Starting phenix.real_space_refine on Fri Aug 7 01:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eax_27989/08_2026/8eax_27989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eax_27989/08_2026/8eax_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2026/8eax_27989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2026/8eax_27989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2026/8eax_27989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2026/8eax_27989.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG: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: {'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU: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: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 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: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2310 Restraints were copied for chains: E, F, G, H Time building chain proxies: 5.97, per 1000 atoms: 0.32 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: 1.65 Conformation dependent library (CDL) restraints added in 1.0 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: 0.47 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: 2.87 Time building geometry restraints manager: 2.20 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG B 583 TYR 0.017 0.002 TYR A 544 PHE 0.029 0.003 PHE D 533 TRP 0.012 0.002 TRP D 630 HIS 0.012 0.001 HIS G 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (18794) covalent geometry : angle 0.83366 / 0.42 (25400) hydrogen bonds : bond 0.32953 / 22.04 ( 893) hydrogen bonds : angle 7.99310 / 5.67 ( 2643) *********************** 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 : 0.683 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: 0.7284 (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: 0.7916 (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: 0.7272 (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: 0.6953 (tm-30) cc_final: 0.6718 (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: 0.6672 (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: 0.4861 (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: 0.8100 (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: 0.1453 time to fit residues: 143.6949 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 : 0.630 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 467 HIS F 523 GLN F 534 GLN F 547 HIS G 446 ASN G 523 GLN 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 = 0.4156 r_free = 0.4156 target = 0.160754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128642 restraints weight = 35486.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133999 restraints weight = 18355.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137428 restraints weight = 11911.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140020 restraints weight = 9008.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141323 restraints weight = 7367.548| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18794 Z= 0.166 Angle : 0.768 12.731 25400 Z= 0.380 Chirality : 0.044 0.186 2910 Planarity : 0.005 0.051 3248 Dihedral : 4.690 43.088 2500 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 2.43 % Allowed : 14.60 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2296 helix: -0.97 (0.12), residues: 1560 sheet: None (None), residues: 0 loop : -1.93 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 693 TYR 0.017 0.002 TYR D 554 PHE 0.027 0.002 PHE C 516 TRP 0.016 0.001 TRP B 448 HIS 0.011 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (18794) covalent geometry : angle 0.76845 / 0.38 (25400) hydrogen bonds : bond 0.06866 / 4.58 ( 893) hydrogen bonds : angle 4.96691 / 3.55 ( 2643) *********************** 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 650 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 601 time to evaluate : 0.672 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 419 LYS cc_start: 0.8042 (tppt) cc_final: 0.7709 (tppt) REVERT: A 440 GLN cc_start: 0.8184 (mt0) cc_final: 0.7705 (mt0) REVERT: A 460 LYS cc_start: 0.8448 (mttt) cc_final: 0.7907 (mtmm) REVERT: A 476 PHE cc_start: 0.8065 (t80) cc_final: 0.7838 (t80) REVERT: A 491 ASN cc_start: 0.7669 (m-40) cc_final: 0.7350 (m-40) REVERT: A 629 LYS cc_start: 0.7279 (ptmm) cc_final: 0.7058 (ptmm) REVERT: A 645 MET cc_start: 0.7459 (mmm) cc_final: 0.7245 (mmm) REVERT: A 666 GLN cc_start: 0.8066 (tp40) cc_final: 0.7845 (tp40) REVERT: A 670 ASP cc_start: 0.7936 (p0) cc_final: 0.7673 (p0) REVERT: A 695 GLU cc_start: 0.7245 (tp30) cc_final: 0.6638 (tp30) REVERT: A 700 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6402 (mm-30) REVERT: A 710 MET cc_start: 0.7319 (mmm) cc_final: 0.7034 (mmm) REVERT: B 442 ILE cc_start: 0.8615 (mt) cc_final: 0.8359 (tp) REVERT: B 527 ASN cc_start: 0.7968 (p0) cc_final: 0.7642 (p0) REVERT: B 536 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6696 (tm-30) REVERT: B 539 ASP cc_start: 0.8017 (t0) cc_final: 0.7758 (t0) REVERT: B 567 SER cc_start: 0.7949 (m) cc_final: 0.7610 (p) REVERT: B 682 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7561 (mmm-85) REVERT: C 427 ASP cc_start: 0.8031 (t0) cc_final: 0.7825 (t0) REVERT: C 428 TYR cc_start: 0.8001 (t80) cc_final: 0.7676 (t80) REVERT: C 474 ASP cc_start: 0.7861 (t70) cc_final: 0.7621 (t0) REVERT: C 530 MET cc_start: 0.7249 (mtt) cc_final: 0.6181 (mtt) REVERT: C 627 GLU cc_start: 0.5595 (mp0) cc_final: 0.4904 (tm-30) REVERT: C 645 MET cc_start: 0.6854 (mmm) cc_final: 0.6571 (mpp) REVERT: C 649 ASN cc_start: 0.7936 (m110) cc_final: 0.7675 (m-40) REVERT: D 442 ILE cc_start: 0.8387 (mt) cc_final: 0.8183 (tp) REVERT: D 464 ARG cc_start: 0.7222 (ttp80) cc_final: 0.6857 (ttp80) REVERT: D 469 SER cc_start: 0.8056 (p) cc_final: 0.7618 (t) REVERT: D 508 LYS cc_start: 0.8179 (tppt) cc_final: 0.7886 (tppt) REVERT: D 536 GLN cc_start: 0.6848 (tm-30) cc_final: 0.6583 (tm-30) REVERT: D 540 LEU cc_start: 0.8078 (mt) cc_final: 0.7861 (mm) REVERT: D 594 THR cc_start: 0.7957 (m) cc_final: 0.7690 (p) REVERT: D 686 MET cc_start: 0.7483 (mmp) cc_final: 0.6862 (mmp) REVERT: D 687 ASP cc_start: 0.7739 (t70) cc_final: 0.6864 (t0) REVERT: D 691 GLN cc_start: 0.8172 (mt0) cc_final: 0.7793 (mt0) REVERT: E 419 LYS cc_start: 0.7973 (tppt) cc_final: 0.7581 (tppt) REVERT: E 438 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7589 (mtt180) REVERT: E 440 GLN cc_start: 0.8134 (mt0) cc_final: 0.7709 (mt0) REVERT: E 460 LYS cc_start: 0.8437 (mttt) cc_final: 0.7999 (mtmm) REVERT: E 476 PHE cc_start: 0.7860 (t80) cc_final: 0.7650 (t80) REVERT: E 491 ASN cc_start: 0.7563 (m-40) cc_final: 0.7226 (m-40) REVERT: E 629 LYS cc_start: 0.7226 (ptmm) cc_final: 0.6804 (ptmm) REVERT: E 635 ILE cc_start: 0.8044 (mt) cc_final: 0.7705 (tt) REVERT: E 670 ASP cc_start: 0.7978 (p0) cc_final: 0.7611 (p0) REVERT: E 695 GLU cc_start: 0.7121 (tp30) cc_final: 0.5860 (tp30) REVERT: E 696 ILE cc_start: 0.8700 (mm) cc_final: 0.8427 (tp) REVERT: E 698 ARG cc_start: 0.6878 (mtm110) cc_final: 0.6017 (mtm180) REVERT: E 700 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6270 (mm-30) REVERT: E 710 MET cc_start: 0.7278 (mmm) cc_final: 0.7004 (mmm) REVERT: E 715 GLU cc_start: 0.7833 (mp0) cc_final: 0.7207 (mp0) REVERT: F 469 SER cc_start: 0.8348 (p) cc_final: 0.8003 (t) REVERT: F 515 GLU cc_start: 0.6335 (pt0) cc_final: 0.6128 (pt0) REVERT: F 527 ASN cc_start: 0.8100 (p0) cc_final: 0.7837 (p0) REVERT: F 534 GLN cc_start: 0.7590 (mt0) cc_final: 0.7032 (mt0) REVERT: F 536 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6802 (tm-30) REVERT: F 539 ASP cc_start: 0.8046 (t0) cc_final: 0.7798 (t0) REVERT: F 666 GLN cc_start: 0.7805 (mp10) cc_final: 0.7428 (pm20) REVERT: F 682 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7442 (mmm-85) REVERT: G 427 ASP cc_start: 0.8023 (t0) cc_final: 0.7817 (t0) REVERT: G 428 TYR cc_start: 0.8062 (t80) cc_final: 0.7831 (t80) REVERT: G 456 VAL cc_start: 0.8303 (m) cc_final: 0.7971 (t) REVERT: G 559 ASP cc_start: 0.7440 (t0) cc_final: 0.7163 (t0) REVERT: G 574 LEU cc_start: 0.8002 (mt) cc_final: 0.7769 (tt) REVERT: G 627 GLU cc_start: 0.5445 (mp0) cc_final: 0.5157 (mp0) REVERT: H 460 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8153 (mtpp) REVERT: H 469 SER cc_start: 0.8122 (p) cc_final: 0.7689 (t) REVERT: H 539 ASP cc_start: 0.7516 (t0) cc_final: 0.7081 (t0) REVERT: H 551 GLU cc_start: 0.6338 (tm-30) cc_final: 0.6115 (tm-30) REVERT: H 597 LEU cc_start: 0.7758 (tp) cc_final: 0.7554 (tp) REVERT: H 647 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7531 (mm) REVERT: H 686 MET cc_start: 0.7328 (mmp) cc_final: 0.6729 (mmp) REVERT: H 687 ASP cc_start: 0.7790 (t0) cc_final: 0.7430 (t0) outliers start: 49 outliers final: 20 residues processed: 618 average time/residue: 0.1473 time to fit residues: 135.0021 Evaluate side-chains 592 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 571 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 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 115 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 209 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 106 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.4474 > 50:) chunk 27 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 171 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 G 649 ASN ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 644 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.160670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128264 restraints weight = 36219.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135451 restraints weight = 19038.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137906 restraints weight = 10904.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139446 restraints weight = 8841.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.140764 restraints weight = 7515.626| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18794 Z= 0.138 Angle : 0.705 12.314 25400 Z= 0.347 Chirality : 0.041 0.181 2910 Planarity : 0.004 0.048 3248 Dihedral : 4.331 25.967 2498 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.18 % Allowed : 18.22 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 2296 helix: -0.44 (0.13), residues: 1570 sheet: None (None), residues: 0 loop : -1.64 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 693 TYR 0.016 0.001 TYR D 554 PHE 0.050 0.002 PHE C 516 TRP 0.014 0.001 TRP B 448 HIS 0.009 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (18794) covalent geometry : angle 0.70462 / 0.35 (25400) hydrogen bonds : bond 0.05349 / 3.59 ( 893) hydrogen bonds : angle 4.46140 / 3.18 ( 2643) *********************** 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 638 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 594 time to evaluate : 0.646 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: A 440 GLN cc_start: 0.8132 (mt0) cc_final: 0.7646 (mt0) REVERT: A 460 LYS cc_start: 0.8342 (mttt) cc_final: 0.7917 (mtmm) REVERT: A 484 ARG cc_start: 0.6201 (pmt-80) cc_final: 0.5785 (pmt-80) REVERT: A 491 ASN cc_start: 0.7647 (m-40) cc_final: 0.7342 (m-40) REVERT: A 515 GLU cc_start: 0.7384 (tp30) cc_final: 0.7137 (tp30) REVERT: A 670 ASP cc_start: 0.7788 (p0) cc_final: 0.7335 (p0) REVERT: A 695 GLU cc_start: 0.7273 (tp30) cc_final: 0.6830 (tp30) REVERT: A 700 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6646 (mm-30) REVERT: A 710 MET cc_start: 0.7093 (mmm) cc_final: 0.6886 (mmm) REVERT: B 508 LYS cc_start: 0.8201 (tttp) cc_final: 0.7912 (ttpp) REVERT: B 527 ASN cc_start: 0.7913 (p0) cc_final: 0.7606 (p0) REVERT: B 536 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6686 (tm-30) REVERT: B 539 ASP cc_start: 0.8010 (t0) cc_final: 0.7729 (t0) REVERT: B 567 SER cc_start: 0.7923 (m) cc_final: 0.7616 (p) REVERT: B 682 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7567 (mmm-85) REVERT: C 428 TYR cc_start: 0.8032 (t80) cc_final: 0.7757 (t80) REVERT: C 474 ASP cc_start: 0.7810 (t70) cc_final: 0.7591 (t0) REVERT: C 596 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7839 (tt) REVERT: C 670 ASP cc_start: 0.6705 (m-30) cc_final: 0.6328 (m-30) REVERT: D 464 ARG cc_start: 0.7042 (ttp80) cc_final: 0.6808 (ttp80) REVERT: D 469 SER cc_start: 0.7980 (p) cc_final: 0.7638 (t) REVERT: D 508 LYS cc_start: 0.8169 (tppt) cc_final: 0.7861 (tppt) REVERT: D 536 GLN cc_start: 0.6755 (tm-30) cc_final: 0.6481 (tm-30) REVERT: D 572 LEU cc_start: 0.8816 (mt) cc_final: 0.8612 (mp) REVERT: D 666 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.5726 (pm20) REVERT: D 685 MET cc_start: 0.7250 (tpt) cc_final: 0.6549 (tpt) REVERT: D 686 MET cc_start: 0.7535 (mmp) cc_final: 0.6946 (mmp) REVERT: D 687 ASP cc_start: 0.7764 (t70) cc_final: 0.7374 (t0) REVERT: E 438 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7543 (mtt180) REVERT: E 440 GLN cc_start: 0.8064 (mt0) cc_final: 0.7678 (mt0) REVERT: E 455 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8525 (mmtp) REVERT: E 460 LYS cc_start: 0.8314 (mttt) cc_final: 0.7881 (mtmm) REVERT: E 474 ASP cc_start: 0.7696 (t0) cc_final: 0.7468 (t0) REVERT: E 476 PHE cc_start: 0.7885 (t80) cc_final: 0.7679 (t80) REVERT: E 491 ASN cc_start: 0.7552 (m-40) cc_final: 0.7186 (m-40) REVERT: E 527 ASN cc_start: 0.7508 (t0) cc_final: 0.7285 (t0) REVERT: E 629 LYS cc_start: 0.7122 (ptmm) cc_final: 0.6794 (ptmm) REVERT: E 635 ILE cc_start: 0.8030 (mt) cc_final: 0.7696 (tt) REVERT: E 670 ASP cc_start: 0.7865 (p0) cc_final: 0.7534 (p0) REVERT: E 695 GLU cc_start: 0.7066 (tp30) cc_final: 0.5972 (tp30) REVERT: E 698 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6115 (mtm180) REVERT: E 715 GLU cc_start: 0.7807 (mp0) cc_final: 0.7183 (mp0) REVERT: F 468 ASN cc_start: 0.7856 (m-40) cc_final: 0.7580 (m110) REVERT: F 471 LEU cc_start: 0.7506 (pp) cc_final: 0.7283 (tp) REVERT: F 536 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6777 (tm-30) REVERT: F 539 ASP cc_start: 0.8045 (t0) cc_final: 0.7837 (t0) REVERT: F 557 MET cc_start: 0.7532 (ttm) cc_final: 0.7316 (ttt) REVERT: F 626 ASP cc_start: 0.6685 (p0) cc_final: 0.5812 (t70) REVERT: F 682 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: G 428 TYR cc_start: 0.8108 (t80) cc_final: 0.7853 (t80) REVERT: G 437 VAL cc_start: 0.9066 (p) cc_final: 0.8858 (t) REVERT: G 530 MET cc_start: 0.7220 (mtt) cc_final: 0.6248 (mtt) REVERT: G 539 ASP cc_start: 0.7983 (t0) cc_final: 0.7450 (m-30) REVERT: G 574 LEU cc_start: 0.8142 (mt) cc_final: 0.7926 (tt) REVERT: G 602 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6476 (mt0) REVERT: G 627 GLU cc_start: 0.5257 (mp0) cc_final: 0.4942 (mp0) REVERT: G 663 GLU cc_start: 0.6732 (pm20) cc_final: 0.6467 (pm20) REVERT: H 460 LYS cc_start: 0.8391 (mtmm) cc_final: 0.7942 (mtpp) REVERT: H 508 LYS cc_start: 0.8148 (tppt) cc_final: 0.7844 (tppt) REVERT: H 539 ASP cc_start: 0.7588 (t0) cc_final: 0.7005 (t0) REVERT: H 551 GLU cc_start: 0.6294 (tm-30) cc_final: 0.6055 (tm-30) REVERT: H 572 LEU cc_start: 0.8778 (mt) cc_final: 0.8565 (mm) REVERT: H 647 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7405 (mm) REVERT: H 686 MET cc_start: 0.7411 (mmp) cc_final: 0.6845 (mmp) outliers start: 44 outliers final: 27 residues processed: 612 average time/residue: 0.1476 time to fit residues: 134.2949 Evaluate side-chains 602 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 572 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 557 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 596 LEU 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 489 THR 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 429 ILE Chi-restraints excluded: chain E residue 572 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 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 626 ASP Chi-restraints excluded: chain H residue 647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 218 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 183 optimal weight: 0.3980 chunk 200 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 162 optimal weight: 0.0170 chunk 119 optimal weight: 0.6980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 HIS A 527 ASN A 644 HIS C 649 ASN D 564 GLN D 636 HIS D 664 GLN E 477 GLN E 644 HIS E 657 HIS F 534 GLN ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS H 666 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.161454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129205 restraints weight = 45301.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135509 restraints weight = 21303.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137166 restraints weight = 12772.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138156 restraints weight = 11040.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138971 restraints weight = 10040.716| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 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 = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18794 Z= 0.125 Angle : 0.679 13.782 25400 Z= 0.331 Chirality : 0.040 0.263 2910 Planarity : 0.004 0.047 3248 Dihedral : 4.176 22.585 2498 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.72 % Allowed : 19.41 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2296 helix: -0.16 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 438 TYR 0.012 0.001 TYR D 554 PHE 0.049 0.001 PHE C 516 TRP 0.014 0.001 TRP B 448 HIS 0.008 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (18794) covalent geometry : angle 0.67880 / 0.33 (25400) hydrogen bonds : bond 0.04638 / 3.11 ( 893) hydrogen bonds : angle 4.24702 / 3.03 ( 2643) *********************** 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 640 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 585 time to evaluate : 0.563 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: 0.7932 (mtm-85) cc_final: 0.7560 (mtt90) REVERT: A 440 GLN cc_start: 0.8018 (mt0) cc_final: 0.7659 (mt0) REVERT: A 460 LYS cc_start: 0.8307 (mttt) cc_final: 0.7824 (mtmm) REVERT: A 484 ARG cc_start: 0.6337 (pmt-80) cc_final: 0.5764 (pmt-80) REVERT: A 491 ASN cc_start: 0.7595 (m-40) cc_final: 0.7312 (m-40) REVERT: A 515 GLU cc_start: 0.7425 (tp30) cc_final: 0.7163 (tp30) REVERT: A 666 GLN cc_start: 0.8119 (tp40) cc_final: 0.7764 (tp40) REVERT: A 670 ASP cc_start: 0.7794 (p0) cc_final: 0.7405 (p0) REVERT: A 685 MET cc_start: 0.7991 (ttt) cc_final: 0.7735 (ttm) REVERT: A 700 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6630 (mm-30) REVERT: B 527 ASN cc_start: 0.7920 (p0) cc_final: 0.7657 (p0) REVERT: B 536 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6698 (tm-30) REVERT: B 539 ASP cc_start: 0.8057 (t0) cc_final: 0.7738 (t0) REVERT: B 682 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: C 428 TYR cc_start: 0.7991 (t80) cc_final: 0.7741 (t80) REVERT: C 574 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7882 (tt) REVERT: C 602 GLN cc_start: 0.6570 (mm-40) cc_final: 0.6280 (mt0) REVERT: C 673 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: D 464 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6791 (ttp80) REVERT: D 469 SER cc_start: 0.7946 (p) cc_final: 0.7536 (t) REVERT: D 508 LYS cc_start: 0.8261 (tppt) cc_final: 0.7943 (tppt) REVERT: D 536 GLN cc_start: 0.6646 (tm-30) cc_final: 0.6405 (tm-30) REVERT: D 572 LEU cc_start: 0.8763 (mt) cc_final: 0.8505 (mm) REVERT: D 663 GLU cc_start: 0.7570 (pm20) cc_final: 0.7056 (pm20) REVERT: D 667 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: D 687 ASP cc_start: 0.7762 (t70) cc_final: 0.7461 (t0) REVERT: E 419 LYS cc_start: 0.7950 (tppt) cc_final: 0.7638 (tppt) REVERT: E 438 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7592 (mtt180) REVERT: E 440 GLN cc_start: 0.7933 (mt0) cc_final: 0.7551 (mt0) REVERT: E 460 LYS cc_start: 0.8329 (mttt) cc_final: 0.7883 (mtmm) REVERT: E 474 ASP cc_start: 0.7683 (t0) cc_final: 0.7402 (t0) REVERT: E 491 ASN cc_start: 0.7544 (m-40) cc_final: 0.7205 (m-40) REVERT: E 629 LYS cc_start: 0.7136 (ptmm) cc_final: 0.6801 (ptmm) REVERT: E 670 ASP cc_start: 0.7830 (p0) cc_final: 0.7514 (p0) REVERT: E 695 GLU cc_start: 0.7006 (tp30) cc_final: 0.6048 (tp30) REVERT: E 696 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8507 (tt) REVERT: E 698 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6217 (mtm180) REVERT: E 715 GLU cc_start: 0.7820 (mp0) cc_final: 0.7199 (mp0) REVERT: F 460 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7960 (mttp) REVERT: F 534 GLN cc_start: 0.7442 (mt0) cc_final: 0.7037 (mt0) REVERT: F 536 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6794 (tm-30) REVERT: F 539 ASP cc_start: 0.8117 (t0) cc_final: 0.7880 (t0) REVERT: F 557 MET cc_start: 0.7524 (ttm) cc_final: 0.7314 (ttt) REVERT: F 595 ARG cc_start: 0.7766 (ptp90) cc_final: 0.7023 (ptp90) REVERT: F 682 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: F 691 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8190 (tm-30) REVERT: G 428 TYR cc_start: 0.8032 (t80) cc_final: 0.7811 (t80) REVERT: G 530 MET cc_start: 0.7153 (mtt) cc_final: 0.6111 (mtt) REVERT: G 539 ASP cc_start: 0.7743 (t0) cc_final: 0.7109 (m-30) REVERT: G 574 LEU cc_start: 0.8057 (mt) cc_final: 0.7806 (tt) REVERT: G 602 GLN cc_start: 0.6706 (mm-40) cc_final: 0.6470 (mt0) REVERT: G 627 GLU cc_start: 0.5502 (mp0) cc_final: 0.5113 (mp0) REVERT: G 663 GLU cc_start: 0.6679 (pm20) cc_final: 0.6372 (pm20) REVERT: G 696 ILE cc_start: 0.8546 (tt) cc_final: 0.8219 (tt) REVERT: H 443 ASP cc_start: 0.7613 (p0) cc_final: 0.7409 (p0) REVERT: H 460 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8110 (mtpp) REVERT: H 508 LYS cc_start: 0.8114 (tppt) cc_final: 0.7896 (tppt) REVERT: H 539 ASP cc_start: 0.7450 (t0) cc_final: 0.7032 (t0) REVERT: H 551 GLU cc_start: 0.6227 (tm-30) cc_final: 0.5980 (tm-30) REVERT: H 560 GLN cc_start: 0.7999 (tt0) cc_final: 0.7738 (tt0) REVERT: H 572 LEU cc_start: 0.8758 (mt) cc_final: 0.8511 (mm) REVERT: H 647 LEU cc_start: 0.7603 (mp) cc_final: 0.7400 (mm) REVERT: H 666 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5963 (pm20) REVERT: H 686 MET cc_start: 0.7421 (mmp) cc_final: 0.7212 (mmp) outliers start: 55 outliers final: 32 residues processed: 609 average time/residue: 0.1411 time to fit residues: 128.0614 Evaluate side-chains 609 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 572 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL 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 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 574 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 692 LEU 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 540 LEU Chi-restraints excluded: chain D residue 667 PHE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 586 ILE 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 696 ILE 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 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 666 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 0.2980 chunk 31 optimal weight: 0.0980 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 649 ASN D 545 ASN D 636 HIS D 666 GLN E 527 ASN E 644 HIS F 467 HIS ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129405 restraints weight = 40837.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136679 restraints weight = 19476.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139175 restraints weight = 11255.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140582 restraints weight = 9136.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.142358 restraints weight = 7714.038| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4268 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= 0.124 Angle : 0.680 15.291 25400 Z= 0.329 Chirality : 0.040 0.265 2910 Planarity : 0.004 0.044 3248 Dihedral : 4.086 20.780 2498 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.67 % Allowed : 20.84 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2296 helix: -0.02 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 450 TYR 0.012 0.001 TYR D 554 PHE 0.025 0.001 PHE G 516 TRP 0.013 0.001 TRP F 448 HIS 0.008 0.001 HIS D 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (18794) covalent geometry : angle 0.68014 / 0.33 (25400) hydrogen bonds : bond 0.04336 / 2.91 ( 893) hydrogen bonds : angle 4.16479 / 2.99 ( 2643) *********************** 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 627 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 573 time to evaluate : 0.531 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: 0.7918 (mtm-85) cc_final: 0.7536 (mtt90) REVERT: A 440 GLN cc_start: 0.8031 (mt0) cc_final: 0.7645 (mt0) REVERT: A 460 LYS cc_start: 0.8233 (mttt) cc_final: 0.7832 (mtmm) REVERT: A 476 PHE cc_start: 0.8051 (t80) cc_final: 0.7807 (t80) REVERT: A 484 ARG cc_start: 0.6305 (pmt-80) cc_final: 0.5742 (pmt-80) REVERT: A 491 ASN cc_start: 0.7595 (m-40) cc_final: 0.7294 (m-40) REVERT: A 515 GLU cc_start: 0.7382 (tp30) cc_final: 0.7107 (tp30) REVERT: A 666 GLN cc_start: 0.8067 (tp40) cc_final: 0.7711 (tp40) REVERT: A 670 ASP cc_start: 0.7785 (p0) cc_final: 0.7388 (p0) REVERT: A 685 MET cc_start: 0.7989 (ttt) cc_final: 0.7741 (ttm) REVERT: A 700 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6558 (mm-30) REVERT: B 527 ASN cc_start: 0.7870 (p0) cc_final: 0.7578 (p0) REVERT: B 536 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6690 (tm-30) REVERT: B 539 ASP cc_start: 0.8080 (t0) cc_final: 0.7788 (t0) REVERT: B 595 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7177 (ptp90) REVERT: B 666 GLN cc_start: 0.7786 (mp10) cc_final: 0.7496 (pm20) REVERT: C 428 TYR cc_start: 0.8043 (t80) cc_final: 0.7746 (t80) REVERT: C 574 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7910 (tt) REVERT: C 602 GLN cc_start: 0.6599 (mm-40) cc_final: 0.6304 (mt0) REVERT: C 670 ASP cc_start: 0.6749 (m-30) cc_final: 0.6503 (m-30) REVERT: C 673 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: D 464 ARG cc_start: 0.7038 (ttp80) cc_final: 0.6778 (ttp80) REVERT: D 508 LYS cc_start: 0.8183 (tppt) cc_final: 0.7885 (tppt) REVERT: D 536 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6071 (tm-30) REVERT: D 540 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7556 (mm) REVERT: D 572 LEU cc_start: 0.8669 (mt) cc_final: 0.8394 (mm) REVERT: D 666 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: D 667 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 670 ASP cc_start: 0.7270 (p0) cc_final: 0.7021 (p0) REVERT: E 419 LYS cc_start: 0.7823 (tppt) cc_final: 0.7461 (tppt) REVERT: E 440 GLN cc_start: 0.7954 (mt0) cc_final: 0.7575 (mt0) REVERT: E 460 LYS cc_start: 0.8269 (mttt) cc_final: 0.7816 (mtmm) REVERT: E 474 ASP cc_start: 0.7632 (t0) cc_final: 0.7310 (t0) REVERT: E 491 ASN cc_start: 0.7547 (m-40) cc_final: 0.7200 (m-40) REVERT: E 629 LYS cc_start: 0.7109 (ptmm) cc_final: 0.6778 (ptmm) REVERT: E 670 ASP cc_start: 0.7832 (p0) cc_final: 0.7521 (p0) REVERT: E 696 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8453 (tt) REVERT: E 698 ARG cc_start: 0.7041 (mtm110) cc_final: 0.6627 (mtm180) REVERT: E 715 GLU cc_start: 0.7742 (mp0) cc_final: 0.7168 (mp0) REVERT: F 460 LYS cc_start: 0.8307 (mtpt) cc_final: 0.8005 (mttp) REVERT: F 469 SER cc_start: 0.8302 (p) cc_final: 0.7924 (t) REVERT: F 471 LEU cc_start: 0.7456 (pp) cc_final: 0.7189 (tp) REVERT: F 534 GLN cc_start: 0.7464 (mt0) cc_final: 0.7033 (mt0) REVERT: F 536 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6790 (tm-30) REVERT: F 539 ASP cc_start: 0.8103 (t0) cc_final: 0.7862 (t0) REVERT: F 557 MET cc_start: 0.7482 (ttm) cc_final: 0.7280 (ttt) REVERT: F 595 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7088 (ptp90) REVERT: F 682 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: G 428 TYR cc_start: 0.8100 (t80) cc_final: 0.7886 (t80) REVERT: G 530 MET cc_start: 0.7156 (mtt) cc_final: 0.6164 (mtt) REVERT: G 602 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6484 (mt0) REVERT: G 627 GLU cc_start: 0.5402 (mp0) cc_final: 0.4994 (mp0) REVERT: G 693 ARG cc_start: 0.7345 (mtt90) cc_final: 0.7138 (mtt90) REVERT: H 443 ASP cc_start: 0.7593 (p0) cc_final: 0.7382 (p0) REVERT: H 460 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8068 (mtpp) REVERT: H 508 LYS cc_start: 0.8180 (tppt) cc_final: 0.7904 (tppt) REVERT: H 551 GLU cc_start: 0.6243 (tm-30) cc_final: 0.5995 (tm-30) REVERT: H 572 LEU cc_start: 0.8655 (mt) cc_final: 0.8422 (mm) REVERT: H 667 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7923 (m-10) REVERT: H 685 MET cc_start: 0.7281 (tpt) cc_final: 0.6890 (mmm) REVERT: H 686 MET cc_start: 0.7506 (mmp) cc_final: 0.7257 (mmp) outliers start: 54 outliers final: 33 residues processed: 596 average time/residue: 0.1298 time to fit residues: 115.1970 Evaluate side-chains 605 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 565 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 574 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 716 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 666 GLN 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 456 VAL Chi-restraints excluded: chain E residue 526 MET 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 E residue 696 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 637 MET Chi-restraints excluded: chain F residue 693 ARG 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 490 HIS 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 48 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 636 HIS E 477 GLN E 527 ASN E 644 HIS 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 = 0.4122 r_free = 0.4122 target = 0.158604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127453 restraints weight = 30115.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132319 restraints weight = 16597.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135570 restraints weight = 11266.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137484 restraints weight = 8678.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139080 restraints weight = 7305.042| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 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 = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18794 Z= 0.169 Angle : 0.727 16.104 25400 Z= 0.355 Chirality : 0.043 0.224 2910 Planarity : 0.004 0.046 3248 Dihedral : 4.231 17.987 2498 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.07 % Allowed : 21.63 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2296 helix: 0.05 (0.13), residues: 1610 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 450 TYR 0.020 0.001 TYR H 504 PHE 0.030 0.002 PHE D 441 TRP 0.020 0.001 TRP B 448 HIS 0.007 0.001 HIS G 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (18794) covalent geometry : angle 0.72731 / 0.36 (25400) hydrogen bonds : bond 0.05662 / 3.79 ( 893) hydrogen bonds : angle 4.39792 / 3.13 ( 2643) *********************** 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 649 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 587 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8063 (mt0) cc_final: 0.7665 (mt0) REVERT: A 484 ARG cc_start: 0.6422 (pmt-80) cc_final: 0.5853 (pmt-80) REVERT: A 491 ASN cc_start: 0.7611 (m-40) cc_final: 0.7271 (m-40) REVERT: A 515 GLU cc_start: 0.7539 (tp30) cc_final: 0.7262 (tp30) REVERT: A 666 GLN cc_start: 0.8037 (tp40) cc_final: 0.7663 (tp40) REVERT: A 670 ASP cc_start: 0.7870 (p0) cc_final: 0.7401 (p0) REVERT: A 698 ARG cc_start: 0.7227 (mtm110) cc_final: 0.6640 (mtm180) REVERT: A 700 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6468 (mm-30) REVERT: B 527 ASN cc_start: 0.7899 (p0) cc_final: 0.7613 (p0) REVERT: B 536 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6735 (tm-30) REVERT: B 539 ASP cc_start: 0.8105 (t0) cc_final: 0.7797 (t0) REVERT: B 595 ARG cc_start: 0.7945 (ptp90) cc_final: 0.7298 (ptp90) REVERT: C 428 TYR cc_start: 0.8059 (t80) cc_final: 0.7851 (t80) REVERT: C 530 MET cc_start: 0.7311 (mtt) cc_final: 0.6318 (mtt) REVERT: C 574 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 645 MET cc_start: 0.7296 (mmm) cc_final: 0.6929 (mmt) REVERT: C 670 ASP cc_start: 0.6739 (m-30) cc_final: 0.6419 (m-30) REVERT: C 673 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: D 464 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6924 (ttp80) REVERT: D 469 SER cc_start: 0.8093 (p) cc_final: 0.7765 (t) REVERT: D 508 LYS cc_start: 0.8222 (tppt) cc_final: 0.7903 (tppt) REVERT: D 525 VAL cc_start: 0.7419 (t) cc_final: 0.7218 (p) REVERT: D 536 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6367 (tm-30) REVERT: D 540 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7872 (mm) REVERT: D 572 LEU cc_start: 0.8769 (mt) cc_final: 0.8428 (mm) REVERT: D 663 GLU cc_start: 0.7669 (pm20) cc_final: 0.7265 (pm20) REVERT: D 667 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: E 419 LYS cc_start: 0.7790 (tppt) cc_final: 0.7456 (tppt) REVERT: E 440 GLN cc_start: 0.7982 (mt0) cc_final: 0.7568 (mt0) REVERT: E 474 ASP cc_start: 0.7644 (t0) cc_final: 0.7441 (t0) REVERT: E 486 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8034 (mmmt) REVERT: E 491 ASN cc_start: 0.7629 (m-40) cc_final: 0.7277 (m-40) REVERT: E 629 LYS cc_start: 0.7221 (ptmm) cc_final: 0.6893 (ptmm) REVERT: E 670 ASP cc_start: 0.7904 (p0) cc_final: 0.7641 (p0) REVERT: E 695 GLU cc_start: 0.7103 (tp30) cc_final: 0.6382 (tp30) REVERT: E 696 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8537 (tt) REVERT: E 698 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6364 (mtm180) REVERT: E 715 GLU cc_start: 0.7752 (mp0) cc_final: 0.7220 (mp0) REVERT: F 450 ARG cc_start: 0.6593 (mmt-90) cc_final: 0.6181 (mmt-90) REVERT: F 529 ILE cc_start: 0.7934 (mm) cc_final: 0.7672 (mt) REVERT: F 536 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6738 (tm-30) REVERT: F 539 ASP cc_start: 0.8127 (t0) cc_final: 0.7864 (t0) REVERT: G 530 MET cc_start: 0.7313 (mtt) cc_final: 0.6176 (mtt) REVERT: G 602 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6439 (mt0) REVERT: H 443 ASP cc_start: 0.7632 (p0) cc_final: 0.7360 (p0) REVERT: H 460 LYS cc_start: 0.8392 (mtmm) cc_final: 0.7928 (mtpp) REVERT: H 466 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7543 (tp) REVERT: H 508 LYS cc_start: 0.8187 (tppt) cc_final: 0.7857 (tppt) REVERT: H 551 GLU cc_start: 0.6339 (tm-30) cc_final: 0.6094 (tm-30) REVERT: H 572 LEU cc_start: 0.8740 (mt) cc_final: 0.8484 (mm) REVERT: H 667 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: H 686 MET cc_start: 0.7499 (mmp) cc_final: 0.7296 (mmp) outliers start: 62 outliers final: 42 residues processed: 609 average time/residue: 0.1423 time to fit residues: 128.4020 Evaluate side-chains 631 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 582 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 540 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 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 574 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 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 540 LEU Chi-restraints excluded: chain D residue 574 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 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 E residue 686 MET Chi-restraints excluded: chain E residue 696 ILE 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 648 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 667 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 108 optimal weight: 0.0770 chunk 184 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN C 649 ASN D 636 HIS D 666 GLN E 644 HIS 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 = 0.4147 r_free = 0.4147 target = 0.160492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127648 restraints weight = 40792.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134932 restraints weight = 19795.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137083 restraints weight = 11442.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139400 restraints weight = 9221.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139888 restraints weight = 7941.847| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18794 Z= 0.140 Angle : 0.726 16.445 25400 Z= 0.348 Chirality : 0.041 0.211 2910 Planarity : 0.004 0.045 3248 Dihedral : 4.183 16.419 2498 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.22 % Allowed : 22.28 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2296 helix: 0.20 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.64 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 655 TYR 0.011 0.001 TYR H 504 PHE 0.030 0.002 PHE D 441 TRP 0.015 0.001 TRP B 448 HIS 0.007 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (18794) covalent geometry : angle 0.72568 / 0.35 (25400) hydrogen bonds : bond 0.04815 / 3.23 ( 893) hydrogen bonds : angle 4.28796 / 3.05 ( 2643) *********************** 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 643 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 578 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8026 (mt0) cc_final: 0.7613 (mt0) REVERT: A 484 ARG cc_start: 0.6513 (pmt-80) cc_final: 0.5922 (pmt-80) REVERT: A 491 ASN cc_start: 0.7625 (m-40) cc_final: 0.7296 (m-40) REVERT: A 515 GLU cc_start: 0.7514 (tp30) cc_final: 0.7235 (tp30) REVERT: A 666 GLN cc_start: 0.7997 (tp40) cc_final: 0.7736 (tp40) REVERT: A 670 ASP cc_start: 0.7852 (p0) cc_final: 0.7466 (p0) REVERT: A 698 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6698 (mtm180) REVERT: A 700 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6582 (mm-30) REVERT: B 419 LYS cc_start: 0.7513 (tppt) cc_final: 0.6989 (tppt) REVERT: B 460 LYS cc_start: 0.8082 (mttt) cc_final: 0.7821 (mttp) REVERT: B 508 LYS cc_start: 0.8240 (tttp) cc_final: 0.8006 (ttmt) REVERT: B 527 ASN cc_start: 0.7936 (p0) cc_final: 0.7644 (p0) REVERT: B 536 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6734 (tm-30) REVERT: B 539 ASP cc_start: 0.8057 (t0) cc_final: 0.7727 (t0) REVERT: B 567 SER cc_start: 0.7921 (m) cc_final: 0.7478 (p) REVERT: B 595 ARG cc_start: 0.7931 (ptp90) cc_final: 0.7298 (ptp90) REVERT: B 693 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7101 (ptt-90) REVERT: C 428 TYR cc_start: 0.8061 (t80) cc_final: 0.7825 (t80) REVERT: C 574 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 645 MET cc_start: 0.7215 (mmm) cc_final: 0.6827 (mmt) REVERT: C 673 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: D 460 LYS cc_start: 0.8435 (mttt) cc_final: 0.8177 (mttt) REVERT: D 464 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6908 (ttp80) REVERT: D 466 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7746 (tp) REVERT: D 469 SER cc_start: 0.8097 (p) cc_final: 0.7812 (t) REVERT: D 508 LYS cc_start: 0.8277 (tppt) cc_final: 0.7931 (tppt) REVERT: D 525 VAL cc_start: 0.7368 (t) cc_final: 0.7158 (p) REVERT: D 536 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6293 (tm-30) REVERT: D 540 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7806 (mm) REVERT: D 572 LEU cc_start: 0.8759 (mt) cc_final: 0.8411 (mm) REVERT: D 663 GLU cc_start: 0.7761 (pm20) cc_final: 0.7325 (pm20) REVERT: D 667 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: E 419 LYS cc_start: 0.7755 (tppt) cc_final: 0.7417 (tppt) REVERT: E 440 GLN cc_start: 0.7976 (mt0) cc_final: 0.7558 (mt0) REVERT: E 474 ASP cc_start: 0.7673 (t0) cc_final: 0.7351 (t0) REVERT: E 486 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8094 (mmmt) REVERT: E 491 ASN cc_start: 0.7650 (m-40) cc_final: 0.7296 (m-40) REVERT: E 629 LYS cc_start: 0.7269 (ptmm) cc_final: 0.6912 (ptmm) REVERT: E 670 ASP cc_start: 0.7802 (p0) cc_final: 0.7497 (p0) REVERT: E 695 GLU cc_start: 0.7115 (tp30) cc_final: 0.6267 (tp30) REVERT: E 696 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8467 (tt) REVERT: E 698 ARG cc_start: 0.7125 (mtm110) cc_final: 0.6288 (mtm180) REVERT: E 715 GLU cc_start: 0.7755 (mp0) cc_final: 0.7197 (mp0) REVERT: F 536 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6663 (tm-30) REVERT: F 539 ASP cc_start: 0.8098 (t0) cc_final: 0.7860 (t0) REVERT: F 557 MET cc_start: 0.7532 (ttm) cc_final: 0.7310 (ttt) REVERT: G 547 HIS cc_start: 0.7849 (t-90) cc_final: 0.7428 (m-70) REVERT: G 602 GLN cc_start: 0.6818 (mm-40) cc_final: 0.6455 (mt0) REVERT: G 663 GLU cc_start: 0.6722 (pm20) cc_final: 0.6490 (pm20) REVERT: H 441 PHE cc_start: 0.8187 (t80) cc_final: 0.7942 (t80) REVERT: H 460 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8047 (mtpp) REVERT: H 466 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7056 (mt) REVERT: H 508 LYS cc_start: 0.8209 (tppt) cc_final: 0.7887 (tppt) REVERT: H 551 GLU cc_start: 0.6236 (tm-30) cc_final: 0.6008 (tm-30) REVERT: H 572 LEU cc_start: 0.8730 (mt) cc_final: 0.8434 (mm) REVERT: H 667 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7977 (m-80) outliers start: 65 outliers final: 44 residues processed: 602 average time/residue: 0.1301 time to fit residues: 116.4773 Evaluate side-chains 621 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 568 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 540 LEU 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 421 VAL 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 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 574 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 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 540 LEU Chi-restraints excluded: chain D residue 574 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 562 THR 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 E residue 660 MET Chi-restraints excluded: chain E residue 696 ILE 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 590 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET Chi-restraints excluded: chain G residue 648 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 667 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 209 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS C 649 ASN D 636 HIS D 664 GLN D 666 GLN E 644 HIS H 636 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.159806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126103 restraints weight = 45418.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133327 restraints weight = 21901.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136236 restraints weight = 12081.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136400 restraints weight = 10671.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137407 restraints weight = 9561.143| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18794 Z= 0.149 Angle : 0.744 16.061 25400 Z= 0.357 Chirality : 0.042 0.229 2910 Planarity : 0.004 0.045 3248 Dihedral : 4.206 18.039 2498 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.22 % Allowed : 22.87 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2296 helix: 0.25 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 438 TYR 0.013 0.001 TYR H 504 PHE 0.028 0.002 PHE D 441 TRP 0.014 0.001 TRP B 448 HIS 0.007 0.001 HIS B 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (18794) covalent geometry : angle 0.74355 / 0.36 (25400) hydrogen bonds : bond 0.05021 / 3.37 ( 893) hydrogen bonds : angle 4.31658 / 3.07 ( 2643) *********************** 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 645 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 580 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8021 (mt0) cc_final: 0.7594 (mt0) REVERT: A 484 ARG cc_start: 0.6645 (pmt-80) cc_final: 0.6060 (pmt-80) REVERT: A 491 ASN cc_start: 0.7610 (m-40) cc_final: 0.7273 (m-40) REVERT: A 515 GLU cc_start: 0.7500 (tp30) cc_final: 0.7238 (tp30) REVERT: A 524 GLU cc_start: 0.7688 (mp0) cc_final: 0.7431 (mp0) REVERT: A 666 GLN cc_start: 0.7967 (tp40) cc_final: 0.7704 (tp40) REVERT: A 670 ASP cc_start: 0.7847 (p0) cc_final: 0.7465 (p0) REVERT: A 698 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6669 (mtm180) REVERT: A 700 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6570 (mm-30) REVERT: B 527 ASN cc_start: 0.7950 (p0) cc_final: 0.7644 (p0) REVERT: B 530 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: B 536 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6706 (tm-30) REVERT: B 539 ASP cc_start: 0.8079 (t0) cc_final: 0.7755 (t0) REVERT: B 567 SER cc_start: 0.7944 (m) cc_final: 0.7494 (p) REVERT: B 595 ARG cc_start: 0.7880 (ptp90) cc_final: 0.7236 (ptp90) REVERT: B 601 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.7166 (t80) REVERT: B 643 SER cc_start: 0.7350 (m) cc_final: 0.6742 (p) REVERT: B 693 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6953 (ptt-90) REVERT: C 428 TYR cc_start: 0.8060 (t80) cc_final: 0.7815 (t80) REVERT: C 574 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8094 (tt) REVERT: C 645 MET cc_start: 0.7265 (mmm) cc_final: 0.6881 (mmt) REVERT: C 670 ASP cc_start: 0.6885 (m-30) cc_final: 0.6608 (m-30) REVERT: C 673 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: D 460 LYS cc_start: 0.8478 (mttt) cc_final: 0.8243 (mttt) REVERT: D 464 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6882 (ttp80) REVERT: D 466 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7894 (tp) REVERT: D 469 SER cc_start: 0.8085 (p) cc_final: 0.7768 (t) REVERT: D 508 LYS cc_start: 0.8278 (tppt) cc_final: 0.7958 (tppt) REVERT: D 536 GLN cc_start: 0.6775 (tm-30) cc_final: 0.6284 (tm-30) REVERT: D 540 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7819 (mm) REVERT: D 572 LEU cc_start: 0.8769 (mt) cc_final: 0.8430 (mm) REVERT: D 667 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: E 419 LYS cc_start: 0.7870 (tppt) cc_final: 0.7489 (tppt) REVERT: E 440 GLN cc_start: 0.7928 (mt0) cc_final: 0.7536 (mt0) REVERT: E 474 ASP cc_start: 0.7664 (t0) cc_final: 0.7347 (t0) REVERT: E 486 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8126 (mmmt) REVERT: E 491 ASN cc_start: 0.7685 (m-40) cc_final: 0.7344 (m-40) REVERT: E 629 LYS cc_start: 0.7327 (ptmm) cc_final: 0.6959 (ptmm) REVERT: E 670 ASP cc_start: 0.7817 (p0) cc_final: 0.7486 (p0) REVERT: E 695 GLU cc_start: 0.7084 (tp30) cc_final: 0.6474 (tp30) REVERT: E 698 ARG cc_start: 0.7119 (mtm110) cc_final: 0.6286 (mtm180) REVERT: E 715 GLU cc_start: 0.7806 (mp0) cc_final: 0.7229 (mp0) REVERT: F 514 MET cc_start: 0.7144 (tpp) cc_final: 0.6808 (tpp) REVERT: F 529 ILE cc_start: 0.7914 (mm) cc_final: 0.7628 (mt) REVERT: F 536 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6664 (tm-30) REVERT: F 539 ASP cc_start: 0.8106 (t0) cc_final: 0.7884 (t0) REVERT: F 557 MET cc_start: 0.7567 (ttm) cc_final: 0.7328 (ttt) REVERT: G 547 HIS cc_start: 0.7838 (t-90) cc_final: 0.7393 (m-70) REVERT: G 602 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6453 (mt0) REVERT: G 711 ARG cc_start: 0.8134 (mmt90) cc_final: 0.7879 (mmt180) REVERT: H 441 PHE cc_start: 0.8170 (t80) cc_final: 0.7860 (t80) REVERT: H 460 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8011 (mtpp) REVERT: H 466 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7143 (mt) REVERT: H 508 LYS cc_start: 0.8264 (tppt) cc_final: 0.7948 (tppt) REVERT: H 551 GLU cc_start: 0.6249 (tm-30) cc_final: 0.6031 (tm-30) REVERT: H 572 LEU cc_start: 0.8721 (mt) cc_final: 0.8415 (mm) REVERT: H 667 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (m-80) outliers start: 65 outliers final: 48 residues processed: 604 average time/residue: 0.1262 time to fit residues: 113.5178 Evaluate side-chains 630 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 572 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 562 THR 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 B residue 421 VAL Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 530 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 B residue 693 ARG 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 574 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 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 540 LEU Chi-restraints excluded: chain D residue 574 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 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 E residue 696 ILE 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 570 THR Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET 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 530 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 179 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 636 HIS E 644 HIS F 523 GLN H 636 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.159930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129042 restraints weight = 40699.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133645 restraints weight = 19357.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135413 restraints weight = 12915.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136105 restraints weight = 10674.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139019 restraints weight = 9826.384| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 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 = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18794 Z= 0.142 Angle : 0.743 16.536 25400 Z= 0.357 Chirality : 0.042 0.183 2910 Planarity : 0.004 0.047 3248 Dihedral : 4.171 17.947 2498 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.02 % Allowed : 23.47 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2296 helix: 0.36 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 438 TYR 0.011 0.001 TYR H 504 PHE 0.027 0.002 PHE F 516 TRP 0.013 0.001 TRP B 448 HIS 0.007 0.001 HIS D 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (18794) covalent geometry : angle 0.74270 / 0.36 (25400) hydrogen bonds : bond 0.04751 / 3.20 ( 893) hydrogen bonds : angle 4.29390 / 3.06 ( 2643) *********************** 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 635 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 574 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7492 (mtt90) REVERT: A 440 GLN cc_start: 0.8012 (mt0) cc_final: 0.7622 (mt0) REVERT: A 484 ARG cc_start: 0.6674 (pmt-80) cc_final: 0.6074 (pmt-80) REVERT: A 491 ASN cc_start: 0.7603 (m-40) cc_final: 0.7274 (m-40) REVERT: A 515 GLU cc_start: 0.7510 (tp30) cc_final: 0.7239 (tp30) REVERT: A 524 GLU cc_start: 0.7723 (mp0) cc_final: 0.7463 (mp0) REVERT: A 660 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6051 (ptp) REVERT: A 666 GLN cc_start: 0.7928 (tp40) cc_final: 0.7625 (tp40) REVERT: A 670 ASP cc_start: 0.7839 (p0) cc_final: 0.7351 (p0) REVERT: A 698 ARG cc_start: 0.7297 (mtm110) cc_final: 0.6700 (mtm180) REVERT: A 700 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6598 (mm-30) REVERT: B 527 ASN cc_start: 0.7902 (p0) cc_final: 0.7607 (p0) REVERT: B 530 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8055 (mtm) REVERT: B 536 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6683 (tm-30) REVERT: B 539 ASP cc_start: 0.8083 (t0) cc_final: 0.7742 (t0) REVERT: B 595 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7275 (ptp90) REVERT: B 693 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7065 (ptt-90) REVERT: C 428 TYR cc_start: 0.8091 (t80) cc_final: 0.7859 (t80) REVERT: C 450 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7832 (ttp-110) REVERT: C 574 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8143 (tt) REVERT: C 645 MET cc_start: 0.7234 (mmm) cc_final: 0.6879 (mmt) REVERT: C 670 ASP cc_start: 0.6863 (m-30) cc_final: 0.6592 (m-30) REVERT: C 673 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: D 460 LYS cc_start: 0.8425 (mttt) cc_final: 0.8191 (mttt) REVERT: D 464 ARG cc_start: 0.7211 (ttp80) cc_final: 0.6931 (ttp80) REVERT: D 466 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 469 SER cc_start: 0.8062 (p) cc_final: 0.7800 (t) REVERT: D 508 LYS cc_start: 0.8265 (tppt) cc_final: 0.7933 (tppt) REVERT: D 536 GLN cc_start: 0.6848 (tm-30) cc_final: 0.6338 (tm-30) REVERT: D 540 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7872 (mm) REVERT: D 572 LEU cc_start: 0.8741 (mt) cc_final: 0.8389 (mm) REVERT: D 667 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: E 440 GLN cc_start: 0.7998 (mt0) cc_final: 0.7611 (mt0) REVERT: E 474 ASP cc_start: 0.7680 (t0) cc_final: 0.7361 (t0) REVERT: E 486 LYS cc_start: 0.8451 (mmmt) cc_final: 0.8105 (mmmt) REVERT: E 491 ASN cc_start: 0.7698 (m-40) cc_final: 0.7327 (m-40) REVERT: E 629 LYS cc_start: 0.7365 (ptmm) cc_final: 0.7034 (ptmm) REVERT: E 670 ASP cc_start: 0.7839 (p0) cc_final: 0.7480 (p0) REVERT: E 695 GLU cc_start: 0.7110 (tp30) cc_final: 0.5975 (tp30) REVERT: E 698 ARG cc_start: 0.7140 (mtm110) cc_final: 0.6134 (mtm180) REVERT: E 715 GLU cc_start: 0.7789 (mp0) cc_final: 0.7172 (mp0) REVERT: F 514 MET cc_start: 0.7114 (tpp) cc_final: 0.6906 (ttm) REVERT: F 529 ILE cc_start: 0.7773 (mm) cc_final: 0.7506 (mt) REVERT: F 536 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6626 (tm-30) REVERT: F 539 ASP cc_start: 0.8096 (t0) cc_final: 0.7843 (t0) REVERT: F 557 MET cc_start: 0.7518 (ttm) cc_final: 0.7288 (ttt) REVERT: G 510 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7926 (tt) REVERT: G 547 HIS cc_start: 0.7819 (t-90) cc_final: 0.7382 (m-70) REVERT: G 559 ASP cc_start: 0.7491 (t0) cc_final: 0.7058 (t0) REVERT: G 595 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6570 (mmp80) REVERT: G 602 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6471 (mt0) REVERT: G 711 ARG cc_start: 0.8090 (mmt90) cc_final: 0.7865 (mmt180) REVERT: H 441 PHE cc_start: 0.8210 (t80) cc_final: 0.7893 (t80) REVERT: H 460 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8064 (mtpp) REVERT: H 466 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7116 (mt) REVERT: H 508 LYS cc_start: 0.8220 (tppt) cc_final: 0.7876 (tppt) REVERT: H 525 VAL cc_start: 0.7371 (t) cc_final: 0.7154 (p) REVERT: H 551 GLU cc_start: 0.6264 (tm-30) cc_final: 0.6056 (tm-30) REVERT: H 572 LEU cc_start: 0.8700 (mt) cc_final: 0.8375 (mm) REVERT: H 667 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7971 (m-80) outliers start: 61 outliers final: 43 residues processed: 598 average time/residue: 0.1362 time to fit residues: 122.5681 Evaluate side-chains 622 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 567 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP 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 421 VAL Chi-restraints excluded: chain B residue 530 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 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 574 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 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 540 LEU Chi-restraints excluded: chain D residue 574 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 562 THR 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 E residue 660 MET Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET 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 530 MET 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 138 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 636 HIS 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 = 0.4118 r_free = 0.4118 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125805 restraints weight = 45045.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130859 restraints weight = 21633.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134397 restraints weight = 13269.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134568 restraints weight = 11129.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135255 restraints weight = 10257.179| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 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 = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18794 Z= 0.184 Angle : 0.785 16.521 25400 Z= 0.381 Chirality : 0.044 0.188 2910 Planarity : 0.004 0.054 3248 Dihedral : 4.276 18.053 2498 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.02 % Allowed : 23.86 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2296 helix: 0.28 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 655 TYR 0.018 0.002 TYR H 504 PHE 0.024 0.002 PHE B 441 TRP 0.013 0.001 TRP B 448 HIS 0.007 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (18794) covalent geometry : angle 0.78518 / 0.38 (25400) hydrogen bonds : bond 0.05556 / 3.75 ( 893) hydrogen bonds : angle 4.44671 / 3.15 ( 2643) ********************** 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 634 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 573 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8026 (mt0) cc_final: 0.7638 (mt0) REVERT: A 484 ARG cc_start: 0.6702 (pmt-80) cc_final: 0.6097 (pmt-80) REVERT: A 491 ASN cc_start: 0.7614 (m-40) cc_final: 0.7272 (m-40) REVERT: A 515 GLU cc_start: 0.7589 (tp30) cc_final: 0.7322 (tp30) REVERT: A 524 GLU cc_start: 0.7724 (mp0) cc_final: 0.7417 (mp0) REVERT: A 660 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6312 (ptp) REVERT: A 666 GLN cc_start: 0.7947 (tp40) cc_final: 0.7722 (tp40) REVERT: A 670 ASP cc_start: 0.7884 (p0) cc_final: 0.7491 (p0) REVERT: A 698 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6722 (mtm180) REVERT: A 700 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 432 MET cc_start: 0.7461 (mmp) cc_final: 0.7191 (mmm) REVERT: B 527 ASN cc_start: 0.7931 (p0) cc_final: 0.7645 (p0) REVERT: B 530 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8119 (mtm) REVERT: B 536 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6620 (tm-30) REVERT: B 539 ASP cc_start: 0.8101 (t0) cc_final: 0.7804 (t0) REVERT: B 595 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7349 (ptp90) REVERT: B 601 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7224 (t80) REVERT: B 693 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7096 (ptt-90) REVERT: C 428 TYR cc_start: 0.8066 (t80) cc_final: 0.7859 (t80) REVERT: C 526 MET cc_start: 0.7181 (ttm) cc_final: 0.6899 (ttm) REVERT: C 574 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8170 (tt) REVERT: C 645 MET cc_start: 0.7361 (mmm) cc_final: 0.7007 (mmt) REVERT: C 670 ASP cc_start: 0.6886 (m-30) cc_final: 0.6526 (m-30) REVERT: C 673 GLU cc_start: 0.7961 (pm20) cc_final: 0.7719 (pm20) REVERT: D 464 ARG cc_start: 0.7291 (ttp80) cc_final: 0.6982 (ttp80) REVERT: D 466 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7874 (tp) REVERT: D 469 SER cc_start: 0.8068 (p) cc_final: 0.7780 (t) REVERT: D 508 LYS cc_start: 0.8292 (tppt) cc_final: 0.7929 (tppt) REVERT: D 536 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6457 (tm-30) REVERT: D 540 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7912 (mm) REVERT: D 572 LEU cc_start: 0.8810 (mt) cc_final: 0.8541 (mp) REVERT: D 667 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: E 440 GLN cc_start: 0.8007 (mt0) cc_final: 0.7603 (mt0) REVERT: E 474 ASP cc_start: 0.7682 (t0) cc_final: 0.7361 (t0) REVERT: E 491 ASN cc_start: 0.7691 (m-40) cc_final: 0.7294 (m-40) REVERT: E 629 LYS cc_start: 0.7391 (ptmm) cc_final: 0.7021 (ptmm) REVERT: E 670 ASP cc_start: 0.7869 (p0) cc_final: 0.7520 (p0) REVERT: E 695 GLU cc_start: 0.7239 (tp30) cc_final: 0.6147 (tp30) REVERT: E 698 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6210 (mtm180) REVERT: E 711 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7468 (mmm160) REVERT: E 715 GLU cc_start: 0.7860 (mp0) cc_final: 0.7231 (mp0) REVERT: F 529 ILE cc_start: 0.7835 (mm) cc_final: 0.7564 (mt) REVERT: F 536 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6654 (tm-30) REVERT: F 539 ASP cc_start: 0.8119 (t0) cc_final: 0.7912 (t0) REVERT: F 557 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7340 (ttt) REVERT: G 547 HIS cc_start: 0.7936 (t-90) cc_final: 0.7564 (m-70) REVERT: G 559 ASP cc_start: 0.7498 (t0) cc_final: 0.7036 (t0) REVERT: G 595 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6585 (mmp80) REVERT: G 602 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6473 (mt0) REVERT: G 711 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7859 (mmt180) REVERT: H 460 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7983 (mtpp) REVERT: H 466 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7135 (mt) REVERT: H 508 LYS cc_start: 0.8249 (tppt) cc_final: 0.7895 (tppt) REVERT: H 539 ASP cc_start: 0.7228 (t0) cc_final: 0.6947 (t0) REVERT: H 551 GLU cc_start: 0.6367 (tm-30) cc_final: 0.6130 (tm-30) REVERT: H 572 LEU cc_start: 0.8734 (mt) cc_final: 0.8391 (mm) REVERT: H 667 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (m-80) outliers start: 61 outliers final: 43 residues processed: 597 average time/residue: 0.1217 time to fit residues: 108.1308 Evaluate side-chains 627 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 572 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 530 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 B residue 693 ARG 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 574 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 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 540 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 562 THR 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 E residue 660 MET Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 557 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 538 MET Chi-restraints excluded: chain G residue 570 THR Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 607 TYR Chi-restraints excluded: chain G residue 637 MET 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 530 MET 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 146 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 136 optimal weight: 0.0060 chunk 89 optimal weight: 0.0010 chunk 176 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN C 649 ASN D 636 HIS E 644 HIS F 468 ASN 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 = 0.4143 r_free = 0.4143 target = 0.160144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127238 restraints weight = 47414.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135060 restraints weight = 22529.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136773 restraints weight = 12285.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137434 restraints weight = 10448.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139524 restraints weight = 9616.369| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 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 = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18794 Z= 0.138 Angle : 0.765 16.680 25400 Z= 0.365 Chirality : 0.041 0.172 2910 Planarity : 0.004 0.057 3248 Dihedral : 4.197 17.821 2498 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.57 % Allowed : 24.36 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.18), residues: 2296 helix: 0.44 (0.13), residues: 1622 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 464 TYR 0.010 0.001 TYR D 554 PHE 0.027 0.002 PHE B 667 TRP 0.014 0.001 TRP B 448 HIS 0.008 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18794) covalent geometry : angle 0.76467 / 0.37 (25400) hydrogen bonds : bond 0.04662 / 3.14 ( 893) hydrogen bonds : angle 4.30391 / 3.06 ( 2643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.99 seconds wall clock time: 63 minutes 2.46 seconds (3782.46 seconds total)