdb=" N GLN C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 562 removed outlier: 3.632A pdb=" N TYR C 555 " --> pdb=" O GLU C 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 561 " --> pdb=" O MET C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.082A pdb=" N PHE C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.880A pdb=" N GLN C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 607 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 643 through 658 removed outlier: 3.561A pdb=" N LEU C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 654 " --> pdb=" O VAL C 650 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 673 removed outlier: 3.535A pdb=" N GLU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 700 removed outlier: 4.245A pdb=" N ASP C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 691 " --> pdb=" O ASP C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.536A pdb=" N LEU C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 714 " --> pdb=" O MET C 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 709 through 714' Processing helix chain 'D' and resid 415 through 423 removed outlier: 3.793A pdb=" N LYS D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 421 " --> pdb=" O PHE D 417 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 423' Processing helix chain 'D' and resid 423 through 431 removed outlier: 3.814A pdb=" N SER D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 3.941A pdb=" N ILE D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 478 removed outlier: 4.606A pdb=" N LYS D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 471 " --> pdb=" O HIS D 467 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 removed outlier: 3.570A pdb=" N ILE D 492 " --> pdb=" O THR D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 514 removed outlier: 3.830A pdb=" N TYR D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 507 " --> pdb=" O THR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 545 removed outlier: 3.879A pdb=" N VAL D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 530 " --> pdb=" O MET D 526 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.667A pdb=" N TYR D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG D 556 " --> pdb=" O GLU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 4.035A pdb=" N PHE D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 568 " --> pdb=" O GLN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 611 removed outlier: 3.574A pdb=" N SER D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS D 589 " --> pdb=" O LYS D 585 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 592 " --> pdb=" O SER D 588 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 593 " --> pdb=" O CYS D 589 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS D 604 " --> pdb=" O CYS D 600 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 607 " --> pdb=" O ILE D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 Processing helix chain 'D' and resid 643 through 649 removed outlier: 3.645A pdb=" N LEU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 676 removed outlier: 3.516A pdb=" N VAL D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 669 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU D 674 " --> pdb=" O ASP D 670 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 703 removed outlier: 3.535A pdb=" N ARG D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS D 689 " --> pdb=" O MET D 685 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 690 " --> pdb=" O MET D 686 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 701 " --> pdb=" O GLY D 697 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 703 " --> pdb=" O ILE D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 717 removed outlier: 4.018A pdb=" N LEU D 714 " --> pdb=" O ARG D 711 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 717 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 423 removed outlier: 3.899A pdb=" N ALA E 420 " --> pdb=" O PHE E 416 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 422 " --> pdb=" O GLU E 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 423 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 431 removed outlier: 3.669A pdb=" N TYR E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 429 " --> pdb=" O PRO E 425 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 450 removed outlier: 3.553A pdb=" N ALA E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 445 " --> pdb=" O PHE E 441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 447 " --> pdb=" O ASP E 443 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 478 removed outlier: 3.595A pdb=" N VAL E 456 " --> pdb=" O PRO E 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS E 458 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL E 465 " --> pdb=" O ASP E 461 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 494 removed outlier: 3.622A pdb=" N PHE E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 515 removed outlier: 3.719A pdb=" N THR E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 499 " --> pdb=" O SER E 495 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN E 500 " --> pdb=" O ALA E 496 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE E 507 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 508 " --> pdb=" O TYR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 Processing helix chain 'E' and resid 530 through 546 removed outlier: 3.551A pdb=" N GLN E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN E 536 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR E 544 " --> pdb=" O LEU E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 562 removed outlier: 3.576A pdb=" N TYR E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 574 removed outlier: 4.020A pdb=" N PHE E 566 " --> pdb=" O THR E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 610 removed outlier: 3.674A pdb=" N LEU E 593 " --> pdb=" O CYS E 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN E 602 " --> pdb=" O GLY E 598 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP E 605 " --> pdb=" O PHE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 Processing helix chain 'E' and resid 643 through 658 removed outlier: 3.600A pdb=" N SER E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR E 653 " --> pdb=" O ASN E 649 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY E 654 " --> pdb=" O VAL E 650 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG E 655 " --> pdb=" O LEU E 651 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 675 removed outlier: 3.904A pdb=" N PHE E 667 " --> pdb=" O GLU E 663 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 701 removed outlier: 4.377A pdb=" N ASP E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 688 " --> pdb=" O VAL E 684 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS E 689 " --> pdb=" O MET E 685 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 690 " --> pdb=" O MET E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 Processing helix chain 'E' and resid 715 through 718 removed outlier: 3.999A pdb=" N ARG E 718 " --> pdb=" O GLU E 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 718' Processing helix chain 'F' and resid 415 through 423 removed outlier: 3.630A pdb=" N VAL F 421 " --> pdb=" O PHE F 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 removed outlier: 3.526A pdb=" N ASP F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 450 removed outlier: 3.687A pdb=" N ILE F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP F 443 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 445 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN F 446 " --> pdb=" O ILE F 442 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP F 447 " --> pdb=" O ASP F 443 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 477 removed outlier: 4.249A pdb=" N LYS F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 473 " --> pdb=" O SER F 469 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 removed outlier: 3.518A pdb=" N ILE F 492 " --> pdb=" O THR F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 514 removed outlier: 3.924A pdb=" N TYR F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 507 " --> pdb=" O THR F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 545 removed outlier: 3.605A pdb=" N SER F 528 " --> pdb=" O GLU F 524 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE F 533 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP F 539 " --> pdb=" O GLY F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 removed outlier: 4.411A pdb=" N ARG F 556 " --> pdb=" O GLU F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 572 removed outlier: 4.124A pdb=" N PHE F 566 " --> pdb=" O THR F 562 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 589 Processing helix chain 'F' and resid 590 through 611 removed outlier: 3.614A pdb=" N GLN F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 636 removed outlier: 3.545A pdb=" N HIS F 636 " --> pdb=" O LEU F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 649 removed outlier: 3.910A pdb=" N ASN F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 676 removed outlier: 3.645A pdb=" N LEU F 669 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 672 " --> pdb=" O VAL F 668 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU F 673 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU F 675 " --> pdb=" O ILE F 671 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 676 " --> pdb=" O ILE F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 693 removed outlier: 3.614A pdb=" N THR F 681 " --> pdb=" O SER F 677 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG F 682 " --> pdb=" O LEU F 678 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 688 " --> pdb=" O VAL F 684 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS F 689 " --> pdb=" O MET F 685 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL F 690 " --> pdb=" O MET F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 703 removed outlier: 3.622A pdb=" N ILE F 699 " --> pdb=" O GLU F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 714 removed outlier: 4.299A pdb=" N LEU F 714 " --> pdb=" O MET F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 717 No H-bonds generated for 'chain 'F' and resid 715 through 717' Processing helix chain 'G' and resid 415 through 419 Processing helix chain 'G' and resid 423 through 429 removed outlier: 3.709A pdb=" N ILE G 429 " --> pdb=" O PRO G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 450 removed outlier: 4.512A pdb=" N ASP G 447 " --> pdb=" O ASP G 443 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP G 448 " --> pdb=" O ALA G 444 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G 449 " --> pdb=" O LEU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 478 removed outlier: 3.602A pdb=" N VAL G 456 " --> pdb=" O PRO G 452 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS G 458 " --> pdb=" O VAL G 454 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS G 460 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 461 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 462 " --> pdb=" O LYS G 458 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL G 465 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 472 " --> pdb=" O ASN G 468 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 473 " --> pdb=" O SER G 469 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE G 476 " --> pdb=" O LEU G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 494 removed outlier: 3.952A pdb=" N ILE G 492 " --> pdb=" O SER G 488 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 493 " --> pdb=" O THR G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 517 removed outlier: 3.607A pdb=" N THR G 498 " --> pdb=" O GLY G 494 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL G 499 " --> pdb=" O SER G 495 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN G 500 " --> pdb=" O ALA G 496 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE G 507 " --> pdb=" O THR G 503 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 525 removed outlier: 3.935A pdb=" N GLU G 524 " --> pdb=" O SER G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 546 removed outlier: 3.680A pdb=" N GLN G 534 " --> pdb=" O MET G 530 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN G 536 " --> pdb=" O LEU G 532 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP G 539 " --> pdb=" O GLY G 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR G 544 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 562 removed outlier: 3.632A pdb=" N TYR G 555 " --> pdb=" O GLU G 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 561 " --> pdb=" O MET G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 575 removed outlier: 4.082A pdb=" N PHE G 566 " --> pdb=" O THR G 562 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 586 through 610 removed outlier: 3.880A pdb=" N GLN G 602 " --> pdb=" O GLY G 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 603 " --> pdb=" O ARG G 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR G 607 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 638 Processing helix chain 'G' and resid 643 through 658 removed outlier: 3.561A pdb=" N LEU G 647 " --> pdb=" O SER G 643 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY G 654 " --> pdb=" O VAL G 650 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 655 " --> pdb=" O LEU G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 663 through 673 removed outlier: 3.535A pdb=" N GLU G 673 " --> pdb=" O LEU G 669 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 700 removed outlier: 4.245A pdb=" N ASP G 687 " --> pdb=" O SER G 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL G 690 " --> pdb=" O MET G 686 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN G 691 " --> pdb=" O ASP G 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 714 removed outlier: 3.536A pdb=" N LEU G 713 " --> pdb=" O ALA G 709 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 714 " --> pdb=" O MET G 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 709 through 714' Processing helix chain 'H' and resid 415 through 423 removed outlier: 3.793A pdb=" N LYS H 419 " --> pdb=" O ILE H 415 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA H 420 " --> pdb=" O PHE H 416 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL H 421 " --> pdb=" O PHE H 417 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU H 423 " --> pdb=" O LYS H 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 415 through 423' Processing helix chain 'H' and resid 423 through 431 removed outlier: 3.814A pdb=" N SER H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 450 removed outlier: 3.941A pdb=" N ILE H 442 " --> pdb=" O ARG H 438 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP H 443 " --> pdb=" O ASP H 439 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP H 447 " --> pdb=" O ASP H 443 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 478 removed outlier: 4.606A pdb=" N LYS H 458 " --> pdb=" O VAL H 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 471 " --> pdb=" O HIS H 467 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE H 476 " --> pdb=" O LEU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 removed outlier: 3.570A pdb=" N ILE H 492 " --> pdb=" O THR H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 514 removed outlier: 3.830A pdb=" N TYR H 504 " --> pdb=" O ASN H 500 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 507 " --> pdb=" O THR H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 545 removed outlier: 3.879A pdb=" N VAL H 525 " --> pdb=" O SER H 521 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 529 " --> pdb=" O VAL H 525 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET H 530 " --> pdb=" O MET H 526 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE H 531 " --> pdb=" O ASN H 527 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU H 532 " --> pdb=" O SER H 528 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE H 533 " --> pdb=" O ILE H 529 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN H 534 " --> pdb=" O MET H 530 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP H 539 " --> pdb=" O GLY H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 562 removed outlier: 3.667A pdb=" N TYR H 555 " --> pdb=" O GLU H 551 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG H 556 " --> pdb=" O GLU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 572 removed outlier: 4.035A pdb=" N PHE H 566 " --> pdb=" O THR H 562 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE H 568 " --> pdb=" O GLN H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 611 removed outlier: 3.574A pdb=" N SER H 588 " --> pdb=" O THR H 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS H 589 " --> pdb=" O LYS H 585 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 590 " --> pdb=" O ILE H 586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG H 592 " --> pdb=" O SER H 588 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU H 593 " --> pdb=" O CYS H 589 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS H 604 " --> pdb=" O CYS H 600 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 607 " --> pdb=" O ILE H 603 " (cutoff:3.500A) Processing helix chain 'H' and resid 631 through 636 Processing helix chain 'H' and resid 643 through 649 removed outlier: 3.645A pdb=" N LEU H 647 " --> pdb=" O SER H 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN H 649 " --> pdb=" O MET H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 676 removed outlier: 3.516A pdb=" N VAL H 668 " --> pdb=" O GLN H 664 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU H 669 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU H 673 " --> pdb=" O LEU H 669 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU H 674 " --> pdb=" O ASP H 670 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU H 675 " --> pdb=" O ILE H 671 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 676 " --> pdb=" O ILE H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 676 through 703 removed outlier: 3.535A pdb=" N ARG H 682 " --> pdb=" O LEU H 678 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP H 687 " --> pdb=" O SER H 683 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS H 689 " --> pdb=" O MET H 685 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL H 690 " --> pdb=" O MET H 686 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 694 " --> pdb=" O VAL H 690 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY H 697 " --> pdb=" O ARG H 693 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE H 701 " --> pdb=" O GLY H 697 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU H 702 " --> pdb=" O ARG H 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU H 703 " --> pdb=" O ILE H 699 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 717 removed outlier: 4.018A pdb=" N LEU H 714 " --> pdb=" O ARG H 711 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 717 " --> pdb=" O LEU H 714 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2643 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: 4.84 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6124 1.34 - 1.46: 3484 1.46 - 1.58: 8970 1.58 - 1.70: 0 1.70 - 1.81: 216 Bond restraints: 18794 Sorted by residual: bond pdb=" CA PRO D 582 " pdb=" C PRO D 582 " ideal model delta sigma weight residual 1.528 1.519 0.010 9.10e-03 1.21e+04 1.12e+00 bond pdb=" CA PRO H 582 " pdb=" C PRO H 582 " ideal model delta sigma weight residual 1.528 1.519 0.010 9.10e-03 1.21e+04 1.12e+00 bond pdb=" CA ILE F 581 " pdb=" CB ILE F 581 " ideal model delta sigma weight residual 1.540 1.567 -0.027 2.70e-02 1.37e+03 1.02e+00 bond pdb=" CA ILE B 581 " pdb=" CB ILE B 581 " ideal model delta sigma weight residual 1.540 1.567 -0.027 2.70e-02 1.37e+03 1.02e+00 bond pdb=" CB ILE H 507 " pdb=" CG2 ILE H 507 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.84e-01 ... (remaining 18789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 24622 2.08 - 4.17: 642 4.17 - 6.25: 94 6.25 - 8.33: 30 8.33 - 10.42: 12 Bond angle restraints: 25400 Sorted by residual: angle pdb=" CA MET H 710 " pdb=" CB MET H 710 " pdb=" CG MET H 710 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA MET D 710 " pdb=" CB MET D 710 " pdb=" CG MET D 710 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA LEU B 610 " pdb=" CB LEU B 610 " pdb=" CG LEU B 610 " ideal model delta sigma weight residual 116.30 126.72 -10.42 3.50e+00 8.16e-02 8.86e+00 angle pdb=" CA LEU F 610 " pdb=" CB LEU F 610 " pdb=" CG LEU F 610 " ideal model delta sigma weight residual 116.30 126.72 -10.42 3.50e+00 8.16e-02 8.86e+00 angle pdb=" CA LYS C 676 " pdb=" CB LYS C 676 " pdb=" CG LYS C 676 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.62e+00 ... (remaining 25395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10334 17.84 - 35.68: 842 35.68 - 53.52: 166 53.52 - 71.36: 38 71.36 - 89.20: 40 Dihedral angle restraints: 11420 sinusoidal: 4604 harmonic: 6816 Sorted by residual: dihedral pdb=" CA THR F 653 " pdb=" C THR F 653 " pdb=" N GLY F 654 " pdb=" CA GLY F 654 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA THR B 653 " pdb=" C THR B 653 " pdb=" N GLY B 654 " pdb=" CA GLY B 654 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA THR C 661 " pdb=" C THR C 661 " pdb=" N LEU C 662 " pdb=" CA LEU C 662 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1892 0.045 - 0.089: 882 0.089 - 0.133: 120 0.133 - 0.178: 14 0.178 - 0.222: 2 Chirality restraints: 2910 Sorted by residual: chirality pdb=" CB ILE B 581 " pdb=" CA ILE B 581 " pdb=" CG1 ILE B 581 " pdb=" CG2 ILE B 581 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE F 581 " pdb=" CA ILE F 581 " pdb=" CG1 ILE F 581 " pdb=" CG2 ILE F 581 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU D 482 " pdb=" CB LEU D 482 " pdb=" CD1 LEU D 482 " pdb=" CD2 LEU D 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 2907 not shown) Planarity restraints: 3248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 451 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO D 452 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 452 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 451 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO H 452 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 452 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 452 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 581 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 582 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 582 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 582 " 0.026 5.00e-02 4.00e+02 ... (remaining 3245 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2840 2.75 - 3.29: 20086 3.29 - 3.83: 27423 3.83 - 4.36: 33849 4.36 - 4.90: 53418 Nonbonded interactions: 137616 Sorted by model distance: nonbonded pdb=" O MET G 660 " pdb=" OG1 THR G 661 " model vdw 2.213 3.040 nonbonded pdb=" O MET C 660 " pdb=" OG1 THR C 661 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP A 606 " pdb=" OG SER A 631 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP E 606 " pdb=" OG SER E 631 " model vdw 2.246 3.040 nonbonded pdb=" O VAL C 650 " pdb=" OG1 THR C 653 " model vdw 2.249 3.040 ... (remaining 137611 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 48.010 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.004 0.033 18794 Z= 0.201 Angle : 0.834 10.416 25400 Z= 0.421 Chirality : 0.046 0.222 2910 Planarity : 0.005 0.048 3248 Dihedral : 14.959 89.197 6988 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.77 % Favored : 89.79 % Rotamer: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2296 helix: -2.50 (0.10), residues: 1514 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 630 HIS 0.012 0.001 HIS G 467 PHE 0.029 0.003 PHE D 533 TYR 0.017 0.002 TYR A 544 ARG 0.005 0.001 ARG B 583 Details of bonding type rmsd hydrogen bonds : bond 0.32953 ( 893) hydrogen bonds : angle 7.99310 ( 2643) covalent geometry : bond 0.00448 (18794) covalent geometry : angle 0.83366 (25400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 656 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 439 ASP cc_start: 0.8567 (p0) cc_final: 0.8308 (p0) REVERT: A 460 LYS cc_start: 0.8698 (mttt) cc_final: 0.8432 (mttt) REVERT: A 475 ASP cc_start: 0.7968 (t0) cc_final: 0.7766 (t0) REVERT: A 486 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7839 (mmmt) REVERT: A 491 ASN cc_start: 0.7708 (m-40) cc_final: 0.7389 (m-40) REVERT: A 524 GLU cc_start: 0.8161 (mp0) cc_final: 0.7662 (mp0) REVERT: A 556 ARG cc_start: 0.6200 (tmt170) cc_final: 0.5946 (tmt170) REVERT: A 629 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7131 (ptmm) REVERT: A 645 MET cc_start: 0.7658 (mmm) cc_final: 0.7403 (mmm) REVERT: A 670 ASP cc_start: 0.8196 (p0) cc_final: 0.7821 (p0) REVERT: A 695 GLU cc_start: 0.7285 (tp30) cc_final: 0.6522 (tp30) REVERT: A 700 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6728 (mm-30) REVERT: A 715 GLU cc_start: 0.7911 (mp0) cc_final: 0.7459 (mp0) REVERT: B 440 GLN cc_start: 0.7936 (pp30) cc_final: 0.7675 (pp30) REVERT: B 441 PHE cc_start: 0.8808 (t80) cc_final: 0.8566 (t80) REVERT: B 527 ASN cc_start: 0.7922 (p0) cc_final: 0.7457 (p0) REVERT: B 530 MET cc_start: 0.8201 (mtt) cc_final: 0.7915 (mtm) REVERT: B 536 GLN cc_start: 0.7676 (tm-30) cc_final: 0.6887 (tm-30) REVERT: B 539 ASP cc_start: 0.8033 (t0) cc_final: 0.7747 (t0) REVERT: B 573 LEU cc_start: 0.8329 (tp) cc_final: 0.8050 (tp) REVERT: C 427 ASP cc_start: 0.8014 (t0) cc_final: 0.7607 (t0) REVERT: C 428 TYR cc_start: 0.7844 (t80) cc_final: 0.7576 (t80) REVERT: C 474 ASP cc_start: 0.7770 (t70) cc_final: 0.7461 (t0) REVERT: C 478 ASP cc_start: 0.7130 (m-30) cc_final: 0.6922 (m-30) REVERT: C 679 ASP cc_start: 0.8281 (t0) cc_final: 0.7766 (t0) REVERT: D 503 THR cc_start: 0.8255 (t) cc_final: 0.8053 (m) REVERT: D 506 ILE cc_start: 0.7649 (pt) cc_final: 0.7271 (mt) REVERT: D 536 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6606 (tm-30) REVERT: D 540 LEU cc_start: 0.8036 (mt) cc_final: 0.7695 (mm) REVERT: D 551 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6717 (tm-30) REVERT: D 637 MET cc_start: 0.7500 (ppp) cc_final: 0.7164 (ppp) REVERT: D 685 MET cc_start: 0.7449 (tpt) cc_final: 0.7103 (tpt) REVERT: D 686 MET cc_start: 0.7748 (mmp) cc_final: 0.7460 (mmp) REVERT: D 687 ASP cc_start: 0.7690 (t0) cc_final: 0.7083 (t0) REVERT: E 460 LYS cc_start: 0.8693 (mttt) cc_final: 0.8314 (mtpp) REVERT: E 463 VAL cc_start: 0.8295 (p) cc_final: 0.8086 (m) REVERT: E 468 ASN cc_start: 0.7788 (m110) cc_final: 0.7556 (m110) REVERT: E 484 ARG cc_start: 0.6842 (pmt-80) cc_final: 0.6423 (pmt-80) REVERT: E 491 ASN cc_start: 0.7603 (m-40) cc_final: 0.7231 (m-40) REVERT: E 500 ASN cc_start: 0.8511 (t0) cc_final: 0.8292 (t0) REVERT: E 524 GLU cc_start: 0.8116 (mp0) cc_final: 0.7624 (mp0) REVERT: E 539 ASP cc_start: 0.7675 (t70) cc_final: 0.7453 (t0) REVERT: E 670 ASP cc_start: 0.8119 (p0) cc_final: 0.7829 (p0) REVERT: E 695 GLU cc_start: 0.7236 (tp30) cc_final: 0.5892 (tp30) REVERT: E 698 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6109 (mtm110) REVERT: E 700 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6772 (mm-30) REVERT: E 715 GLU cc_start: 0.7895 (mp0) cc_final: 0.7373 (mp0) REVERT: F 440 GLN cc_start: 0.7946 (pp30) cc_final: 0.7586 (pp30) REVERT: F 441 PHE cc_start: 0.8754 (t80) cc_final: 0.8480 (t80) REVERT: F 463 VAL cc_start: 0.8859 (t) cc_final: 0.8592 (p) REVERT: F 527 ASN cc_start: 0.8058 (p0) cc_final: 0.7661 (p0) REVERT: F 530 MET cc_start: 0.8095 (mtt) cc_final: 0.7833 (mtm) REVERT: F 536 GLN cc_start: 0.7694 (tm-30) cc_final: 0.6848 (tm-30) REVERT: F 539 ASP cc_start: 0.8135 (t0) cc_final: 0.7876 (t0) REVERT: F 544 TYR cc_start: 0.7093 (t80) cc_final: 0.6671 (t80) REVERT: F 560 GLN cc_start: 0.7932 (tt0) cc_final: 0.7721 (tt0) REVERT: F 586 ILE cc_start: 0.8410 (pt) cc_final: 0.7913 (mp) REVERT: G 428 TYR cc_start: 0.7938 (t80) cc_final: 0.7723 (t80) REVERT: G 450 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8193 (ttp-110) REVERT: G 464 ARG cc_start: 0.7279 (ttp80) cc_final: 0.7045 (ttp80) REVERT: G 474 ASP cc_start: 0.7747 (t70) cc_final: 0.7507 (t0) REVERT: G 515 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7104 (tm-30) REVERT: G 602 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6663 (mm-40) REVERT: G 627 GLU cc_start: 0.5582 (mp0) cc_final: 0.4860 (mp0) REVERT: G 673 GLU cc_start: 0.7697 (pt0) cc_final: 0.7453 (pt0) REVERT: G 679 ASP cc_start: 0.8232 (t0) cc_final: 0.7478 (t0) REVERT: H 506 ILE cc_start: 0.7536 (pt) cc_final: 0.7111 (mt) REVERT: H 536 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6910 (tm-30) REVERT: H 541 PHE cc_start: 0.8289 (t80) cc_final: 0.8052 (t80) REVERT: H 551 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6843 (tm-30) REVERT: H 591 HIS cc_start: 0.7792 (m170) cc_final: 0.7528 (m-70) REVERT: H 637 MET cc_start: 0.7507 (ppp) cc_final: 0.7276 (ppp) REVERT: H 647 LEU cc_start: 0.8313 (mp) cc_final: 0.8101 (mp) REVERT: H 686 MET cc_start: 0.7669 (mmp) cc_final: 0.7440 (mmp) outliers start: 6 outliers final: 1 residues processed: 661 average time/residue: 0.3235 time to fit residues: 314.7259 Evaluate side-chains 574 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 573 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 657 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 0.0370 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A 440 GLN A 468 ASN A 477 GLN A 479 ASN A 527 ASN A 536 GLN A 591 HIS A 644 HIS A 649 ASN A 666 GLN B 467 HIS B 523 GLN B 547 HIS B 591 HIS C 446 ASN C 467 HIS C 523 GLN C 587 GLN C 664 GLN D 414 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN D 644 HIS D 691 GLN E 414 HIS E 440 GLN E 468 ASN E 477 GLN E 479 ASN E 527 ASN E 536 GLN E 644 HIS E 649 ASN E 666 GLN F 523 GLN F 534 GLN F 547 HIS G 446 ASN G 523 GLN G 649 ASN G 664 GLN H 414 HIS ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 GLN H 636 HIS H 641 GLN H 644 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131231 restraints weight = 43447.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135558 restraints weight = 19772.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137187 restraints weight = 13455.343| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18794 Z= 0.160 Angle : 0.763 12.766 25400 Z= 0.377 Chirality : 0.043 0.188 2910 Planarity : 0.005 0.051 3248 Dihedral : 4.685 43.008 2500 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 2.38 % Allowed : 14.70 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2296 helix: -0.97 (0.12), residues: 1572 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 448 HIS 0.011 0.001 HIS B 657 PHE 0.028 0.002 PHE H 441 TYR 0.018 0.002 TYR D 554 ARG 0.007 0.001 ARG E 693 Details of bonding type rmsd hydrogen bonds : bond 0.06410 ( 893) hydrogen bonds : angle 4.92536 ( 2643) covalent geometry : bond 0.00333 (18794) covalent geometry : angle 0.76287 (25400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 599 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8156 (mt0) cc_final: 0.7712 (mt0) REVERT: A 460 LYS cc_start: 0.8473 (mttt) cc_final: 0.7943 (mtmm) REVERT: A 476 PHE cc_start: 0.8041 (t80) cc_final: 0.7801 (t80) REVERT: A 491 ASN cc_start: 0.7661 (m-40) cc_final: 0.7336 (m-40) REVERT: A 629 LYS cc_start: 0.7311 (ptmm) cc_final: 0.7086 (ptmm) REVERT: A 645 MET cc_start: 0.7483 (mmm) cc_final: 0.7278 (mmm) REVERT: A 665 LYS cc_start: 0.8090 (tppt) cc_final: 0.7878 (mmtm) REVERT: A 666 GLN cc_start: 0.8111 (tp40) cc_final: 0.7907 (tp40) REVERT: A 670 ASP cc_start: 0.7973 (p0) cc_final: 0.7699 (p0) REVERT: A 695 GLU cc_start: 0.7265 (tp30) cc_final: 0.6651 (tp30) REVERT: A 700 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6566 (mm-30) REVERT: A 710 MET cc_start: 0.7326 (mmm) cc_final: 0.7036 (mmm) REVERT: B 527 ASN cc_start: 0.8028 (p0) cc_final: 0.7719 (p0) REVERT: B 536 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6670 (tm-30) REVERT: B 539 ASP cc_start: 0.8022 (t0) cc_final: 0.7714 (t0) REVERT: B 682 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7593 (mmm-85) REVERT: C 428 TYR cc_start: 0.7948 (t80) cc_final: 0.7639 (t80) REVERT: C 432 MET cc_start: 0.6258 (mmm) cc_final: 0.5981 (mtm) REVERT: C 474 ASP cc_start: 0.7831 (t70) cc_final: 0.7597 (t0) REVERT: C 559 ASP cc_start: 0.7552 (t0) cc_final: 0.6938 (t0) REVERT: C 593 LEU cc_start: 0.8540 (tt) cc_final: 0.8338 (tp) REVERT: C 627 GLU cc_start: 0.5484 (mp0) cc_final: 0.5238 (mp0) REVERT: C 645 MET cc_start: 0.6867 (mmm) cc_final: 0.6505 (mmt) REVERT: C 649 ASN cc_start: 0.7983 (m110) cc_final: 0.7690 (m-40) REVERT: C 665 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8480 (mtpt) REVERT: D 464 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6824 (ttp80) REVERT: D 469 SER cc_start: 0.8077 (p) cc_final: 0.7560 (t) REVERT: D 508 LYS cc_start: 0.8250 (tppt) cc_final: 0.7956 (tppt) REVERT: D 573 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 594 THR cc_start: 0.7875 (m) cc_final: 0.7613 (p) REVERT: D 686 MET cc_start: 0.7582 (mmp) cc_final: 0.6934 (mmp) REVERT: D 687 ASP cc_start: 0.7815 (t70) cc_final: 0.6893 (t0) REVERT: D 691 GLN cc_start: 0.8209 (mt0) cc_final: 0.7813 (mt0) REVERT: E 419 LYS cc_start: 0.7990 (tppt) cc_final: 0.7670 (tppt) REVERT: E 438 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7592 (mtt180) REVERT: E 440 GLN cc_start: 0.8114 (mt0) cc_final: 0.7703 (mt0) REVERT: E 460 LYS cc_start: 0.8452 (mttt) cc_final: 0.8029 (mtmm) REVERT: E 476 PHE cc_start: 0.7813 (t80) cc_final: 0.7556 (t80) REVERT: E 491 ASN cc_start: 0.7562 (m-40) cc_final: 0.7222 (m-40) REVERT: E 629 LYS cc_start: 0.7236 (ptmm) cc_final: 0.6803 (ptmm) REVERT: E 635 ILE cc_start: 0.8063 (mt) cc_final: 0.7747 (tt) REVERT: E 670 ASP cc_start: 0.8016 (p0) cc_final: 0.7615 (p0) REVERT: E 695 GLU cc_start: 0.7094 (tp30) cc_final: 0.5818 (tp30) REVERT: E 696 ILE cc_start: 0.8692 (mm) cc_final: 0.8466 (tp) REVERT: E 698 ARG cc_start: 0.6903 (mtm110) cc_final: 0.6028 (mtm180) REVERT: E 700 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6406 (mm-30) REVERT: E 710 MET cc_start: 0.7318 (mmm) cc_final: 0.7040 (mmm) REVERT: E 715 GLU cc_start: 0.7970 (mp0) cc_final: 0.7276 (mp0) REVERT: F 469 SER cc_start: 0.8334 (p) cc_final: 0.7961 (t) REVERT: F 527 ASN cc_start: 0.8147 (p0) cc_final: 0.7886 (p0) REVERT: F 534 GLN cc_start: 0.7527 (mt0) cc_final: 0.7015 (mt0) REVERT: F 536 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6789 (tm-30) REVERT: F 539 ASP cc_start: 0.8041 (t0) cc_final: 0.7781 (t0) REVERT: F 666 GLN cc_start: 0.7875 (mp10) cc_final: 0.7471 (pm20) REVERT: F 682 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: G 428 TYR cc_start: 0.8015 (t80) cc_final: 0.7791 (t80) REVERT: G 456 VAL cc_start: 0.8285 (m) cc_final: 0.7950 (t) REVERT: G 559 ASP cc_start: 0.7420 (t0) cc_final: 0.7208 (t0) REVERT: G 560 GLN cc_start: 0.7768 (mt0) cc_final: 0.7567 (mt0) REVERT: G 574 LEU cc_start: 0.8008 (mt) cc_final: 0.7762 (tt) REVERT: G 627 GLU cc_start: 0.5367 (mp0) cc_final: 0.5109 (mp0) REVERT: G 667 PHE cc_start: 0.7286 (t80) cc_final: 0.7072 (t80) REVERT: H 460 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8202 (mtpp) REVERT: H 469 SER cc_start: 0.8145 (p) cc_final: 0.7613 (t) REVERT: H 508 LYS cc_start: 0.8159 (tppt) cc_final: 0.7910 (tppt) REVERT: H 539 ASP cc_start: 0.7563 (t0) cc_final: 0.6988 (t0) REVERT: H 551 GLU cc_start: 0.6282 (tm-30) cc_final: 0.6074 (tm-30) REVERT: H 573 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8630 (mt) REVERT: H 597 LEU cc_start: 0.7686 (tp) cc_final: 0.7473 (tp) REVERT: H 637 MET cc_start: 0.7190 (ppp) cc_final: 0.6972 (ppp) REVERT: H 647 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7471 (mm) REVERT: H 686 MET cc_start: 0.7400 (mmp) cc_final: 0.6789 (mmp) REVERT: H 687 ASP cc_start: 0.7842 (t0) cc_final: 0.7483 (t0) outliers start: 48 outliers final: 21 residues processed: 616 average time/residue: 0.3492 time to fit residues: 315.7407 Evaluate side-chains 597 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 573 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 678 LEU Chi-restraints excluded: chain H residue 573 LEU Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 202 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 125 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 88 optimal weight: 0.0000 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 664 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 HIS D 666 GLN E 644 HIS E 664 GLN ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 644 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129414 restraints weight = 33401.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134523 restraints weight = 17608.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137983 restraints weight = 11659.142| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18794 Z= 0.136 Angle : 0.701 11.954 25400 Z= 0.345 Chirality : 0.041 0.162 2910 Planarity : 0.004 0.048 3248 Dihedral : 4.288 25.690 2498 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.08 % Allowed : 18.07 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2296 helix: -0.41 (0.13), residues: 1568 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 448 HIS 0.009 0.001 HIS B 657 PHE 0.051 0.002 PHE C 516 TYR 0.016 0.001 TYR D 554 ARG 0.006 0.000 ARG A 693 Details of bonding type rmsd hydrogen bonds : bond 0.05357 ( 893) hydrogen bonds : angle 4.43660 ( 2643) covalent geometry : bond 0.00287 (18794) covalent geometry : angle 0.70127 (25400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 599 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8143 (mt0) cc_final: 0.7686 (mt0) REVERT: A 460 LYS cc_start: 0.8352 (mttt) cc_final: 0.7922 (mtmm) REVERT: A 491 ASN cc_start: 0.7646 (m-40) cc_final: 0.7332 (m-40) REVERT: A 515 GLU cc_start: 0.7466 (tp30) cc_final: 0.7198 (tp30) REVERT: A 670 ASP cc_start: 0.7822 (p0) cc_final: 0.7443 (p0) REVERT: A 695 GLU cc_start: 0.7258 (tp30) cc_final: 0.6791 (tp30) REVERT: A 696 ILE cc_start: 0.8616 (mm) cc_final: 0.8313 (tp) REVERT: A 700 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6618 (mm-30) REVERT: A 710 MET cc_start: 0.7133 (mmm) cc_final: 0.6921 (mmm) REVERT: B 508 LYS cc_start: 0.8174 (tttp) cc_final: 0.7910 (ttpp) REVERT: B 527 ASN cc_start: 0.7953 (p0) cc_final: 0.7622 (p0) REVERT: B 536 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6692 (tm-30) REVERT: B 539 ASP cc_start: 0.8040 (t0) cc_final: 0.7737 (t0) REVERT: B 567 SER cc_start: 0.7915 (m) cc_final: 0.7610 (p) REVERT: B 682 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7545 (mmm-85) REVERT: C 428 TYR cc_start: 0.8024 (t80) cc_final: 0.7744 (t80) REVERT: C 474 ASP cc_start: 0.7787 (t70) cc_final: 0.7578 (t0) REVERT: C 670 ASP cc_start: 0.6750 (m-30) cc_final: 0.6364 (m-30) REVERT: D 464 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6812 (ttp80) REVERT: D 469 SER cc_start: 0.7954 (p) cc_final: 0.7599 (t) REVERT: D 508 LYS cc_start: 0.8172 (tppt) cc_final: 0.7875 (tppt) REVERT: D 572 LEU cc_start: 0.8789 (mt) cc_final: 0.8556 (mm) REVERT: D 666 GLN cc_start: 0.6523 (OUTLIER) cc_final: 0.5745 (pm20) REVERT: D 685 MET cc_start: 0.7250 (tpt) cc_final: 0.6523 (tpt) REVERT: D 686 MET cc_start: 0.7562 (mmp) cc_final: 0.6965 (mmp) REVERT: D 687 ASP cc_start: 0.7809 (t70) cc_final: 0.7434 (t0) REVERT: E 419 LYS cc_start: 0.7988 (tppt) cc_final: 0.7669 (tppt) REVERT: E 438 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7549 (mtt180) REVERT: E 440 GLN cc_start: 0.8028 (mt0) cc_final: 0.7624 (mt0) REVERT: E 460 LYS cc_start: 0.8352 (mttt) cc_final: 0.7910 (mtmm) REVERT: E 474 ASP cc_start: 0.7659 (t0) cc_final: 0.7429 (t0) REVERT: E 476 PHE cc_start: 0.7807 (t80) cc_final: 0.7557 (t80) REVERT: E 491 ASN cc_start: 0.7535 (m-40) cc_final: 0.7164 (m-40) REVERT: E 526 MET cc_start: 0.7802 (tpp) cc_final: 0.7562 (tpp) REVERT: E 527 ASN cc_start: 0.7566 (t0) cc_final: 0.7347 (t0) REVERT: E 629 LYS cc_start: 0.7133 (ptmm) cc_final: 0.6813 (ptmm) REVERT: E 635 ILE cc_start: 0.8044 (mt) cc_final: 0.7705 (tt) REVERT: E 670 ASP cc_start: 0.7906 (p0) cc_final: 0.7559 (p0) REVERT: E 695 GLU cc_start: 0.7098 (tp30) cc_final: 0.6006 (tp30) REVERT: E 698 ARG cc_start: 0.7032 (mtm110) cc_final: 0.6184 (mtm180) REVERT: E 700 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6561 (mm-30) REVERT: E 715 GLU cc_start: 0.7831 (mp0) cc_final: 0.7204 (mp0) REVERT: F 460 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7924 (mttp) REVERT: F 468 ASN cc_start: 0.7833 (m-40) cc_final: 0.7495 (m110) REVERT: F 469 SER cc_start: 0.8324 (p) cc_final: 0.7991 (t) REVERT: F 471 LEU cc_start: 0.7477 (pp) cc_final: 0.7272 (tp) REVERT: F 534 GLN cc_start: 0.7513 (mt0) cc_final: 0.7004 (mt0) REVERT: F 536 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6786 (tm-30) REVERT: F 539 ASP cc_start: 0.8063 (t0) cc_final: 0.7851 (t0) REVERT: F 557 MET cc_start: 0.7568 (ttm) cc_final: 0.7352 (ttt) REVERT: F 626 ASP cc_start: 0.6640 (p0) cc_final: 0.5749 (t70) REVERT: F 682 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: G 428 TYR cc_start: 0.8092 (t80) cc_final: 0.7858 (t80) REVERT: G 456 VAL cc_start: 0.8321 (m) cc_final: 0.7986 (t) REVERT: G 530 MET cc_start: 0.7233 (mtt) cc_final: 0.6249 (mtt) REVERT: G 539 ASP cc_start: 0.7965 (t0) cc_final: 0.7437 (m-30) REVERT: G 559 ASP cc_start: 0.7446 (t0) cc_final: 0.6549 (t0) REVERT: G 627 GLU cc_start: 0.5313 (mp0) cc_final: 0.5004 (mp0) REVERT: G 663 GLU cc_start: 0.6787 (pm20) cc_final: 0.6507 (pm20) REVERT: H 460 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7992 (mtpp) REVERT: H 508 LYS cc_start: 0.8167 (tppt) cc_final: 0.7882 (tppt) REVERT: H 539 ASP cc_start: 0.7529 (t0) cc_final: 0.6918 (t0) REVERT: H 551 GLU cc_start: 0.6353 (tm-30) cc_final: 0.6120 (tm-30) REVERT: H 572 LEU cc_start: 0.8789 (mt) cc_final: 0.8526 (mm) REVERT: H 637 MET cc_start: 0.7129 (ppp) cc_final: 0.6895 (ppp) REVERT: H 647 LEU cc_start: 0.7699 (mp) cc_final: 0.7447 (mm) REVERT: H 686 MET cc_start: 0.7489 (mmp) cc_final: 0.6892 (mmp) outliers start: 42 outliers final: 24 residues processed: 618 average time/residue: 0.3297 time to fit residues: 297.1698 Evaluate side-chains 602 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 577 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 526 MET Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 666 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 626 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 172 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 HIS A 527 ASN A 644 HIS C 649 ASN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 HIS D 664 GLN E 644 HIS E 657 HIS H 636 HIS H 644 HIS H 666 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.160017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126048 restraints weight = 53180.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134120 restraints weight = 24181.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136230 restraints weight = 12744.868| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18794 Z= 0.141 Angle : 0.700 13.901 25400 Z= 0.340 Chirality : 0.041 0.320 2910 Planarity : 0.004 0.047 3248 Dihedral : 4.229 22.657 2498 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.02 % Allowed : 19.36 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2296 helix: -0.19 (0.13), residues: 1574 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 448 HIS 0.009 0.001 HIS H 644 PHE 0.051 0.002 PHE G 516 TYR 0.014 0.001 TYR H 504 ARG 0.006 0.000 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 893) hydrogen bonds : angle 4.35034 ( 2643) covalent geometry : bond 0.00307 (18794) covalent geometry : angle 0.69996 (25400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 600 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7557 (mtt90) REVERT: A 440 GLN cc_start: 0.8042 (mt0) cc_final: 0.7615 (mt0) REVERT: A 474 ASP cc_start: 0.7585 (t0) cc_final: 0.7380 (t0) REVERT: A 491 ASN cc_start: 0.7586 (m-40) cc_final: 0.7279 (m-40) REVERT: A 515 GLU cc_start: 0.7489 (tp30) cc_final: 0.7215 (tp30) REVERT: A 590 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7941 (mm) REVERT: A 670 ASP cc_start: 0.7855 (p0) cc_final: 0.7463 (p0) REVERT: A 700 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6640 (mm-30) REVERT: B 460 LYS cc_start: 0.8206 (mttt) cc_final: 0.7922 (mttp) REVERT: B 508 LYS cc_start: 0.8311 (tttp) cc_final: 0.8050 (ttmt) REVERT: B 527 ASN cc_start: 0.7963 (p0) cc_final: 0.7687 (p0) REVERT: B 536 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6713 (tm-30) REVERT: B 539 ASP cc_start: 0.8079 (t0) cc_final: 0.7763 (t0) REVERT: B 682 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7636 (mmm-85) REVERT: C 428 TYR cc_start: 0.8006 (t80) cc_final: 0.7753 (t80) REVERT: C 673 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: D 464 ARG cc_start: 0.7099 (ttp80) cc_final: 0.6844 (ttp80) REVERT: D 469 SER cc_start: 0.7991 (p) cc_final: 0.7577 (t) REVERT: D 508 LYS cc_start: 0.8329 (tppt) cc_final: 0.7955 (tppt) REVERT: D 536 GLN cc_start: 0.6809 (tm-30) cc_final: 0.6380 (tm-30) REVERT: D 540 LEU cc_start: 0.8233 (mm) cc_final: 0.7847 (mm) REVERT: D 572 LEU cc_start: 0.8818 (mt) cc_final: 0.8585 (mm) REVERT: D 663 GLU cc_start: 0.7678 (pm20) cc_final: 0.7190 (pm20) REVERT: D 667 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 687 ASP cc_start: 0.7828 (t70) cc_final: 0.7512 (t0) REVERT: E 419 LYS cc_start: 0.7993 (tppt) cc_final: 0.7707 (tppt) REVERT: E 438 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7565 (mtt90) REVERT: E 440 GLN cc_start: 0.7976 (mt0) cc_final: 0.7600 (mt0) REVERT: E 460 LYS cc_start: 0.8341 (mttt) cc_final: 0.7894 (mtmm) REVERT: E 474 ASP cc_start: 0.7699 (t0) cc_final: 0.7431 (t0) REVERT: E 491 ASN cc_start: 0.7562 (m-40) cc_final: 0.7203 (m-40) REVERT: E 526 MET cc_start: 0.7693 (tpp) cc_final: 0.7425 (tpp) REVERT: E 629 LYS cc_start: 0.7202 (ptmm) cc_final: 0.6836 (ptmm) REVERT: E 670 ASP cc_start: 0.7871 (p0) cc_final: 0.7561 (p0) REVERT: E 695 GLU cc_start: 0.7022 (tp30) cc_final: 0.6084 (tp30) REVERT: E 696 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8537 (tt) REVERT: E 698 ARG cc_start: 0.7054 (mtm110) cc_final: 0.6219 (mtm180) REVERT: E 700 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6554 (mm-30) REVERT: E 715 GLU cc_start: 0.7918 (mp0) cc_final: 0.7279 (mp0) REVERT: F 419 LYS cc_start: 0.7682 (tppt) cc_final: 0.7199 (tppt) REVERT: F 534 GLN cc_start: 0.7488 (mt0) cc_final: 0.7011 (mt0) REVERT: F 536 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6797 (tm-30) REVERT: F 539 ASP cc_start: 0.8114 (t0) cc_final: 0.7900 (t0) REVERT: F 666 GLN cc_start: 0.7792 (mp10) cc_final: 0.7553 (pm20) REVERT: F 682 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7541 (mmm-85) REVERT: F 691 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8256 (tm-30) REVERT: F 693 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6900 (ptt-90) REVERT: G 428 TYR cc_start: 0.8086 (t80) cc_final: 0.7874 (t80) REVERT: G 530 MET cc_start: 0.7298 (mtt) cc_final: 0.6309 (mtt) REVERT: G 539 ASP cc_start: 0.7784 (t0) cc_final: 0.7168 (m-30) REVERT: G 627 GLU cc_start: 0.5445 (mp0) cc_final: 0.5008 (mp0) REVERT: H 460 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8196 (mtpp) REVERT: H 470 SER cc_start: 0.8818 (m) cc_final: 0.8355 (p) REVERT: H 508 LYS cc_start: 0.8260 (tppt) cc_final: 0.7935 (tppt) REVERT: H 539 ASP cc_start: 0.7470 (t0) cc_final: 0.7139 (t0) REVERT: H 551 GLU cc_start: 0.6350 (tm-30) cc_final: 0.6093 (tm-30) REVERT: H 560 GLN cc_start: 0.8090 (tt0) cc_final: 0.7810 (tt0) REVERT: H 572 LEU cc_start: 0.8754 (mt) cc_final: 0.8516 (mm) REVERT: H 637 MET cc_start: 0.7128 (ppp) cc_final: 0.6893 (ppp) REVERT: H 645 MET cc_start: 0.7964 (mtt) cc_final: 0.7653 (mtp) REVERT: H 647 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7361 (mm) REVERT: H 666 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6289 (pm20) REVERT: H 667 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: H 686 MET cc_start: 0.7450 (mmp) cc_final: 0.7247 (mmp) outliers start: 61 outliers final: 28 residues processed: 625 average time/residue: 0.3484 time to fit residues: 319.8086 Evaluate side-chains 619 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 583 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 666 GLN Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 218 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 150 optimal weight: 0.0770 chunk 198 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 657 HIS C 649 ASN D 636 HIS D 666 GLN E 644 HIS F 468 ASN ** H 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.159967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128407 restraints weight = 45784.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134512 restraints weight = 20624.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135918 restraints weight = 12693.199| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18794 Z= 0.145 Angle : 0.703 15.249 25400 Z= 0.342 Chirality : 0.041 0.229 2910 Planarity : 0.004 0.046 3248 Dihedral : 4.208 21.094 2498 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.42 % Allowed : 20.35 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2296 helix: -0.07 (0.13), residues: 1604 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 448 HIS 0.008 0.001 HIS D 644 PHE 0.042 0.002 PHE G 516 TYR 0.015 0.001 TYR H 504 ARG 0.005 0.000 ARG G 655 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 893) hydrogen bonds : angle 4.33168 ( 2643) covalent geometry : bond 0.00321 (18794) covalent geometry : angle 0.70286 (25400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 582 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8073 (mt0) cc_final: 0.7646 (mt0) REVERT: A 460 LYS cc_start: 0.8313 (mttt) cc_final: 0.7894 (mtmm) REVERT: A 491 ASN cc_start: 0.7614 (m-40) cc_final: 0.7293 (m-40) REVERT: A 515 GLU cc_start: 0.7601 (tp30) cc_final: 0.7312 (tp30) REVERT: A 590 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 670 ASP cc_start: 0.7882 (p0) cc_final: 0.7502 (p0) REVERT: A 700 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6693 (mm-30) REVERT: B 463 VAL cc_start: 0.8156 (t) cc_final: 0.7802 (m) REVERT: B 512 GLN cc_start: 0.7797 (mt0) cc_final: 0.7588 (mt0) REVERT: B 527 ASN cc_start: 0.7960 (p0) cc_final: 0.7694 (p0) REVERT: B 536 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6694 (tm-30) REVERT: B 539 ASP cc_start: 0.8110 (t0) cc_final: 0.7792 (t0) REVERT: B 595 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7229 (ptp90) REVERT: B 666 GLN cc_start: 0.7848 (mp10) cc_final: 0.7513 (pm20) REVERT: B 682 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7691 (mmm-85) REVERT: C 428 TYR cc_start: 0.8043 (t80) cc_final: 0.7783 (t80) REVERT: C 645 MET cc_start: 0.7322 (mmm) cc_final: 0.6950 (mmt) REVERT: C 670 ASP cc_start: 0.6811 (m-30) cc_final: 0.6579 (m-30) REVERT: C 673 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: C 691 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: D 460 LYS cc_start: 0.8442 (mttt) cc_final: 0.8212 (mttt) REVERT: D 464 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6882 (ttp80) REVERT: D 469 SER cc_start: 0.8072 (p) cc_final: 0.7691 (t) REVERT: D 508 LYS cc_start: 0.8357 (tppt) cc_final: 0.7987 (tppt) REVERT: D 536 GLN cc_start: 0.6780 (tm-30) cc_final: 0.6298 (tm-30) REVERT: D 540 LEU cc_start: 0.8217 (mm) cc_final: 0.7793 (mm) REVERT: D 572 LEU cc_start: 0.8837 (mt) cc_final: 0.8622 (mp) REVERT: D 663 GLU cc_start: 0.7673 (pm20) cc_final: 0.7349 (pm20) REVERT: D 667 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: D 687 ASP cc_start: 0.7810 (t70) cc_final: 0.7506 (t0) REVERT: E 419 LYS cc_start: 0.7888 (tppt) cc_final: 0.7593 (tppt) REVERT: E 440 GLN cc_start: 0.7998 (mt0) cc_final: 0.7603 (mt0) REVERT: E 460 LYS cc_start: 0.8336 (mttt) cc_final: 0.7901 (mtmm) REVERT: E 474 ASP cc_start: 0.7661 (t0) cc_final: 0.7337 (t0) REVERT: E 491 ASN cc_start: 0.7625 (m-40) cc_final: 0.7260 (m-40) REVERT: E 629 LYS cc_start: 0.7315 (ptmm) cc_final: 0.6960 (ptmm) REVERT: E 670 ASP cc_start: 0.7900 (p0) cc_final: 0.7523 (p0) REVERT: E 698 ARG cc_start: 0.7172 (mtm110) cc_final: 0.6779 (mtm180) REVERT: E 700 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6583 (mm-30) REVERT: E 711 ARG cc_start: 0.7594 (mmt180) cc_final: 0.7337 (mmm160) REVERT: E 715 GLU cc_start: 0.7906 (mp0) cc_final: 0.7264 (mp0) REVERT: F 419 LYS cc_start: 0.7566 (tppt) cc_final: 0.7093 (tppt) REVERT: F 460 LYS cc_start: 0.8213 (mtpt) cc_final: 0.8007 (mttp) REVERT: F 534 GLN cc_start: 0.7589 (mt0) cc_final: 0.7111 (mt0) REVERT: F 536 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6799 (tm-30) REVERT: F 666 GLN cc_start: 0.7854 (mp10) cc_final: 0.7630 (pm20) REVERT: F 682 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: F 691 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8265 (tm-30) REVERT: G 530 MET cc_start: 0.7338 (mtt) cc_final: 0.6282 (mtt) REVERT: G 627 GLU cc_start: 0.5430 (mp0) cc_final: 0.4930 (mp0) REVERT: H 460 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8170 (mtpp) REVERT: H 470 SER cc_start: 0.8807 (m) cc_final: 0.8361 (p) REVERT: H 508 LYS cc_start: 0.8261 (tppt) cc_final: 0.7931 (tppt) REVERT: H 539 ASP cc_start: 0.7564 (t0) cc_final: 0.6865 (t0) REVERT: H 551 GLU cc_start: 0.6352 (tm-30) cc_final: 0.6087 (tm-30) REVERT: H 560 GLN cc_start: 0.8072 (tt0) cc_final: 0.7820 (tt0) REVERT: H 572 LEU cc_start: 0.8782 (mt) cc_final: 0.8512 (mm) REVERT: H 637 MET cc_start: 0.7186 (ppp) cc_final: 0.6922 (ppp) REVERT: H 645 MET cc_start: 0.7937 (mtt) cc_final: 0.7650 (mtp) REVERT: H 647 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7308 (mm) REVERT: H 667 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7991 (m-80) outliers start: 69 outliers final: 45 residues processed: 611 average time/residue: 0.4288 time to fit residues: 390.7724 Evaluate side-chains 627 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 576 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 637 MET Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 113 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 215 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 GLN C 649 ASN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS G 707 ASN ** H 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125523 restraints weight = 45700.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132106 restraints weight = 22359.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134816 restraints weight = 13435.982| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18794 Z= 0.150 Angle : 0.704 16.222 25400 Z= 0.342 Chirality : 0.041 0.202 2910 Planarity : 0.004 0.046 3248 Dihedral : 4.214 18.276 2498 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.47 % Allowed : 21.44 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2296 helix: -0.00 (0.13), residues: 1618 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 448 HIS 0.007 0.001 HIS D 644 PHE 0.032 0.002 PHE D 441 TYR 0.015 0.001 TYR H 504 ARG 0.005 0.000 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.05237 ( 893) hydrogen bonds : angle 4.36612 ( 2643) covalent geometry : bond 0.00334 (18794) covalent geometry : angle 0.70369 (25400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 577 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8046 (mt0) cc_final: 0.7633 (mt0) REVERT: A 491 ASN cc_start: 0.7636 (m-40) cc_final: 0.7317 (m-40) REVERT: A 515 GLU cc_start: 0.7633 (tp30) cc_final: 0.7343 (tp30) REVERT: A 670 ASP cc_start: 0.7849 (p0) cc_final: 0.7464 (p0) REVERT: A 700 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6678 (mm-30) REVERT: B 463 VAL cc_start: 0.8253 (t) cc_final: 0.7883 (m) REVERT: B 527 ASN cc_start: 0.8044 (p0) cc_final: 0.7755 (p0) REVERT: B 536 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6707 (tm-30) REVERT: B 539 ASP cc_start: 0.8092 (t0) cc_final: 0.7770 (t0) REVERT: B 595 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7199 (ptp90) REVERT: B 666 GLN cc_start: 0.7843 (mp10) cc_final: 0.7536 (pm20) REVERT: B 682 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7716 (mmm-85) REVERT: C 428 TYR cc_start: 0.8030 (t80) cc_final: 0.7783 (t80) REVERT: C 645 MET cc_start: 0.7358 (mmm) cc_final: 0.6988 (mmt) REVERT: C 670 ASP cc_start: 0.6858 (m-30) cc_final: 0.6648 (m-30) REVERT: C 673 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: D 460 LYS cc_start: 0.8459 (mttt) cc_final: 0.8229 (mttt) REVERT: D 464 ARG cc_start: 0.7096 (ttp80) cc_final: 0.6873 (ttp80) REVERT: D 466 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7551 (tp) REVERT: D 469 SER cc_start: 0.8067 (p) cc_final: 0.7723 (t) REVERT: D 508 LYS cc_start: 0.8318 (tppt) cc_final: 0.7982 (tppt) REVERT: D 536 GLN cc_start: 0.6697 (tm-30) cc_final: 0.6233 (tm-30) REVERT: D 540 LEU cc_start: 0.8287 (mm) cc_final: 0.7864 (mm) REVERT: D 572 LEU cc_start: 0.8837 (mt) cc_final: 0.8610 (mp) REVERT: D 663 GLU cc_start: 0.7479 (pm20) cc_final: 0.7129 (pm20) REVERT: D 667 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: D 687 ASP cc_start: 0.7814 (t70) cc_final: 0.7613 (t0) REVERT: E 419 LYS cc_start: 0.7813 (tppt) cc_final: 0.7506 (tppt) REVERT: E 440 GLN cc_start: 0.7961 (mt0) cc_final: 0.7553 (mt0) REVERT: E 460 LYS cc_start: 0.8352 (mttt) cc_final: 0.7898 (mtmm) REVERT: E 474 ASP cc_start: 0.7602 (t0) cc_final: 0.7302 (t0) REVERT: E 491 ASN cc_start: 0.7641 (m-40) cc_final: 0.7295 (m-40) REVERT: E 629 LYS cc_start: 0.7324 (ptmm) cc_final: 0.6881 (ptmm) REVERT: E 670 ASP cc_start: 0.7860 (p0) cc_final: 0.7535 (p0) REVERT: E 695 GLU cc_start: 0.7071 (tp30) cc_final: 0.6258 (tp30) REVERT: E 696 ILE cc_start: 0.8753 (tp) cc_final: 0.8508 (tp) REVERT: E 698 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6360 (mtm180) REVERT: E 700 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6487 (mm-30) REVERT: E 715 GLU cc_start: 0.7942 (mp0) cc_final: 0.7321 (mp0) REVERT: F 419 LYS cc_start: 0.7569 (tppt) cc_final: 0.7096 (tppt) REVERT: F 529 ILE cc_start: 0.7898 (mm) cc_final: 0.7620 (mt) REVERT: F 534 GLN cc_start: 0.7580 (mt0) cc_final: 0.7058 (mt0) REVERT: F 536 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6717 (tm-30) REVERT: F 682 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7568 (mmm-85) REVERT: F 692 LEU cc_start: 0.8653 (tp) cc_final: 0.8363 (tt) REVERT: G 530 MET cc_start: 0.7313 (mtt) cc_final: 0.6264 (mtt) REVERT: G 663 GLU cc_start: 0.6833 (pm20) cc_final: 0.6539 (pm20) REVERT: H 460 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8183 (mtpp) REVERT: H 466 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7559 (tp) REVERT: H 470 SER cc_start: 0.8861 (m) cc_final: 0.8417 (p) REVERT: H 508 LYS cc_start: 0.8259 (tppt) cc_final: 0.7941 (tppt) REVERT: H 551 GLU cc_start: 0.6283 (tm-30) cc_final: 0.6048 (tm-30) REVERT: H 560 GLN cc_start: 0.8127 (tt0) cc_final: 0.7881 (tt0) REVERT: H 572 LEU cc_start: 0.8797 (mt) cc_final: 0.8518 (mm) REVERT: H 637 MET cc_start: 0.7187 (ppp) cc_final: 0.6908 (ppp) REVERT: H 645 MET cc_start: 0.7903 (mtt) cc_final: 0.7639 (mtp) REVERT: H 647 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7296 (mm) REVERT: H 667 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8027 (m-80) outliers start: 70 outliers final: 46 residues processed: 601 average time/residue: 0.5054 time to fit residues: 453.5798 Evaluate side-chains 628 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 576 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 591 HIS Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain E residue 660 MET Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 197 optimal weight: 0.5980 chunk 218 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN D 636 HIS ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 HIS H 636 HIS H 644 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.158912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126868 restraints weight = 36330.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132132 restraints weight = 18768.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135802 restraints weight = 12235.032| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18794 Z= 0.154 Angle : 0.720 16.552 25400 Z= 0.349 Chirality : 0.042 0.203 2910 Planarity : 0.004 0.046 3248 Dihedral : 4.237 19.485 2498 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.32 % Allowed : 21.88 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2296 helix: 0.01 (0.13), residues: 1646 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 448 HIS 0.007 0.001 HIS D 644 PHE 0.029 0.002 PHE D 441 TYR 0.015 0.001 TYR H 504 ARG 0.007 0.000 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 893) hydrogen bonds : angle 4.36884 ( 2643) covalent geometry : bond 0.00347 (18794) covalent geometry : angle 0.72049 (25400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 595 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8048 (mt0) cc_final: 0.7619 (mt0) REVERT: A 491 ASN cc_start: 0.7640 (m-40) cc_final: 0.7303 (m-40) REVERT: A 515 GLU cc_start: 0.7617 (tp30) cc_final: 0.7341 (tp30) REVERT: A 670 ASP cc_start: 0.7888 (p0) cc_final: 0.7485 (p0) REVERT: A 698 ARG cc_start: 0.7338 (mtm110) cc_final: 0.6737 (mtm180) REVERT: A 700 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6632 (mm-30) REVERT: B 419 LYS cc_start: 0.7707 (tppt) cc_final: 0.7247 (tppt) REVERT: B 460 LYS cc_start: 0.8143 (mttt) cc_final: 0.7866 (mttp) REVERT: B 508 LYS cc_start: 0.8297 (tttp) cc_final: 0.8034 (ttmt) REVERT: B 527 ASN cc_start: 0.7962 (p0) cc_final: 0.7673 (p0) REVERT: B 536 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6686 (tm-30) REVERT: B 539 ASP cc_start: 0.8119 (t0) cc_final: 0.7807 (t0) REVERT: B 595 ARG cc_start: 0.7963 (ptp90) cc_final: 0.7368 (ptp90) REVERT: B 601 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 682 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7648 (mmm-85) REVERT: C 428 TYR cc_start: 0.8050 (t80) cc_final: 0.7794 (t80) REVERT: C 645 MET cc_start: 0.7285 (mmm) cc_final: 0.6934 (mmt) REVERT: C 673 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: D 460 LYS cc_start: 0.8418 (mttt) cc_final: 0.8184 (mttt) REVERT: D 464 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6910 (ttp80) REVERT: D 466 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7445 (tp) REVERT: D 469 SER cc_start: 0.8060 (p) cc_final: 0.7802 (t) REVERT: D 508 LYS cc_start: 0.8216 (tppt) cc_final: 0.7911 (tppt) REVERT: D 536 GLN cc_start: 0.6912 (tm-30) cc_final: 0.6367 (tm-30) REVERT: D 540 LEU cc_start: 0.8265 (mm) cc_final: 0.7789 (mm) REVERT: D 663 GLU cc_start: 0.7443 (pm20) cc_final: 0.7073 (pm20) REVERT: D 667 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: E 419 LYS cc_start: 0.7765 (tppt) cc_final: 0.7433 (tppt) REVERT: E 440 GLN cc_start: 0.7986 (mt0) cc_final: 0.7574 (mt0) REVERT: E 474 ASP cc_start: 0.7648 (t0) cc_final: 0.7328 (t0) REVERT: E 486 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8083 (mmmt) REVERT: E 491 ASN cc_start: 0.7677 (m-40) cc_final: 0.7280 (m-40) REVERT: E 629 LYS cc_start: 0.7339 (ptmm) cc_final: 0.6933 (ptmm) REVERT: E 666 GLN cc_start: 0.8143 (tp40) cc_final: 0.7698 (tp40) REVERT: E 670 ASP cc_start: 0.7824 (p0) cc_final: 0.7431 (p0) REVERT: E 695 GLU cc_start: 0.7129 (tp30) cc_final: 0.6516 (tp30) REVERT: E 696 ILE cc_start: 0.8742 (tp) cc_final: 0.8492 (tp) REVERT: E 698 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6348 (mtm180) REVERT: E 700 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6399 (mm-30) REVERT: E 715 GLU cc_start: 0.7825 (mp0) cc_final: 0.7263 (mp0) REVERT: F 419 LYS cc_start: 0.7600 (tppt) cc_final: 0.7133 (tppt) REVERT: F 508 LYS cc_start: 0.8343 (tttp) cc_final: 0.8099 (ttmt) REVERT: F 529 ILE cc_start: 0.7843 (mm) cc_final: 0.7577 (mt) REVERT: F 536 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6643 (tm-30) REVERT: F 682 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: G 530 MET cc_start: 0.7327 (mtt) cc_final: 0.6236 (mtt) REVERT: G 655 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7204 (ttm170) REVERT: G 711 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7921 (mmt180) REVERT: H 460 LYS cc_start: 0.8426 (mtmm) cc_final: 0.7998 (mtpp) REVERT: H 466 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7442 (tp) REVERT: H 470 SER cc_start: 0.8788 (m) cc_final: 0.8364 (p) REVERT: H 508 LYS cc_start: 0.8140 (tppt) cc_final: 0.7839 (tppt) REVERT: H 539 ASP cc_start: 0.7331 (t0) cc_final: 0.7071 (t0) REVERT: H 551 GLU cc_start: 0.6349 (tm-30) cc_final: 0.6095 (tm-30) REVERT: H 560 GLN cc_start: 0.8064 (tt0) cc_final: 0.7845 (tt0) REVERT: H 572 LEU cc_start: 0.8781 (mt) cc_final: 0.8484 (mm) REVERT: H 637 MET cc_start: 0.7171 (ppp) cc_final: 0.6875 (ppp) REVERT: H 645 MET cc_start: 0.7891 (mtt) cc_final: 0.7634 (mtp) REVERT: H 647 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7298 (mm) REVERT: H 667 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7995 (m-80) outliers start: 67 outliers final: 44 residues processed: 620 average time/residue: 0.4504 time to fit residues: 409.6258 Evaluate side-chains 633 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 582 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 490 HIS Chi-restraints excluded: chain D residue 527 ASN Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 70 optimal weight: 0.3980 chunk 219 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 90 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 overall best weight: 0.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN E 477 GLN E 644 HIS F 468 ASN G 602 GLN H 636 HIS H 644 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.158766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125543 restraints weight = 40749.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131198 restraints weight = 20114.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134900 restraints weight = 12762.130| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18794 Z= 0.130 Angle : 0.701 16.293 25400 Z= 0.340 Chirality : 0.040 0.184 2910 Planarity : 0.004 0.045 3248 Dihedral : 4.111 17.977 2498 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.67 % Allowed : 23.61 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2296 helix: 0.29 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 448 HIS 0.008 0.001 HIS D 644 PHE 0.026 0.002 PHE F 516 TYR 0.010 0.001 TYR D 554 ARG 0.008 0.000 ARG E 438 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 893) hydrogen bonds : angle 4.25515 ( 2643) covalent geometry : bond 0.00289 (18794) covalent geometry : angle 0.70097 (25400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 593 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8019 (mt0) cc_final: 0.7614 (mt0) REVERT: A 491 ASN cc_start: 0.7639 (m-40) cc_final: 0.7294 (m-40) REVERT: A 515 GLU cc_start: 0.7543 (tp30) cc_final: 0.7264 (tp30) REVERT: A 670 ASP cc_start: 0.7873 (p0) cc_final: 0.7443 (p0) REVERT: A 698 ARG cc_start: 0.7291 (mtm110) cc_final: 0.6669 (mtm180) REVERT: A 700 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6629 (mm-30) REVERT: B 419 LYS cc_start: 0.7644 (tppt) cc_final: 0.7188 (tppt) REVERT: B 460 LYS cc_start: 0.8061 (mttt) cc_final: 0.7807 (mttp) REVERT: B 508 LYS cc_start: 0.8319 (tttp) cc_final: 0.7997 (ttmt) REVERT: B 527 ASN cc_start: 0.7932 (p0) cc_final: 0.7643 (p0) REVERT: B 536 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6639 (tm-30) REVERT: B 539 ASP cc_start: 0.8074 (t0) cc_final: 0.7751 (t0) REVERT: B 567 SER cc_start: 0.7949 (m) cc_final: 0.7452 (p) REVERT: B 595 ARG cc_start: 0.7925 (ptp90) cc_final: 0.7312 (ptp90) REVERT: B 601 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7235 (t80) REVERT: B 643 SER cc_start: 0.7416 (m) cc_final: 0.6775 (p) REVERT: B 682 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7671 (mmm-85) REVERT: C 428 TYR cc_start: 0.8078 (t80) cc_final: 0.7798 (t80) REVERT: C 602 GLN cc_start: 0.6645 (mm-40) cc_final: 0.6305 (mt0) REVERT: C 645 MET cc_start: 0.7189 (mmm) cc_final: 0.6810 (mmt) REVERT: C 711 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7847 (mmt180) REVERT: D 464 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6974 (ttp80) REVERT: D 466 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.6915 (mt) REVERT: D 508 LYS cc_start: 0.8233 (tppt) cc_final: 0.7945 (tppt) REVERT: D 536 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6328 (tm-30) REVERT: D 540 LEU cc_start: 0.8177 (mm) cc_final: 0.7731 (mm) REVERT: D 572 LEU cc_start: 0.8841 (mt) cc_final: 0.8638 (mp) REVERT: D 663 GLU cc_start: 0.7492 (pm20) cc_final: 0.7064 (pm20) REVERT: D 667 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: D 670 ASP cc_start: 0.7347 (p0) cc_final: 0.7142 (p0) REVERT: E 438 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7553 (mtt90) REVERT: E 440 GLN cc_start: 0.7998 (mt0) cc_final: 0.7596 (mt0) REVERT: E 474 ASP cc_start: 0.7605 (t0) cc_final: 0.7263 (t0) REVERT: E 486 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8107 (mmmt) REVERT: E 491 ASN cc_start: 0.7691 (m-40) cc_final: 0.7307 (m-40) REVERT: E 629 LYS cc_start: 0.7304 (ptmm) cc_final: 0.6976 (ptmm) REVERT: E 666 GLN cc_start: 0.8112 (tp40) cc_final: 0.7703 (tp40) REVERT: E 670 ASP cc_start: 0.7809 (p0) cc_final: 0.7364 (p0) REVERT: E 696 ILE cc_start: 0.8653 (tp) cc_final: 0.8411 (tp) REVERT: E 698 ARG cc_start: 0.7156 (mtm110) cc_final: 0.6695 (mtm180) REVERT: E 700 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6462 (mm-30) REVERT: E 715 GLU cc_start: 0.7812 (mp0) cc_final: 0.7229 (mp0) REVERT: F 469 SER cc_start: 0.8302 (p) cc_final: 0.7979 (t) REVERT: F 514 MET cc_start: 0.7091 (ttm) cc_final: 0.6846 (ttm) REVERT: F 536 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6622 (tm-30) REVERT: F 682 ARG cc_start: 0.7813 (mmm-85) cc_final: 0.7553 (mmm-85) REVERT: G 530 MET cc_start: 0.7291 (mtt) cc_final: 0.6240 (mtt) REVERT: G 655 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.7186 (ttm170) REVERT: G 679 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7629 (t0) REVERT: G 711 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7860 (mmt180) REVERT: H 460 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8132 (mtpp) REVERT: H 466 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7156 (tp) REVERT: H 470 SER cc_start: 0.8724 (m) cc_final: 0.8298 (p) REVERT: H 508 LYS cc_start: 0.8134 (tppt) cc_final: 0.7865 (tppt) REVERT: H 551 GLU cc_start: 0.6311 (tm-30) cc_final: 0.6102 (tm-30) REVERT: H 572 LEU cc_start: 0.8678 (mt) cc_final: 0.8395 (mm) REVERT: H 637 MET cc_start: 0.7111 (ppp) cc_final: 0.6818 (ppp) REVERT: H 645 MET cc_start: 0.7923 (mtt) cc_final: 0.7656 (mtp) REVERT: H 647 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7285 (mm) outliers start: 54 outliers final: 34 residues processed: 616 average time/residue: 0.3142 time to fit residues: 284.4904 Evaluate side-chains 625 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 585 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 679 ASP Chi-restraints excluded: chain G residue 692 LEU Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 125 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 177 optimal weight: 0.0470 chunk 62 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 207 optimal weight: 0.0670 chunk 168 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN D 636 HIS D 664 GLN E 644 HIS F 534 GLN H 636 HIS H 644 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.159019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125363 restraints weight = 43151.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131123 restraints weight = 20784.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134907 restraints weight = 12970.548| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18794 Z= 0.134 Angle : 0.745 16.296 25400 Z= 0.357 Chirality : 0.041 0.266 2910 Planarity : 0.004 0.044 3248 Dihedral : 4.078 18.047 2498 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.13 % Allowed : 24.85 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2296 helix: 0.36 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 448 HIS 0.007 0.001 HIS D 644 PHE 0.037 0.001 PHE H 441 TYR 0.010 0.001 TYR D 554 ARG 0.007 0.000 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 893) hydrogen bonds : angle 4.28476 ( 2643) covalent geometry : bond 0.00301 (18794) covalent geometry : angle 0.74458 (25400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 577 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7468 (mtt90) REVERT: A 440 GLN cc_start: 0.8007 (mt0) cc_final: 0.7614 (mt0) REVERT: A 491 ASN cc_start: 0.7646 (m-40) cc_final: 0.7262 (m-40) REVERT: A 515 GLU cc_start: 0.7487 (tp30) cc_final: 0.7158 (tp30) REVERT: A 670 ASP cc_start: 0.7894 (p0) cc_final: 0.7519 (p0) REVERT: A 698 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6649 (mtm180) REVERT: A 700 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6631 (mm-30) REVERT: B 463 VAL cc_start: 0.7969 (t) cc_final: 0.7623 (m) REVERT: B 527 ASN cc_start: 0.7910 (p0) cc_final: 0.7636 (p0) REVERT: B 536 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6689 (tm-30) REVERT: B 539 ASP cc_start: 0.8089 (t0) cc_final: 0.7774 (t0) REVERT: B 567 SER cc_start: 0.7966 (m) cc_final: 0.7515 (p) REVERT: B 595 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7302 (ptp90) REVERT: B 643 SER cc_start: 0.7417 (m) cc_final: 0.6776 (p) REVERT: B 682 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7678 (mmm-85) REVERT: B 691 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 428 TYR cc_start: 0.8085 (t80) cc_final: 0.7779 (t80) REVERT: C 450 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7975 (ttp-110) REVERT: C 602 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6308 (mt0) REVERT: C 645 MET cc_start: 0.7141 (mmm) cc_final: 0.6810 (mmt) REVERT: C 711 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7792 (mmt180) REVERT: D 464 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6979 (ttp80) REVERT: D 466 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7116 (mt) REVERT: D 508 LYS cc_start: 0.8228 (tppt) cc_final: 0.7925 (tppt) REVERT: D 536 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6301 (tm-30) REVERT: D 540 LEU cc_start: 0.8176 (mm) cc_final: 0.7777 (mm) REVERT: D 572 LEU cc_start: 0.8820 (mt) cc_final: 0.8550 (mm) REVERT: D 667 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: E 440 GLN cc_start: 0.7947 (mt0) cc_final: 0.7544 (mt0) REVERT: E 474 ASP cc_start: 0.7631 (t0) cc_final: 0.7312 (t0) REVERT: E 486 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8101 (mmmt) REVERT: E 491 ASN cc_start: 0.7671 (m-40) cc_final: 0.7264 (m-40) REVERT: E 629 LYS cc_start: 0.7321 (ptmm) cc_final: 0.7040 (ptmm) REVERT: E 666 GLN cc_start: 0.8065 (tp40) cc_final: 0.7689 (tp40) REVERT: E 670 ASP cc_start: 0.7817 (p0) cc_final: 0.7364 (p0) REVERT: E 696 ILE cc_start: 0.8638 (tp) cc_final: 0.8391 (tp) REVERT: E 698 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6748 (mtm180) REVERT: E 700 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6495 (mm-30) REVERT: E 715 GLU cc_start: 0.7793 (mp0) cc_final: 0.7214 (mp0) REVERT: F 469 SER cc_start: 0.8332 (p) cc_final: 0.8032 (t) REVERT: F 514 MET cc_start: 0.7083 (ttm) cc_final: 0.6840 (ttm) REVERT: F 536 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6595 (tm-30) REVERT: G 530 MET cc_start: 0.7298 (mtt) cc_final: 0.6249 (mtt) REVERT: G 655 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.7168 (ttm170) REVERT: G 679 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7436 (t70) REVERT: G 711 ARG cc_start: 0.8057 (mmt90) cc_final: 0.7838 (mmt180) REVERT: H 460 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8128 (mtpp) REVERT: H 466 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7188 (tp) REVERT: H 470 SER cc_start: 0.8739 (m) cc_final: 0.8316 (p) REVERT: H 508 LYS cc_start: 0.8141 (tppt) cc_final: 0.7840 (tppt) REVERT: H 551 GLU cc_start: 0.6358 (tm-30) cc_final: 0.6144 (tm-30) REVERT: H 572 LEU cc_start: 0.8679 (mt) cc_final: 0.8396 (mm) REVERT: H 637 MET cc_start: 0.7108 (ppp) cc_final: 0.6744 (ppp) REVERT: H 645 MET cc_start: 0.7920 (mtt) cc_final: 0.7642 (mtp) REVERT: H 647 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7397 (mp) REVERT: H 667 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8038 (m-80) outliers start: 43 outliers final: 32 residues processed: 593 average time/residue: 0.3110 time to fit residues: 270.6360 Evaluate side-chains 607 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 569 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 679 ASP Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 221 optimal weight: 0.0980 chunk 129 optimal weight: 0.2980 chunk 135 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 222 optimal weight: 0.0470 chunk 41 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN E 644 HIS F 534 GLN H 644 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.159245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127150 restraints weight = 35681.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132418 restraints weight = 18450.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136009 restraints weight = 12014.072| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18794 Z= 0.135 Angle : 0.747 16.457 25400 Z= 0.360 Chirality : 0.041 0.275 2910 Planarity : 0.004 0.044 3248 Dihedral : 4.084 20.297 2498 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.23 % Allowed : 25.00 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2296 helix: 0.46 (0.14), residues: 1616 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 448 HIS 0.007 0.001 HIS D 644 PHE 0.031 0.002 PHE H 541 TYR 0.011 0.001 TYR H 554 ARG 0.009 0.001 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 893) hydrogen bonds : angle 4.29314 ( 2643) covalent geometry : bond 0.00300 (18794) covalent geometry : angle 0.74685 (25400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 576 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7449 (mtt90) REVERT: A 440 GLN cc_start: 0.7997 (mt0) cc_final: 0.7614 (mt0) REVERT: A 491 ASN cc_start: 0.7652 (m-40) cc_final: 0.7280 (m-40) REVERT: A 515 GLU cc_start: 0.7454 (tp30) cc_final: 0.7128 (tp30) REVERT: A 670 ASP cc_start: 0.7895 (p0) cc_final: 0.7531 (p0) REVERT: A 698 ARG cc_start: 0.7282 (mtm110) cc_final: 0.6651 (mtm180) REVERT: A 700 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6575 (mm-30) REVERT: B 463 VAL cc_start: 0.7957 (t) cc_final: 0.7613 (m) REVERT: B 527 ASN cc_start: 0.7885 (p0) cc_final: 0.7606 (p0) REVERT: B 536 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6681 (tm-30) REVERT: B 539 ASP cc_start: 0.8062 (t0) cc_final: 0.7710 (t0) REVERT: B 567 SER cc_start: 0.7969 (m) cc_final: 0.7543 (p) REVERT: B 595 ARG cc_start: 0.7915 (ptp90) cc_final: 0.7313 (ptp90) REVERT: B 601 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7198 (t80) REVERT: B 643 SER cc_start: 0.7402 (m) cc_final: 0.6769 (p) REVERT: B 682 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7695 (mmm-85) REVERT: B 691 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 428 TYR cc_start: 0.8079 (t80) cc_final: 0.7792 (t80) REVERT: C 602 GLN cc_start: 0.6658 (mm-40) cc_final: 0.6306 (mt0) REVERT: C 645 MET cc_start: 0.7125 (mmm) cc_final: 0.6709 (mmt) REVERT: C 711 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7778 (mmt180) REVERT: D 460 LYS cc_start: 0.8352 (mttt) cc_final: 0.7977 (mtpp) REVERT: D 464 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6975 (ttp80) REVERT: D 466 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7101 (mt) REVERT: D 508 LYS cc_start: 0.8225 (tppt) cc_final: 0.7919 (tppt) REVERT: D 536 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6311 (tm-30) REVERT: D 540 LEU cc_start: 0.8218 (mm) cc_final: 0.7724 (mm) REVERT: D 572 LEU cc_start: 0.8783 (mt) cc_final: 0.8527 (mm) REVERT: D 663 GLU cc_start: 0.7463 (pm20) cc_final: 0.7157 (pm20) REVERT: D 667 PHE cc_start: 0.8331 (m-80) cc_final: 0.7819 (m-80) REVERT: E 440 GLN cc_start: 0.7957 (mt0) cc_final: 0.7586 (mt0) REVERT: E 474 ASP cc_start: 0.7613 (t0) cc_final: 0.7284 (t0) REVERT: E 486 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8068 (mmmt) REVERT: E 491 ASN cc_start: 0.7637 (m-40) cc_final: 0.7244 (m-40) REVERT: E 629 LYS cc_start: 0.7311 (ptmm) cc_final: 0.7048 (ptmm) REVERT: E 666 GLN cc_start: 0.8036 (tp40) cc_final: 0.7678 (tp40) REVERT: E 670 ASP cc_start: 0.7806 (p0) cc_final: 0.7375 (p0) REVERT: E 696 ILE cc_start: 0.8641 (tp) cc_final: 0.8403 (tp) REVERT: E 698 ARG cc_start: 0.7126 (mtm110) cc_final: 0.6591 (mtm180) REVERT: E 700 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6408 (mm-30) REVERT: E 715 GLU cc_start: 0.7785 (mp0) cc_final: 0.7209 (mp0) REVERT: F 469 SER cc_start: 0.8322 (p) cc_final: 0.8023 (t) REVERT: F 514 MET cc_start: 0.7161 (ttm) cc_final: 0.6915 (ttm) REVERT: F 529 ILE cc_start: 0.7679 (mm) cc_final: 0.7400 (mt) REVERT: F 536 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6571 (tm-30) REVERT: G 595 ARG cc_start: 0.7086 (mmp80) cc_final: 0.6826 (mmp80) REVERT: G 655 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7148 (ttm170) REVERT: G 679 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7582 (t0) REVERT: G 711 ARG cc_start: 0.8053 (mmt90) cc_final: 0.7798 (mmt180) REVERT: H 460 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8127 (mtpp) REVERT: H 466 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7157 (tp) REVERT: H 470 SER cc_start: 0.8715 (m) cc_final: 0.8311 (p) REVERT: H 508 LYS cc_start: 0.8127 (tppt) cc_final: 0.7839 (tppt) REVERT: H 551 GLU cc_start: 0.6368 (tm-30) cc_final: 0.6150 (tm-30) REVERT: H 572 LEU cc_start: 0.8640 (mt) cc_final: 0.8364 (mm) REVERT: H 637 MET cc_start: 0.7004 (ppp) cc_final: 0.6682 (ppp) REVERT: H 645 MET cc_start: 0.7910 (mtt) cc_final: 0.7638 (mtp) REVERT: H 667 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7985 (m-80) outliers start: 45 outliers final: 35 residues processed: 593 average time/residue: 0.3093 time to fit residues: 270.9087 Evaluate side-chains 613 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 573 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 653 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 LEU Chi-restraints excluded: chain G residue 679 ASP Chi-restraints excluded: chain G residue 716 LEU Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 490 HIS Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 667 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 121 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 172 optimal weight: 0.1980 chunk 221 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 218 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 129 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN D 636 HIS E 534 GLN E 560 GLN E 644 HIS H 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.159737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125030 restraints weight = 50707.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131171 restraints weight = 22946.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135510 restraints weight = 13825.366| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18794 Z= 0.133 Angle : 0.746 16.505 25400 Z= 0.358 Chirality : 0.041 0.267 2910 Planarity : 0.004 0.044 3248 Dihedral : 4.045 19.040 2498 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.93 % Allowed : 25.45 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2296 helix: 0.54 (0.14), residues: 1616 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 448 HIS 0.008 0.001 HIS D 644 PHE 0.036 0.002 PHE H 441 TYR 0.011 0.001 TYR H 554 ARG 0.009 0.000 ARG G 693 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 893) hydrogen bonds : angle 4.26620 ( 2643) covalent geometry : bond 0.00296 (18794) covalent geometry : angle 0.74586 (25400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8727.04 seconds wall clock time: 154 minutes 41.81 seconds (9281.81 seconds total)