Starting phenix.real_space_refine on Sun Aug 24 08:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eax_27989/08_2025/8eax_27989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eax_27989/08_2025/8eax_27989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2025/8eax_27989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2025/8eax_27989.map" model { file = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2025/8eax_27989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eax_27989/08_2025/8eax_27989.cif" } 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-2.0-5787/lib/python3.9/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: 5.74, per 1000 atoms: 0.31 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: 1.57 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.48 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: 2.92 Time building geometry restraints manager: 2.09 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.100 Find NCS groups from input model: 0.150 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18794 Z= 0.201 Angle : 0.834 10.416 25400 Z= 0.421 Chirality : 0.046 0.222 2910 Planarity : 0.005 0.048 3248 Dihedral : 14.959 89.197 6988 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.77 % Favored : 89.79 % Rotamer: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.00448 (18794) covalent geometry : angle 0.83366 (25400) hydrogen bonds : bond 0.32953 ( 893) hydrogen bonds : angle 7.99310 ( 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 : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 439 ASP cc_start: 0.8567 (p0) cc_final: 0.8308 (p0) REVERT: A 460 LYS cc_start: 0.8698 (mttt) cc_final: 0.8432 (mttt) REVERT: A 475 ASP cc_start: 0.7968 (t0) cc_final: 0.7766 (t0) REVERT: A 486 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7839 (mmmt) REVERT: A 491 ASN cc_start: 0.7708 (m-40) cc_final: 0.7389 (m-40) REVERT: A 524 GLU cc_start: 0.8161 (mp0) cc_final: 0.7662 (mp0) REVERT: A 556 ARG cc_start: 0.6200 (tmt170) cc_final: 0.5946 (tmt170) REVERT: A 629 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7131 (ptmm) REVERT: A 645 MET cc_start: 0.7658 (mmm) cc_final: 0.7403 (mmm) REVERT: A 670 ASP cc_start: 0.8196 (p0) cc_final: 0.7821 (p0) REVERT: A 695 GLU cc_start: 0.7285 (tp30) cc_final: 0.6522 (tp30) REVERT: A 700 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6728 (mm-30) REVERT: A 715 GLU cc_start: 0.7911 (mp0) cc_final: 0.7459 (mp0) REVERT: B 440 GLN cc_start: 0.7936 (pp30) cc_final: 0.7675 (pp30) REVERT: B 441 PHE cc_start: 0.8808 (t80) cc_final: 0.8566 (t80) REVERT: B 527 ASN cc_start: 0.7922 (p0) cc_final: 0.7457 (p0) REVERT: B 530 MET cc_start: 0.8201 (mtt) cc_final: 0.7915 (mtm) REVERT: B 536 GLN cc_start: 0.7676 (tm-30) cc_final: 0.6887 (tm-30) REVERT: B 539 ASP cc_start: 0.8033 (t0) cc_final: 0.7747 (t0) REVERT: B 573 LEU cc_start: 0.8329 (tp) cc_final: 0.8050 (tp) REVERT: C 427 ASP cc_start: 0.8014 (t0) cc_final: 0.7607 (t0) REVERT: C 428 TYR cc_start: 0.7844 (t80) cc_final: 0.7576 (t80) REVERT: C 474 ASP cc_start: 0.7770 (t70) cc_final: 0.7461 (t0) REVERT: C 478 ASP cc_start: 0.7130 (m-30) cc_final: 0.6922 (m-30) REVERT: C 679 ASP cc_start: 0.8281 (t0) cc_final: 0.7766 (t0) REVERT: D 503 THR cc_start: 0.8255 (t) cc_final: 0.8053 (m) REVERT: D 506 ILE cc_start: 0.7649 (pt) cc_final: 0.7271 (mt) REVERT: D 536 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6606 (tm-30) REVERT: D 540 LEU cc_start: 0.8036 (mt) cc_final: 0.7695 (mm) REVERT: D 551 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6717 (tm-30) REVERT: D 637 MET cc_start: 0.7500 (ppp) cc_final: 0.7164 (ppp) REVERT: D 685 MET cc_start: 0.7449 (tpt) cc_final: 0.7103 (tpt) REVERT: D 686 MET cc_start: 0.7748 (mmp) cc_final: 0.7460 (mmp) REVERT: D 687 ASP cc_start: 0.7690 (t0) cc_final: 0.7083 (t0) REVERT: E 460 LYS cc_start: 0.8693 (mttt) cc_final: 0.8314 (mtpp) REVERT: E 463 VAL cc_start: 0.8295 (p) cc_final: 0.8086 (m) REVERT: E 468 ASN cc_start: 0.7788 (m110) cc_final: 0.7556 (m110) REVERT: E 484 ARG cc_start: 0.6842 (pmt-80) cc_final: 0.6423 (pmt-80) REVERT: E 491 ASN cc_start: 0.7603 (m-40) cc_final: 0.7231 (m-40) REVERT: E 500 ASN cc_start: 0.8511 (t0) cc_final: 0.8292 (t0) REVERT: E 524 GLU cc_start: 0.8116 (mp0) cc_final: 0.7624 (mp0) REVERT: E 539 ASP cc_start: 0.7675 (t70) cc_final: 0.7453 (t0) REVERT: E 670 ASP cc_start: 0.8119 (p0) cc_final: 0.7829 (p0) REVERT: E 695 GLU cc_start: 0.7236 (tp30) cc_final: 0.5892 (tp30) REVERT: E 698 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6109 (mtm110) REVERT: E 700 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6772 (mm-30) REVERT: E 715 GLU cc_start: 0.7895 (mp0) cc_final: 0.7373 (mp0) REVERT: F 440 GLN cc_start: 0.7946 (pp30) cc_final: 0.7586 (pp30) REVERT: F 441 PHE cc_start: 0.8754 (t80) cc_final: 0.8480 (t80) REVERT: F 463 VAL cc_start: 0.8859 (t) cc_final: 0.8592 (p) REVERT: F 527 ASN cc_start: 0.8058 (p0) cc_final: 0.7661 (p0) REVERT: F 530 MET cc_start: 0.8095 (mtt) cc_final: 0.7833 (mtm) REVERT: F 536 GLN cc_start: 0.7694 (tm-30) cc_final: 0.6848 (tm-30) REVERT: F 539 ASP cc_start: 0.8135 (t0) cc_final: 0.7876 (t0) REVERT: F 544 TYR cc_start: 0.7093 (t80) cc_final: 0.6671 (t80) REVERT: F 560 GLN cc_start: 0.7932 (tt0) cc_final: 0.7721 (tt0) REVERT: F 586 ILE cc_start: 0.8410 (pt) cc_final: 0.7913 (mp) REVERT: G 428 TYR cc_start: 0.7938 (t80) cc_final: 0.7723 (t80) REVERT: G 450 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8193 (ttp-110) REVERT: G 464 ARG cc_start: 0.7279 (ttp80) cc_final: 0.7045 (ttp80) REVERT: G 474 ASP cc_start: 0.7747 (t70) cc_final: 0.7507 (t0) REVERT: G 515 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7104 (tm-30) REVERT: G 602 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6663 (mm-40) REVERT: G 627 GLU cc_start: 0.5582 (mp0) cc_final: 0.4860 (mp0) REVERT: G 673 GLU cc_start: 0.7697 (pt0) cc_final: 0.7453 (pt0) REVERT: G 679 ASP cc_start: 0.8232 (t0) cc_final: 0.7478 (t0) REVERT: H 506 ILE cc_start: 0.7536 (pt) cc_final: 0.7111 (mt) REVERT: H 536 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6910 (tm-30) REVERT: H 541 PHE cc_start: 0.8289 (t80) cc_final: 0.8052 (t80) REVERT: H 551 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6843 (tm-30) REVERT: H 591 HIS cc_start: 0.7792 (m170) cc_final: 0.7528 (m-70) REVERT: H 637 MET cc_start: 0.7507 (ppp) cc_final: 0.7276 (ppp) REVERT: H 647 LEU cc_start: 0.8313 (mp) cc_final: 0.8101 (mp) REVERT: H 686 MET cc_start: 0.7669 (mmp) cc_final: 0.7440 (mmp) outliers start: 6 outliers final: 1 residues processed: 661 average time/residue: 0.1446 time to fit residues: 141.6164 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 : 0.682 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A 440 GLN A 468 ASN A 477 GLN A 479 ASN A 527 ASN A 536 GLN A 591 HIS A 644 HIS A 649 ASN A 666 GLN B 467 HIS B 523 GLN B 547 HIS B 591 HIS C 446 ASN C 467 HIS C 523 GLN C 587 GLN C 664 GLN D 414 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN D 644 HIS D 691 GLN E 414 HIS E 440 GLN E 468 ASN E 477 GLN E 479 ASN E 527 ASN E 536 GLN E 644 HIS E 649 ASN E 666 GLN F 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 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 aren 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 covalent geometry : bond 0.00348 (18794) covalent geometry : angle 0.76845 (25400) hydrogen bonds : bond 0.06866 ( 893) hydrogen bonds : angle 4.96691 ( 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 : 0.720 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: 0.7672 (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: 0.8018 (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: 0.7622 (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: 0.7617 (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: 0.8133 (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: 0.7649 (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: 0.7279 (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: 0.7970 (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: 0.6114 (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: 0.1466 time to fit residues: 133.3481 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 : 0.674 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4474 > 50: distance: 61 - 66: 23.146 distance: 66 - 67: 6.720 distance: 67 - 68: 9.974 distance: 68 - 69: 22.895 distance: 68 - 70: 20.832 distance: 70 - 71: 27.322 distance: 71 - 72: 5.398 distance: 71 - 74: 16.701 distance: 72 - 73: 24.792 distance: 72 - 79: 21.076 distance: 74 - 75: 33.489 distance: 75 - 76: 31.786 distance: 76 - 77: 15.683 distance: 77 - 78: 55.447 distance: 79 - 80: 15.292 distance: 80 - 81: 27.861 distance: 80 - 83: 18.973 distance: 81 - 82: 17.252 distance: 81 - 93: 4.016 distance: 83 - 84: 4.211 distance: 84 - 86: 5.426 distance: 86 - 89: 9.962 distance: 87 - 88: 5.416 distance: 88 - 90: 5.138 distance: 89 - 91: 9.430 distance: 90 - 92: 13.574 distance: 93 - 94: 21.380 distance: 94 - 95: 26.551 distance: 94 - 97: 23.851 distance: 95 - 96: 24.431 distance: 95 - 99: 14.216 distance: 96 - 120: 13.867 distance: 97 - 98: 28.714 distance: 99 - 100: 19.705 distance: 100 - 101: 18.849 distance: 100 - 103: 21.377 distance: 101 - 102: 4.409 distance: 102 - 128: 15.934 distance: 103 - 104: 27.737 distance: 104 - 105: 54.280 distance: 108 - 109: 38.310 distance: 108 - 111: 4.135 distance: 109 - 112: 4.527 distance: 112 - 113: 12.810 distance: 113 - 114: 12.412 distance: 113 - 116: 11.286 distance: 114 - 115: 20.072 distance: 114 - 120: 27.538 distance: 116 - 117: 32.620 distance: 117 - 118: 18.227 distance: 117 - 119: 25.244 distance: 120 - 121: 13.871 distance: 121 - 122: 15.378 distance: 121 - 124: 11.713 distance: 122 - 123: 31.988 distance: 122 - 128: 7.402 distance: 124 - 125: 26.117 distance: 124 - 126: 19.195 distance: 125 - 127: 24.352 distance: 128 - 129: 24.084 distance: 129 - 130: 23.625 distance: 129 - 132: 8.602 distance: 130 - 131: 27.525 distance: 130 - 138: 39.153 distance: 132 - 133: 20.354 distance: 133 - 134: 35.323 distance: 133 - 135: 11.339 distance: 134 - 136: 15.876 distance: 135 - 137: 32.750 distance: 136 - 137: 24.311 distance: 138 - 139: 18.719 distance: 139 - 140: 9.776 distance: 139 - 142: 9.529 distance: 140 - 141: 8.936 distance: 140 - 146: 10.396 distance: 142 - 143: 21.147