Starting phenix.real_space_refine (version: dev) on Wed May 18 08:08:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/05_2022/7alw_11820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/05_2022/7alw_11820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/05_2022/7alw_11820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/05_2022/7alw_11820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/05_2022/7alw_11820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/05_2022/7alw_11820.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 50148 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 26.61, per 1000 atoms: 0.53 Number of scatterers: 50148 At special positions: 0 Unit cell: (188.238, 189.882, 132.342, 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 162 16.00 O 9576 8.00 N 8442 7.00 C 31968 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 - 3.50 Amino acid : False - 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: 20.83 Conformation dependent library (CDL) restraints added in 7.0 seconds 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11592 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 72 sheets defined 45.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU B 497 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE B 533 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 555 " --> pdb=" O ARG B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU B 615 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG B 672 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU C 481 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU C 497 " --> pdb=" O HIS C 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR C 520 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C 538 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 555 " --> pdb=" O ARG C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA C 568 " --> pdb=" O SER C 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU C 615 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 621 No H-bonds generated for 'chain 'C' and resid 619 through 621' Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG C 672 " --> pdb=" O ARG C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU D 481 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU D 497 " --> pdb=" O HIS D 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS D 500 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE D 533 " --> pdb=" O TYR D 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU D 555 " --> pdb=" O ARG D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA D 568 " --> pdb=" O SER D 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU D 615 " --> pdb=" O ASP D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 637 through 649 Processing helix chain 'D' and resid 664 through 666 No H-bonds generated for 'chain 'D' and resid 664 through 666' Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.527A pdb=" N ARG D 672 " --> pdb=" O ARG D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU E 481 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG E 482 " --> pdb=" O GLU E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS E 500 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG E 506 " --> pdb=" O SER E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR E 520 " --> pdb=" O GLN E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE E 533 " --> pdb=" O TYR E 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG E 538 " --> pdb=" O LYS E 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG E 551 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU E 555 " --> pdb=" O ARG E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP E 572 " --> pdb=" O ALA E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR E 596 " --> pdb=" O ARG E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU E 615 " --> pdb=" O ASP E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 621 No H-bonds generated for 'chain 'E' and resid 619 through 621' Processing helix chain 'E' and resid 637 through 649 Processing helix chain 'E' and resid 664 through 666 No H-bonds generated for 'chain 'E' and resid 664 through 666' Processing helix chain 'E' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG E 672 " --> pdb=" O ARG E 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP F 404 " --> pdb=" O ALA F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU F 481 " --> pdb=" O VAL F 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU F 497 " --> pdb=" O HIS F 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS F 500 " --> pdb=" O VAL F 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG F 506 " --> pdb=" O SER F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG F 519 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR F 520 " --> pdb=" O GLN F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE F 533 " --> pdb=" O TYR F 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG F 538 " --> pdb=" O LYS F 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 555 removed outlier: 3.875A pdb=" N ARG F 551 " --> pdb=" O GLU F 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 555 " --> pdb=" O ARG F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA F 568 " --> pdb=" O SER F 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP F 572 " --> pdb=" O ALA F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR F 596 " --> pdb=" O ARG F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU F 615 " --> pdb=" O ASP F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 637 through 649 Processing helix chain 'F' and resid 664 through 666 No H-bonds generated for 'chain 'F' and resid 664 through 666' Processing helix chain 'F' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG F 672 " --> pdb=" O ARG F 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL G 397 " --> pdb=" O GLU G 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP G 404 " --> pdb=" O ALA G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 458 Processing helix chain 'G' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU G 481 " --> pdb=" O VAL G 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG G 482 " --> pdb=" O GLU G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU G 497 " --> pdb=" O HIS G 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 500 " --> pdb=" O VAL G 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 506 " --> pdb=" O SER G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG G 519 " --> pdb=" O ILE G 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR G 520 " --> pdb=" O GLN G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE G 533 " --> pdb=" O TYR G 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG G 538 " --> pdb=" O LYS G 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG G 551 " --> pdb=" O GLU G 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU G 555 " --> pdb=" O ARG G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA G 568 " --> pdb=" O SER G 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP G 572 " --> pdb=" O ALA G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR G 596 " --> pdb=" O ARG G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU G 615 " --> pdb=" O ASP G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 621 No H-bonds generated for 'chain 'G' and resid 619 through 621' Processing helix chain 'G' and resid 637 through 649 Processing helix chain 'G' and resid 664 through 666 No H-bonds generated for 'chain 'G' and resid 664 through 666' Processing helix chain 'G' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG G 672 " --> pdb=" O ARG G 668 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL H 397 " --> pdb=" O GLU H 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP H 404 " --> pdb=" O ALA H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 458 Processing helix chain 'H' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG H 482 " --> pdb=" O GLU H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU H 497 " --> pdb=" O HIS H 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS H 500 " --> pdb=" O VAL H 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG H 506 " --> pdb=" O SER H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG H 519 " --> pdb=" O ILE H 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR H 520 " --> pdb=" O GLN H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE H 533 " --> pdb=" O TYR H 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG H 538 " --> pdb=" O LYS H 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE H 539 " --> pdb=" O GLU H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG H 551 " --> pdb=" O GLU H 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 555 " --> pdb=" O ARG H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA H 568 " --> pdb=" O SER H 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP H 572 " --> pdb=" O ALA H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR H 596 " --> pdb=" O ARG H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU H 615 " --> pdb=" O ASP H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 621 No H-bonds generated for 'chain 'H' and resid 619 through 621' Processing helix chain 'H' and resid 637 through 649 Processing helix chain 'H' and resid 664 through 666 No H-bonds generated for 'chain 'H' and resid 664 through 666' Processing helix chain 'H' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG H 672 " --> pdb=" O ARG H 668 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL I 397 " --> pdb=" O GLU I 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP I 404 " --> pdb=" O ALA I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 458 Processing helix chain 'I' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU I 481 " --> pdb=" O VAL I 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG I 482 " --> pdb=" O GLU I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU I 497 " --> pdb=" O HIS I 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS I 500 " --> pdb=" O VAL I 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG I 506 " --> pdb=" O SER I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG I 519 " --> pdb=" O ILE I 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR I 520 " --> pdb=" O GLN I 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE I 533 " --> pdb=" O TYR I 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG I 538 " --> pdb=" O LYS I 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 539 " --> pdb=" O GLU I 535 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG I 551 " --> pdb=" O GLU I 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU I 555 " --> pdb=" O ARG I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA I 568 " --> pdb=" O SER I 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP I 572 " --> pdb=" O ALA I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR I 596 " --> pdb=" O ARG I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU I 615 " --> pdb=" O ASP I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 621 No H-bonds generated for 'chain 'I' and resid 619 through 621' Processing helix chain 'I' and resid 637 through 649 Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' Processing helix chain 'I' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG I 672 " --> pdb=" O ARG I 668 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL J 397 " --> pdb=" O GLU J 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP J 404 " --> pdb=" O ALA J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU J 481 " --> pdb=" O VAL J 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG J 482 " --> pdb=" O GLU J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU J 497 " --> pdb=" O HIS J 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS J 500 " --> pdb=" O VAL J 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG J 506 " --> pdb=" O SER J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG J 519 " --> pdb=" O ILE J 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR J 520 " --> pdb=" O GLN J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE J 533 " --> pdb=" O TYR J 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG J 538 " --> pdb=" O LYS J 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG J 551 " --> pdb=" O GLU J 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU J 555 " --> pdb=" O ARG J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA J 568 " --> pdb=" O SER J 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP J 572 " --> pdb=" O ALA J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR J 596 " --> pdb=" O ARG J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU J 615 " --> pdb=" O ASP J 611 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 621 No H-bonds generated for 'chain 'J' and resid 619 through 621' Processing helix chain 'J' and resid 637 through 649 Processing helix chain 'J' and resid 664 through 666 No H-bonds generated for 'chain 'J' and resid 664 through 666' Processing helix chain 'J' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG J 672 " --> pdb=" O ARG J 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL K 397 " --> pdb=" O GLU K 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP K 404 " --> pdb=" O ALA K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 458 Processing helix chain 'K' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU K 481 " --> pdb=" O VAL K 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG K 482 " --> pdb=" O GLU K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU K 497 " --> pdb=" O HIS K 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS K 500 " --> pdb=" O VAL K 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG K 506 " --> pdb=" O SER K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG K 519 " --> pdb=" O ILE K 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR K 520 " --> pdb=" O GLN K 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE K 533 " --> pdb=" O TYR K 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG K 538 " --> pdb=" O LYS K 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE K 539 " --> pdb=" O GLU K 535 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 555 removed outlier: 3.875A pdb=" N ARG K 551 " --> pdb=" O GLU K 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU K 555 " --> pdb=" O ARG K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA K 568 " --> pdb=" O SER K 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP K 572 " --> pdb=" O ALA K 568 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR K 596 " --> pdb=" O ARG K 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU K 615 " --> pdb=" O ASP K 611 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 621 No H-bonds generated for 'chain 'K' and resid 619 through 621' Processing helix chain 'K' and resid 637 through 649 Processing helix chain 'K' and resid 664 through 666 No H-bonds generated for 'chain 'K' and resid 664 through 666' Processing helix chain 'K' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG K 672 " --> pdb=" O ARG K 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL L 397 " --> pdb=" O GLU L 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP L 404 " --> pdb=" O ALA L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 458 Processing helix chain 'L' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU L 481 " --> pdb=" O VAL L 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG L 482 " --> pdb=" O GLU L 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU L 497 " --> pdb=" O HIS L 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS L 500 " --> pdb=" O VAL L 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG L 506 " --> pdb=" O SER L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG L 519 " --> pdb=" O ILE L 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR L 520 " --> pdb=" O GLN L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE L 533 " --> pdb=" O TYR L 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG L 538 " --> pdb=" O LYS L 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG L 551 " --> pdb=" O GLU L 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 555 " --> pdb=" O ARG L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA L 568 " --> pdb=" O SER L 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP L 572 " --> pdb=" O ALA L 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR L 596 " --> pdb=" O ARG L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU L 615 " --> pdb=" O ASP L 611 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 621 No H-bonds generated for 'chain 'L' and resid 619 through 621' Processing helix chain 'L' and resid 637 through 649 Processing helix chain 'L' and resid 664 through 666 No H-bonds generated for 'chain 'L' and resid 664 through 666' Processing helix chain 'L' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG L 672 " --> pdb=" O ARG L 668 " (cutoff:3.500A) Processing helix chain 'M' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL M 397 " --> pdb=" O GLU M 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP M 404 " --> pdb=" O ALA M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 458 Processing helix chain 'M' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU M 481 " --> pdb=" O VAL M 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG M 482 " --> pdb=" O GLU M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU M 497 " --> pdb=" O HIS M 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS M 500 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG M 506 " --> pdb=" O SER M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG M 519 " --> pdb=" O ILE M 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR M 520 " --> pdb=" O GLN M 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE M 533 " --> pdb=" O TYR M 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG M 538 " --> pdb=" O LYS M 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG M 551 " --> pdb=" O GLU M 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU M 555 " --> pdb=" O ARG M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA M 568 " --> pdb=" O SER M 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP M 572 " --> pdb=" O ALA M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER M 588 " --> pdb=" O GLU M 584 " (cutoff:3.500A) Processing helix chain 'M' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR M 596 " --> pdb=" O ARG M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 611 through 618 removed outlier: 3.732A pdb=" N GLU M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 621 No H-bonds generated for 'chain 'M' and resid 619 through 621' Processing helix chain 'M' and resid 637 through 649 Processing helix chain 'M' and resid 664 through 666 No H-bonds generated for 'chain 'M' and resid 664 through 666' Processing helix chain 'M' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG M 672 " --> pdb=" O ARG M 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 393 through 406 removed outlier: 3.622A pdb=" N VAL N 397 " --> pdb=" O GLU N 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP N 404 " --> pdb=" O ALA N 400 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 458 Processing helix chain 'N' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU N 481 " --> pdb=" O VAL N 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG N 482 " --> pdb=" O GLU N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU N 497 " --> pdb=" O HIS N 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS N 500 " --> pdb=" O VAL N 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG N 506 " --> pdb=" O SER N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG N 519 " --> pdb=" O ILE N 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR N 520 " --> pdb=" O GLN N 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE N 533 " --> pdb=" O TYR N 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG N 538 " --> pdb=" O LYS N 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE N 539 " --> pdb=" O GLU N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG N 551 " --> pdb=" O GLU N 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 555 " --> pdb=" O ARG N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA N 568 " --> pdb=" O SER N 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP N 572 " --> pdb=" O ALA N 568 " (cutoff:3.500A) Processing helix chain 'N' and resid 578 through 588 removed outlier: 3.531A pdb=" N SER N 588 " --> pdb=" O GLU N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR N 596 " --> pdb=" O ARG N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU N 615 " --> pdb=" O ASP N 611 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 621 No H-bonds generated for 'chain 'N' and resid 619 through 621' Processing helix chain 'N' and resid 637 through 649 Processing helix chain 'N' and resid 664 through 666 No H-bonds generated for 'chain 'N' and resid 664 through 666' Processing helix chain 'N' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG N 672 " --> pdb=" O ARG N 668 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL O 397 " --> pdb=" O GLU O 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP O 404 " --> pdb=" O ALA O 400 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 458 Processing helix chain 'O' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU O 481 " --> pdb=" O VAL O 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG O 482 " --> pdb=" O GLU O 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU O 497 " --> pdb=" O HIS O 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS O 500 " --> pdb=" O VAL O 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG O 506 " --> pdb=" O SER O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG O 519 " --> pdb=" O ILE O 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR O 520 " --> pdb=" O GLN O 516 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE O 533 " --> pdb=" O TYR O 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG O 538 " --> pdb=" O LYS O 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG O 551 " --> pdb=" O GLU O 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU O 555 " --> pdb=" O ARG O 551 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA O 568 " --> pdb=" O SER O 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP O 572 " --> pdb=" O ALA O 568 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER O 588 " --> pdb=" O GLU O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR O 596 " --> pdb=" O ARG O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU O 615 " --> pdb=" O ASP O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 621 No H-bonds generated for 'chain 'O' and resid 619 through 621' Processing helix chain 'O' and resid 637 through 649 Processing helix chain 'O' and resid 664 through 666 No H-bonds generated for 'chain 'O' and resid 664 through 666' Processing helix chain 'O' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG O 672 " --> pdb=" O ARG O 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL P 397 " --> pdb=" O GLU P 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP P 404 " --> pdb=" O ALA P 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 458 Processing helix chain 'P' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU P 481 " --> pdb=" O VAL P 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG P 482 " --> pdb=" O GLU P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU P 497 " --> pdb=" O HIS P 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS P 500 " --> pdb=" O VAL P 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG P 506 " --> pdb=" O SER P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG P 519 " --> pdb=" O ILE P 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR P 520 " --> pdb=" O GLN P 516 " (cutoff:3.500A) Processing helix chain 'P' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE P 533 " --> pdb=" O TYR P 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG P 538 " --> pdb=" O LYS P 534 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE P 539 " --> pdb=" O GLU P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG P 551 " --> pdb=" O GLU P 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU P 555 " --> pdb=" O ARG P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA P 568 " --> pdb=" O SER P 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP P 572 " --> pdb=" O ALA P 568 " (cutoff:3.500A) Processing helix chain 'P' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER P 588 " --> pdb=" O GLU P 584 " (cutoff:3.500A) Processing helix chain 'P' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR P 596 " --> pdb=" O ARG P 592 " (cutoff:3.500A) Processing helix chain 'P' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU P 615 " --> pdb=" O ASP P 611 " (cutoff:3.500A) Processing helix chain 'P' and resid 619 through 621 No H-bonds generated for 'chain 'P' and resid 619 through 621' Processing helix chain 'P' and resid 637 through 649 Processing helix chain 'P' and resid 664 through 666 No H-bonds generated for 'chain 'P' and resid 664 through 666' Processing helix chain 'P' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG P 672 " --> pdb=" O ARG P 668 " (cutoff:3.500A) Processing helix chain 'Q' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL Q 397 " --> pdb=" O GLU Q 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP Q 404 " --> pdb=" O ALA Q 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 453 through 458 Processing helix chain 'Q' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU Q 481 " --> pdb=" O VAL Q 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG Q 482 " --> pdb=" O GLU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 508 removed outlier: 3.652A pdb=" N LEU Q 497 " --> pdb=" O HIS Q 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS Q 500 " --> pdb=" O VAL Q 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG Q 506 " --> pdb=" O SER Q 502 " (cutoff:3.500A) Processing helix chain 'Q' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG Q 519 " --> pdb=" O ILE Q 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR Q 520 " --> pdb=" O GLN Q 516 " (cutoff:3.500A) Processing helix chain 'Q' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE Q 533 " --> pdb=" O TYR Q 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG Q 538 " --> pdb=" O LYS Q 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE Q 539 " --> pdb=" O GLU Q 535 " (cutoff:3.500A) Processing helix chain 'Q' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG Q 551 " --> pdb=" O GLU Q 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU Q 555 " --> pdb=" O ARG Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA Q 568 " --> pdb=" O SER Q 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP Q 572 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) Processing helix chain 'Q' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER Q 588 " --> pdb=" O GLU Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR Q 596 " --> pdb=" O ARG Q 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU Q 615 " --> pdb=" O ASP Q 611 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 621 No H-bonds generated for 'chain 'Q' and resid 619 through 621' Processing helix chain 'Q' and resid 637 through 649 Processing helix chain 'Q' and resid 664 through 666 No H-bonds generated for 'chain 'Q' and resid 664 through 666' Processing helix chain 'Q' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG Q 672 " --> pdb=" O ARG Q 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL R 397 " --> pdb=" O GLU R 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP R 404 " --> pdb=" O ALA R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 453 through 458 Processing helix chain 'R' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU R 481 " --> pdb=" O VAL R 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG R 482 " --> pdb=" O GLU R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU R 497 " --> pdb=" O HIS R 493 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS R 500 " --> pdb=" O VAL R 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG R 506 " --> pdb=" O SER R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG R 519 " --> pdb=" O ILE R 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR R 520 " --> pdb=" O GLN R 516 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE R 533 " --> pdb=" O TYR R 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG R 538 " --> pdb=" O LYS R 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE R 539 " --> pdb=" O GLU R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG R 551 " --> pdb=" O GLU R 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU R 555 " --> pdb=" O ARG R 551 " (cutoff:3.500A) Processing helix chain 'R' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA R 568 " --> pdb=" O SER R 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP R 572 " --> pdb=" O ALA R 568 " (cutoff:3.500A) Processing helix chain 'R' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER R 588 " --> pdb=" O GLU R 584 " (cutoff:3.500A) Processing helix chain 'R' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR R 596 " --> pdb=" O ARG R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU R 615 " --> pdb=" O ASP R 611 " (cutoff:3.500A) Processing helix chain 'R' and resid 619 through 621 No H-bonds generated for 'chain 'R' and resid 619 through 621' Processing helix chain 'R' and resid 637 through 649 Processing helix chain 'R' and resid 664 through 666 No H-bonds generated for 'chain 'R' and resid 664 through 666' Processing helix chain 'R' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG R 672 " --> pdb=" O ARG R 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU A 373 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 375 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN A 417 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL A 377 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A 424 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR A 425 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A 436 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 427 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG A 447 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 491 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 604 through 605 Processing sheet with id=AA4, first strand: chain 'A' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU A 661 " --> pdb=" O LEU A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU B 373 " --> pdb=" O HIS B 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG B 415 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 375 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN B 417 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL B 377 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU B 424 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR B 425 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 436 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 427 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG B 447 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 491 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AA8, first strand: chain 'B' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU B 661 " --> pdb=" O LEU B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU C 373 " --> pdb=" O HIS C 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG C 415 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE C 375 " --> pdb=" O ARG C 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN C 417 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL C 377 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU C 424 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR C 425 " --> pdb=" O ARG C 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG C 436 " --> pdb=" O TYR C 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 427 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG C 447 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 491 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 604 through 605 Processing sheet with id=AB3, first strand: chain 'C' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU C 661 " --> pdb=" O LEU C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU D 373 " --> pdb=" O HIS D 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG D 415 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 375 " --> pdb=" O ARG D 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 417 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL D 377 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU D 424 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR D 425 " --> pdb=" O ARG D 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG D 436 " --> pdb=" O TYR D 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 427 " --> pdb=" O VAL D 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG D 447 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 491 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 604 through 605 Processing sheet with id=AB7, first strand: chain 'D' and resid 661 through 662 removed outlier: 6.967A pdb=" N LEU D 661 " --> pdb=" O LEU D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU E 373 " --> pdb=" O HIS E 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG E 415 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE E 375 " --> pdb=" O ARG E 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN E 417 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL E 377 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU E 424 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR E 425 " --> pdb=" O ARG E 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG E 436 " --> pdb=" O TYR E 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 427 " --> pdb=" O VAL E 434 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG E 447 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 491 " --> pdb=" O ARG E 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 604 through 605 Processing sheet with id=AC2, first strand: chain 'E' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU E 661 " --> pdb=" O LEU E 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU F 373 " --> pdb=" O HIS F 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG F 415 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE F 375 " --> pdb=" O ARG F 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN F 417 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL F 377 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU F 424 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR F 425 " --> pdb=" O ARG F 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 436 " --> pdb=" O TYR F 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE F 427 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG F 447 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE F 491 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 604 through 605 Processing sheet with id=AC6, first strand: chain 'F' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU F 661 " --> pdb=" O LEU F 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU G 373 " --> pdb=" O HIS G 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG G 415 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE G 375 " --> pdb=" O ARG G 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN G 417 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL G 377 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU G 424 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR G 425 " --> pdb=" O ARG G 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG G 436 " --> pdb=" O TYR G 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE G 427 " --> pdb=" O VAL G 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG G 447 " --> pdb=" O PHE G 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE G 491 " --> pdb=" O ARG G 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 604 through 605 Processing sheet with id=AD1, first strand: chain 'G' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU G 661 " --> pdb=" O LEU G 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU H 373 " --> pdb=" O HIS H 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG H 415 " --> pdb=" O LEU H 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE H 375 " --> pdb=" O ARG H 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN H 417 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL H 377 " --> pdb=" O ASN H 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU H 424 " --> pdb=" O ASP H 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR H 425 " --> pdb=" O ARG H 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG H 436 " --> pdb=" O TYR H 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE H 427 " --> pdb=" O VAL H 434 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG H 447 " --> pdb=" O PHE H 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE H 491 " --> pdb=" O ARG H 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 604 through 605 Processing sheet with id=AD5, first strand: chain 'H' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU H 661 " --> pdb=" O LEU H 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU I 373 " --> pdb=" O HIS I 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG I 415 " --> pdb=" O LEU I 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE I 375 " --> pdb=" O ARG I 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN I 417 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL I 377 " --> pdb=" O ASN I 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU I 424 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR I 425 " --> pdb=" O ARG I 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG I 436 " --> pdb=" O TYR I 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE I 427 " --> pdb=" O VAL I 434 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG I 447 " --> pdb=" O PHE I 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE I 491 " --> pdb=" O ARG I 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 604 through 605 Processing sheet with id=AD9, first strand: chain 'I' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU I 661 " --> pdb=" O LEU I 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU J 373 " --> pdb=" O HIS J 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG J 415 " --> pdb=" O LEU J 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE J 375 " --> pdb=" O ARG J 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN J 417 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL J 377 " --> pdb=" O ASN J 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU J 424 " --> pdb=" O ASP J 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR J 425 " --> pdb=" O ARG J 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG J 436 " --> pdb=" O TYR J 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE J 427 " --> pdb=" O VAL J 434 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG J 447 " --> pdb=" O PHE J 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE J 491 " --> pdb=" O ARG J 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 604 through 605 Processing sheet with id=AE4, first strand: chain 'J' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU J 661 " --> pdb=" O LEU J 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU K 373 " --> pdb=" O HIS K 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG K 415 " --> pdb=" O LEU K 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE K 375 " --> pdb=" O ARG K 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN K 417 " --> pdb=" O ILE K 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL K 377 " --> pdb=" O ASN K 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU K 424 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR K 425 " --> pdb=" O ARG K 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG K 436 " --> pdb=" O TYR K 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE K 427 " --> pdb=" O VAL K 434 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG K 447 " --> pdb=" O PHE K 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE K 491 " --> pdb=" O ARG K 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 604 through 605 Processing sheet with id=AE8, first strand: chain 'K' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU K 661 " --> pdb=" O LEU K 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU L 373 " --> pdb=" O HIS L 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG L 415 " --> pdb=" O LEU L 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE L 375 " --> pdb=" O ARG L 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN L 417 " --> pdb=" O ILE L 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL L 377 " --> pdb=" O ASN L 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU L 424 " --> pdb=" O ASP L 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR L 425 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG L 436 " --> pdb=" O TYR L 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE L 427 " --> pdb=" O VAL L 434 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG L 447 " --> pdb=" O PHE L 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE L 491 " --> pdb=" O ARG L 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 604 through 605 Processing sheet with id=AF3, first strand: chain 'L' and resid 661 through 662 removed outlier: 6.967A pdb=" N LEU L 661 " --> pdb=" O LEU L 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU M 373 " --> pdb=" O HIS M 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE M 375 " --> pdb=" O ARG M 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN M 417 " --> pdb=" O ILE M 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL M 377 " --> pdb=" O ASN M 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU M 424 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR M 425 " --> pdb=" O ARG M 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG M 436 " --> pdb=" O TYR M 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE M 427 " --> pdb=" O VAL M 434 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG M 447 " --> pdb=" O PHE M 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE M 491 " --> pdb=" O ARG M 447 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 604 through 605 Processing sheet with id=AF7, first strand: chain 'M' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU M 661 " --> pdb=" O LEU M 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU N 373 " --> pdb=" O HIS N 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG N 415 " --> pdb=" O LEU N 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE N 375 " --> pdb=" O ARG N 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN N 417 " --> pdb=" O ILE N 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL N 377 " --> pdb=" O ASN N 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU N 424 " --> pdb=" O ASP N 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR N 425 " --> pdb=" O ARG N 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG N 436 " --> pdb=" O TYR N 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE N 427 " --> pdb=" O VAL N 434 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG N 447 " --> pdb=" O PHE N 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE N 491 " --> pdb=" O ARG N 447 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 604 through 605 Processing sheet with id=AG2, first strand: chain 'N' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU N 661 " --> pdb=" O LEU N 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU O 373 " --> pdb=" O HIS O 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG O 415 " --> pdb=" O LEU O 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE O 375 " --> pdb=" O ARG O 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN O 417 " --> pdb=" O ILE O 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL O 377 " --> pdb=" O ASN O 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU O 424 " --> pdb=" O ASP O 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR O 425 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG O 436 " --> pdb=" O TYR O 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE O 427 " --> pdb=" O VAL O 434 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG O 447 " --> pdb=" O PHE O 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE O 491 " --> pdb=" O ARG O 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 604 through 605 Processing sheet with id=AG6, first strand: chain 'O' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU O 661 " --> pdb=" O LEU O 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'P' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU P 373 " --> pdb=" O HIS P 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG P 415 " --> pdb=" O LEU P 373 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE P 375 " --> pdb=" O ARG P 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN P 417 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL P 377 " --> pdb=" O ASN P 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 424 " --> pdb=" O ASP P 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR P 425 " --> pdb=" O ARG P 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG P 436 " --> pdb=" O TYR P 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE P 427 " --> pdb=" O VAL P 434 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG P 447 " --> pdb=" O PHE P 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE P 491 " --> pdb=" O ARG P 447 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 604 through 605 Processing sheet with id=AH1, first strand: chain 'P' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU P 661 " --> pdb=" O LEU P 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'Q' and resid 412 through 417 removed outlier: 7.022A pdb=" N LEU Q 373 " --> pdb=" O HIS Q 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG Q 415 " --> pdb=" O LEU Q 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE Q 375 " --> pdb=" O ARG Q 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN Q 417 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL Q 377 " --> pdb=" O ASN Q 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU Q 424 " --> pdb=" O ASP Q 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR Q 425 " --> pdb=" O ARG Q 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG Q 436 " --> pdb=" O TYR Q 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE Q 427 " --> pdb=" O VAL Q 434 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG Q 447 " --> pdb=" O PHE Q 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE Q 491 " --> pdb=" O ARG Q 447 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 604 through 605 Processing sheet with id=AH5, first strand: chain 'Q' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU Q 661 " --> pdb=" O LEU Q 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'R' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU R 373 " --> pdb=" O HIS R 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG R 415 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE R 375 " --> pdb=" O ARG R 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN R 417 " --> pdb=" O ILE R 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL R 377 " --> pdb=" O ASN R 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU R 424 " --> pdb=" O ASP R 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR R 425 " --> pdb=" O ARG R 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG R 436 " --> pdb=" O TYR R 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE R 427 " --> pdb=" O VAL R 434 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG R 447 " --> pdb=" O PHE R 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE R 491 " --> pdb=" O ARG R 447 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 604 through 605 Processing sheet with id=AH9, first strand: chain 'R' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU R 661 " --> pdb=" O LEU R 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 1584 hydrogen bonds defined for protein. 4698 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: 20.06 Time building geometry restraints manager: 22.05 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: 16786 1.34 - 1.46: 9349 1.46 - 1.57: 24589 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 51012 Sorted by residual: bond pdb=" CB VAL Q 553 " pdb=" CG2 VAL Q 553 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CB VAL E 553 " pdb=" CG2 VAL E 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB VAL D 553 " pdb=" CG2 VAL D 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB VAL A 553 " pdb=" CG2 VAL A 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB VAL M 553 " pdb=" CG2 VAL M 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 ... (remaining 51007 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.40: 810 105.40 - 112.54: 26379 112.54 - 119.68: 17778 119.68 - 126.82: 23542 126.82 - 133.96: 485 Bond angle restraints: 68994 Sorted by residual: angle pdb=" N ALA D 441 " pdb=" CA ALA D 441 " pdb=" C ALA D 441 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" N ALA N 441 " pdb=" CA ALA N 441 " pdb=" C ALA N 441 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" N ALA B 441 " pdb=" CA ALA B 441 " pdb=" C ALA B 441 " ideal model delta sigma weight residual 113.15 107.91 5.24 1.19e+00 7.06e-01 1.94e+01 angle pdb=" N ALA P 441 " pdb=" CA ALA P 441 " pdb=" C ALA P 441 " ideal model delta sigma weight residual 113.15 107.92 5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" N ALA C 441 " pdb=" CA ALA C 441 " pdb=" C ALA C 441 " ideal model delta sigma weight residual 113.15 107.92 5.23 1.19e+00 7.06e-01 1.93e+01 ... (remaining 68989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 27073 16.90 - 33.80: 3238 33.80 - 50.69: 618 50.69 - 67.59: 139 67.59 - 84.49: 90 Dihedral angle restraints: 31158 sinusoidal: 13068 harmonic: 18090 Sorted by residual: dihedral pdb=" CA LEU J 385 " pdb=" C LEU J 385 " pdb=" N GLU J 386 " pdb=" CA GLU J 386 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU K 385 " pdb=" C LEU K 385 " pdb=" N GLU K 386 " pdb=" CA GLU K 386 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU A 385 " pdb=" C LEU A 385 " pdb=" N GLU A 386 " pdb=" CA GLU A 386 " ideal model delta harmonic sigma weight residual 180.00 137.66 42.34 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 31155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4416 0.041 - 0.083: 2567 0.083 - 0.124: 601 0.124 - 0.165: 138 0.165 - 0.207: 36 Chirality restraints: 7758 Sorted by residual: chirality pdb=" CA ILE M 458 " pdb=" N ILE M 458 " pdb=" C ILE M 458 " pdb=" CB ILE M 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE Q 458 " pdb=" N ILE Q 458 " pdb=" C ILE Q 458 " pdb=" CB ILE Q 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE D 458 " pdb=" N ILE D 458 " pdb=" C ILE D 458 " pdb=" CB ILE D 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 7755 not shown) Planarity restraints: 8928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 639 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" CD GLU D 639 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU D 639 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 639 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 639 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" CD GLU K 639 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU K 639 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU K 639 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 639 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" CD GLU C 639 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU C 639 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 639 " 0.009 2.00e-02 2.50e+03 ... (remaining 8925 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3031 2.70 - 3.25: 53341 3.25 - 3.80: 78002 3.80 - 4.35: 100259 4.35 - 4.90: 165771 Nonbonded interactions: 400404 Sorted by model distance: nonbonded pdb=" O LEU B 385 " pdb=" N ALA B 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU D 385 " pdb=" N ALA D 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU I 385 " pdb=" N ALA I 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU L 385 " pdb=" N ALA L 387 " model vdw 2.150 2.520 nonbonded pdb=" O LEU N 385 " pdb=" N ALA N 387 " model vdw 2.151 2.520 ... (remaining 400399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 31968 2.51 5 N 8442 2.21 5 O 9576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.960 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: 0.040 Extract box with map and model: 32.450 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.420 Process input model: 130.630 Find NCS groups from input model: 3.700 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.010 0.056 51012 Z= 0.638 Angle : 0.960 10.433 68994 Z= 0.529 Chirality : 0.052 0.207 7758 Planarity : 0.004 0.036 8928 Dihedral : 15.639 84.488 19566 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.33 % Favored : 82.37 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.45 (0.07), residues: 6156 helix: -4.69 (0.05), residues: 2736 sheet: -3.48 (0.17), residues: 558 loop : -3.96 (0.09), residues: 2862 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 831 time to evaluate : 6.342 Fit side-chains outliers start: 54 outliers final: 0 residues processed: 850 average time/residue: 0.5857 time to fit residues: 827.9753 Evaluate side-chains 507 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 6.244 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 0.9990 chunk 463 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 479 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 357 optimal weight: 0.9980 chunk 555 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS A 561 ASN B 465 HIS B 561 ASN C 465 HIS C 561 ASN D 465 HIS D 561 ASN E 465 HIS ** E 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS F 561 ASN G 465 HIS G 561 ASN G 600 ASN H 465 HIS H 561 ASN I 465 HIS I 561 ASN J 465 HIS J 561 ASN J 600 ASN K 465 HIS K 561 ASN L 465 HIS L 561 ASN M 465 HIS M 561 ASN N 465 HIS N 561 ASN O 465 HIS O 561 ASN P 465 HIS P 561 ASN Q 465 HIS Q 561 ASN R 465 HIS R 561 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 51012 Z= 0.190 Angle : 0.714 11.930 68994 Z= 0.359 Chirality : 0.046 0.216 7758 Planarity : 0.004 0.036 8928 Dihedral : 6.685 39.571 6912 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.75 % Favored : 88.95 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.80 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.09), residues: 6156 helix: -3.04 (0.08), residues: 2862 sheet: -2.79 (0.17), residues: 468 loop : -3.41 (0.11), residues: 2826 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 690 time to evaluate : 6.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 80 residues processed: 790 average time/residue: 0.5522 time to fit residues: 760.1945 Evaluate side-chains 577 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 497 time to evaluate : 6.222 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 8 residues processed: 80 average time/residue: 0.4248 time to fit residues: 73.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 0.8980 chunk 172 optimal weight: 0.0980 chunk 462 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 556 optimal weight: 7.9990 chunk 601 optimal weight: 2.9990 chunk 495 optimal weight: 1.9990 chunk 552 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 446 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS D 452 GLN E 561 ASN G 452 GLN I 500 HIS L 500 HIS M 500 HIS R 452 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 51012 Z= 0.211 Angle : 0.662 11.167 68994 Z= 0.332 Chirality : 0.046 0.184 7758 Planarity : 0.004 0.047 8928 Dihedral : 6.234 38.345 6912 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.18 % Favored : 88.53 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.72 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.09), residues: 6156 helix: -2.42 (0.08), residues: 2880 sheet: -2.44 (0.18), residues: 486 loop : -3.11 (0.11), residues: 2790 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 645 time to evaluate : 7.079 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 41 residues processed: 724 average time/residue: 0.5481 time to fit residues: 687.4560 Evaluate side-chains 544 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 503 time to evaluate : 6.377 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4359 time to fit residues: 41.9593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 0.9980 chunk 418 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 558 optimal weight: 3.9990 chunk 591 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 529 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 500 HIS C 500 HIS D 452 GLN E 500 HIS G 452 GLN H 500 HIS J 452 GLN J 500 HIS K 500 HIS N 500 HIS O 500 HIS P 500 HIS Q 500 HIS R 452 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 51012 Z= 0.305 Angle : 0.713 11.055 68994 Z= 0.355 Chirality : 0.048 0.261 7758 Planarity : 0.004 0.057 8928 Dihedral : 6.194 38.131 6912 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.39 % Favored : 88.32 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.09), residues: 6156 helix: -2.20 (0.08), residues: 2898 sheet: -2.30 (0.19), residues: 486 loop : -3.17 (0.11), residues: 2772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 543 time to evaluate : 6.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 69 residues processed: 657 average time/residue: 0.5324 time to fit residues: 613.5770 Evaluate side-chains 533 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 464 time to evaluate : 6.244 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.4159 time to fit residues: 63.6552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 440 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 504 optimal weight: 6.9990 chunk 408 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 530 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS E 465 HIS ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 HIS G 465 HIS H 465 HIS ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 HIS K 381 GLN K 465 HIS ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 HIS O 465 HIS P 465 HIS Q 465 HIS ** R 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 51012 Z= 0.261 Angle : 0.694 11.185 68994 Z= 0.344 Chirality : 0.048 0.258 7758 Planarity : 0.004 0.064 8928 Dihedral : 6.035 37.295 6912 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.01 % Favored : 88.69 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.80 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.09), residues: 6156 helix: -1.92 (0.09), residues: 2952 sheet: -1.47 (0.25), residues: 306 loop : -3.15 (0.10), residues: 2898 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 555 time to evaluate : 6.736 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 35 residues processed: 647 average time/residue: 0.5403 time to fit residues: 619.9969 Evaluate side-chains 497 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 462 time to evaluate : 6.780 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4577 time to fit residues: 38.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 6.9990 chunk 532 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 347 optimal weight: 0.1980 chunk 146 optimal weight: 7.9990 chunk 592 optimal weight: 1.9990 chunk 491 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 195 optimal weight: 0.2980 chunk 310 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS B 465 HIS D 452 GLN D 465 HIS F 465 HIS G 452 GLN I 465 HIS J 452 GLN L 465 HIS M 465 HIS R 452 GLN R 465 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 51012 Z= 0.170 Angle : 0.665 11.381 68994 Z= 0.332 Chirality : 0.046 0.264 7758 Planarity : 0.004 0.067 8928 Dihedral : 5.655 36.272 6912 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.01 % Favored : 89.70 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.10), residues: 6156 helix: -1.38 (0.09), residues: 2916 sheet: -1.55 (0.19), residues: 666 loop : -3.33 (0.11), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 602 time to evaluate : 6.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 47 residues processed: 667 average time/residue: 0.5745 time to fit residues: 656.4081 Evaluate side-chains 541 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 494 time to evaluate : 6.358 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4206 time to fit residues: 46.6866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 337 optimal weight: 4.9990 chunk 432 optimal weight: 0.0670 chunk 335 optimal weight: 3.9990 chunk 498 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 589 optimal weight: 10.0000 chunk 369 optimal weight: 0.3980 chunk 359 optimal weight: 0.7980 chunk 272 optimal weight: 10.0000 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 381 GLN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 ASN ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 381 GLN ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 452 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 51012 Z= 0.174 Angle : 0.674 11.041 68994 Z= 0.335 Chirality : 0.045 0.243 7758 Planarity : 0.004 0.073 8928 Dihedral : 5.511 34.818 6912 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.14 % Favored : 89.57 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.31 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 6156 helix: -0.94 (0.09), residues: 2916 sheet: -1.34 (0.19), residues: 666 loop : -3.23 (0.11), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 542 time to evaluate : 6.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 43 residues processed: 590 average time/residue: 0.5500 time to fit residues: 569.9802 Evaluate side-chains 542 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 499 time to evaluate : 6.374 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4887 time to fit residues: 48.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 177 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 375 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 463 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN E 417 ASN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 51012 Z= 0.279 Angle : 0.716 11.936 68994 Z= 0.357 Chirality : 0.047 0.240 7758 Planarity : 0.005 0.083 8928 Dihedral : 5.669 36.256 6912 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.41 % Favored : 89.29 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.10), residues: 6156 helix: -1.00 (0.09), residues: 2970 sheet: -1.25 (0.19), residues: 666 loop : -3.13 (0.12), residues: 2520 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 512 time to evaluate : 6.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 544 average time/residue: 0.5426 time to fit residues: 516.2922 Evaluate side-chains 514 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 483 time to evaluate : 6.055 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4316 time to fit residues: 33.6151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 0.2980 chunk 565 optimal weight: 3.9990 chunk 515 optimal weight: 0.0470 chunk 549 optimal weight: 9.9990 chunk 564 optimal weight: 0.9980 chunk 330 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 chunk 431 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 496 optimal weight: 2.9990 chunk 519 optimal weight: 20.0000 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 51012 Z= 0.206 Angle : 0.701 12.737 68994 Z= 0.348 Chirality : 0.046 0.245 7758 Planarity : 0.005 0.099 8928 Dihedral : 5.490 36.415 6912 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.96 % Favored : 89.75 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.10), residues: 6156 helix: -0.44 (0.10), residues: 2808 sheet: -1.12 (0.20), residues: 666 loop : -3.21 (0.11), residues: 2682 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 504 time to evaluate : 6.340 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 28 residues processed: 531 average time/residue: 0.5416 time to fit residues: 504.2143 Evaluate side-chains 506 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 478 time to evaluate : 6.208 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4464 time to fit residues: 32.2719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 0.9980 chunk 360 optimal weight: 1.9990 chunk 581 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 404 optimal weight: 0.9990 chunk 609 optimal weight: 4.9990 chunk 561 optimal weight: 5.9990 chunk 485 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 375 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 381 GLN ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 51012 Z= 0.274 Angle : 0.748 11.985 68994 Z= 0.370 Chirality : 0.047 0.245 7758 Planarity : 0.005 0.099 8928 Dihedral : 5.598 35.201 6912 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.64 % Favored : 89.07 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 6156 helix: -0.54 (0.09), residues: 2862 sheet: -1.74 (0.19), residues: 756 loop : -3.15 (0.12), residues: 2538 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 488 time to evaluate : 6.291 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 495 average time/residue: 0.5609 time to fit residues: 485.2081 Evaluate side-chains 496 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 480 time to evaluate : 6.215 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4296 time to fit residues: 21.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 0.7980 chunk 385 optimal weight: 5.9990 chunk 517 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 447 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 486 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 499 optimal weight: 0.0670 chunk 61 optimal weight: 10.0000 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 GLN ** G 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 381 GLN L 452 GLN ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 452 GLN ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 452 GLN ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107000 restraints weight = 82171.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109642 restraints weight = 51497.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111464 restraints weight = 37418.006| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 51012 Z= 0.219 Angle : 0.727 14.489 68994 Z= 0.358 Chirality : 0.046 0.247 7758 Planarity : 0.005 0.110 8928 Dihedral : 5.430 35.569 6912 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.15 % Favored : 89.55 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.10), residues: 6156 helix: -0.34 (0.10), residues: 2826 sheet: -0.46 (0.24), residues: 486 loop : -3.15 (0.11), residues: 2844 =============================================================================== Job complete usr+sys time: 10991.87 seconds wall clock time: 199 minutes 30.13 seconds (11970.13 seconds total)