Starting phenix.real_space_refine on Mon Sep 23 13:01:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/09_2024/8p2m_17370.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/09_2024/8p2m_17370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/09_2024/8p2m_17370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/09_2024/8p2m_17370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/09_2024/8p2m_17370.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2m_17370/09_2024/8p2m_17370.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 307 5.16 5 C 29840 2.51 5 N 7918 2.21 5 O 8637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 261 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 46702 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5286 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 21, 'TRANS': 637} Chain: "B" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 5177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5177 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 20.94, per 1000 atoms: 0.45 Number of scatterers: 46702 At special positions: 0 Unit cell: (196.56, 194.04, 198.24, 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 307 16.00 O 8637 8.00 N 7918 7.00 C 29840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.55 Conformation dependent library (CDL) restraints added in 4.4 seconds 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11278 Finding SS restraints... Secondary structure from input PDB file: 413 helices and 9 sheets defined 80.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 195 through 226 Processing helix chain 'A' and resid 228 through 248 Processing helix chain 'A' and resid 252 through 267 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.775A pdb=" N ARG A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.644A pdb=" N GLU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.624A pdb=" N HIS A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.694A pdb=" N VAL A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 448 " --> pdb=" O MET A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 455 through 468 removed outlier: 5.638A pdb=" N LYS A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 511 through 517 removed outlier: 4.142A pdb=" N GLN A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.965A pdb=" N ALA A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 561 through 572 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.975A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.525A pdb=" N LEU A 599 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 625 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.542A pdb=" N LEU A 663 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 664 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 679 through 693 removed outlier: 4.090A pdb=" N THR A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 removed outlier: 3.857A pdb=" N LYS A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 removed outlier: 4.183A pdb=" N ASN A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 772 through 776 Processing helix chain 'A' and resid 783 through 796 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 835 through 848 Processing helix chain 'B' and resid 195 through 226 Processing helix chain 'B' and resid 228 through 248 Processing helix chain 'B' and resid 252 through 267 Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 285 through 300 removed outlier: 3.767A pdb=" N ARG B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.686A pdb=" N HIS B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.585A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 412 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.848A pdb=" N LEU B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 455 through 468 removed outlier: 3.560A pdb=" N ASP B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 511 through 517 removed outlier: 4.079A pdb=" N GLN B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.953A pdb=" N ALA B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 removed outlier: 3.541A pdb=" N GLY B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 Processing helix chain 'B' and resid 561 through 572 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 577 through 584 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 595 through 602 Processing helix chain 'B' and resid 607 through 625 Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 644 through 648 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 661 through 666 removed outlier: 4.163A pdb=" N SER B 664 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 666 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.572A pdb=" N ALA B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 733 Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.946A pdb=" N LEU B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 776 Processing helix chain 'B' and resid 783 through 795 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 820 through 826 Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 835 through 849 Processing helix chain 'C' and resid 195 through 226 Processing helix chain 'C' and resid 228 through 249 Processing helix chain 'C' and resid 252 through 267 Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 285 through 300 removed outlier: 3.784A pdb=" N ARG C 289 " --> pdb=" O CYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.586A pdb=" N SER C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.654A pdb=" N HIS C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 388 Processing helix chain 'C' and resid 390 through 400 removed outlier: 3.646A pdb=" N LYS C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 412 Processing helix chain 'C' and resid 414 through 430 Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 434 through 442 Processing helix chain 'C' and resid 442 through 453 removed outlier: 3.938A pdb=" N LEU C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 448 " --> pdb=" O MET C 444 " (cutoff:3.500A) Proline residue: C 449 - end of helix Processing helix chain 'C' and resid 455 through 468 removed outlier: 5.581A pdb=" N LYS C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 511 through 517 removed outlier: 4.089A pdb=" N GLN C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 529 removed outlier: 3.974A pdb=" N ALA C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 561 through 572 Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 577 through 584 Processing helix chain 'C' and resid 589 through 594 Processing helix chain 'C' and resid 595 through 602 Processing helix chain 'C' and resid 607 through 625 Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 649 through 656 Processing helix chain 'C' and resid 659 through 666 removed outlier: 3.543A pdb=" N LEU C 663 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER C 664 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 675 Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 719 through 733 Processing helix chain 'C' and resid 751 through 760 removed outlier: 3.836A pdb=" N LYS C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 776 Processing helix chain 'C' and resid 783 through 795 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 820 through 826 removed outlier: 3.726A pdb=" N THR C 824 " --> pdb=" O ARG C 821 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 826 " --> pdb=" O ILE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 849 removed outlier: 3.954A pdb=" N MET C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C 843 " --> pdb=" O CYS C 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 225 Processing helix chain 'D' and resid 228 through 248 Processing helix chain 'D' and resid 252 through 267 Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.781A pdb=" N ARG D 289 " --> pdb=" O CYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 327 through 342 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.561A pdb=" N GLU D 354 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.633A pdb=" N HIS D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 388 Processing helix chain 'D' and resid 390 through 400 removed outlier: 3.657A pdb=" N LYS D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'D' and resid 414 through 430 Processing helix chain 'D' and resid 434 through 442 Processing helix chain 'D' and resid 442 through 453 removed outlier: 3.956A pdb=" N LEU D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU D 448 " --> pdb=" O MET D 444 " (cutoff:3.500A) Proline residue: D 449 - end of helix Processing helix chain 'D' and resid 455 through 468 removed outlier: 3.690A pdb=" N ASP D 462 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS D 465 " --> pdb=" O ARG D 461 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 511 through 517 removed outlier: 4.087A pdb=" N GLN D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 529 removed outlier: 3.863A pdb=" N ALA D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 546 Processing helix chain 'D' and resid 556 through 560 Processing helix chain 'D' and resid 561 through 572 Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 577 through 584 Processing helix chain 'D' and resid 589 through 594 Processing helix chain 'D' and resid 595 through 602 Processing helix chain 'D' and resid 607 through 625 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 644 through 648 Processing helix chain 'D' and resid 649 through 656 Processing helix chain 'D' and resid 661 through 666 removed outlier: 3.985A pdb=" N SER D 664 " --> pdb=" O SER D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 679 through 693 removed outlier: 3.576A pdb=" N ALA D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 733 removed outlier: 3.711A pdb=" N ASN D 720 " --> pdb=" O ARG D 716 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN D 721 " --> pdb=" O SER D 717 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 759 Processing helix chain 'D' and resid 771 through 776 Processing helix chain 'D' and resid 783 through 795 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 820 through 826 Processing helix chain 'D' and resid 832 through 834 No H-bonds generated for 'chain 'D' and resid 832 through 834' Processing helix chain 'D' and resid 835 through 849 Processing helix chain 'E' and resid 195 through 225 Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 252 through 267 Processing helix chain 'E' and resid 268 through 279 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 285 through 300 removed outlier: 3.754A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 313 through 324 Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 345 through 354 removed outlier: 3.560A pdb=" N GLU E 354 " --> pdb=" O LEU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 368 removed outlier: 3.578A pdb=" N HIS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 388 Processing helix chain 'E' and resid 390 through 400 removed outlier: 3.653A pdb=" N LYS E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 414 through 430 Processing helix chain 'E' and resid 434 through 442 Processing helix chain 'E' and resid 442 through 453 removed outlier: 3.851A pdb=" N LEU E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 448 " --> pdb=" O MET E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 455 through 468 removed outlier: 3.929A pdb=" N ASP E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS E 465 " --> pdb=" O ARG E 461 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 479 Processing helix chain 'E' and resid 480 through 483 Processing helix chain 'E' and resid 487 through 508 Processing helix chain 'E' and resid 511 through 517 removed outlier: 4.075A pdb=" N GLN E 515 " --> pdb=" O LEU E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 529 removed outlier: 3.970A pdb=" N ALA E 522 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 546 Processing helix chain 'E' and resid 556 through 560 Processing helix chain 'E' and resid 561 through 572 Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 577 through 584 Processing helix chain 'E' and resid 587 through 594 Processing helix chain 'E' and resid 595 through 602 Processing helix chain 'E' and resid 607 through 625 Processing helix chain 'E' and resid 634 through 643 Processing helix chain 'E' and resid 644 through 648 Processing helix chain 'E' and resid 649 through 656 Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 667 through 674 Processing helix chain 'E' and resid 679 through 692 removed outlier: 3.557A pdb=" N ALA E 689 " --> pdb=" O LYS E 685 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE E 690 " --> pdb=" O LEU E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 732 Processing helix chain 'E' and resid 740 through 744 Processing helix chain 'E' and resid 750 through 759 removed outlier: 4.354A pdb=" N LEU E 754 " --> pdb=" O ASP E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 776 removed outlier: 4.071A pdb=" N ARG E 774 " --> pdb=" O SER E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 795 Processing helix chain 'E' and resid 812 through 816 Processing helix chain 'E' and resid 820 through 826 removed outlier: 3.618A pdb=" N TYR E 826 " --> pdb=" O ILE E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 849 Processing helix chain 'F' and resid 195 through 225 Processing helix chain 'F' and resid 228 through 248 Processing helix chain 'F' and resid 252 through 267 Processing helix chain 'F' and resid 268 through 279 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 285 through 300 removed outlier: 3.764A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 327 through 342 Processing helix chain 'F' and resid 345 through 354 removed outlier: 3.544A pdb=" N GLU F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 368 removed outlier: 3.708A pdb=" N HIS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 388 Processing helix chain 'F' and resid 390 through 400 removed outlier: 3.633A pdb=" N LYS F 400 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 412 Processing helix chain 'F' and resid 414 through 430 Processing helix chain 'F' and resid 431 through 433 No H-bonds generated for 'chain 'F' and resid 431 through 433' Processing helix chain 'F' and resid 434 through 440 Processing helix chain 'F' and resid 442 through 453 removed outlier: 3.889A pdb=" N GLU F 448 " --> pdb=" O MET F 444 " (cutoff:3.500A) Proline residue: F 449 - end of helix Processing helix chain 'F' and resid 455 through 468 removed outlier: 5.651A pdb=" N LYS F 465 " --> pdb=" O ARG F 461 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 479 Processing helix chain 'F' and resid 480 through 483 Processing helix chain 'F' and resid 487 through 508 Processing helix chain 'F' and resid 511 through 517 removed outlier: 4.095A pdb=" N GLN F 515 " --> pdb=" O LEU F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 529 removed outlier: 3.966A pdb=" N ALA F 522 " --> pdb=" O GLY F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 546 removed outlier: 3.522A pdb=" N GLY F 546 " --> pdb=" O LEU F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 560 Processing helix chain 'F' and resid 561 through 572 Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 577 through 584 Processing helix chain 'F' and resid 587 through 594 Processing helix chain 'F' and resid 595 through 602 Processing helix chain 'F' and resid 607 through 625 Processing helix chain 'F' and resid 634 through 643 Processing helix chain 'F' and resid 644 through 648 Processing helix chain 'F' and resid 649 through 656 Processing helix chain 'F' and resid 661 through 666 removed outlier: 4.266A pdb=" N SER F 664 " --> pdb=" O SER F 661 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 666 " --> pdb=" O LEU F 663 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 674 Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 715 through 733 removed outlier: 6.313A pdb=" N GLN F 721 " --> pdb=" O SER F 717 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU F 722 " --> pdb=" O THR F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 754 Processing helix chain 'F' and resid 754 through 760 removed outlier: 3.660A pdb=" N GLN F 758 " --> pdb=" O LEU F 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 776 Processing helix chain 'F' and resid 783 through 795 Processing helix chain 'F' and resid 812 through 816 Processing helix chain 'F' and resid 817 through 822 removed outlier: 4.582A pdb=" N MET F 822 " --> pdb=" O ASN F 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 826 Processing helix chain 'F' and resid 832 through 834 No H-bonds generated for 'chain 'F' and resid 832 through 834' Processing helix chain 'F' and resid 835 through 849 Processing helix chain 'G' and resid 195 through 226 Processing helix chain 'G' and resid 228 through 248 Processing helix chain 'G' and resid 252 through 267 Processing helix chain 'G' and resid 268 through 279 Processing helix chain 'G' and resid 280 through 284 Processing helix chain 'G' and resid 285 through 299 removed outlier: 3.691A pdb=" N ARG G 289 " --> pdb=" O CYS G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 313 through 324 Processing helix chain 'G' and resid 327 through 342 Processing helix chain 'G' and resid 345 through 354 removed outlier: 3.663A pdb=" N GLU G 354 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 removed outlier: 3.596A pdb=" N HIS G 360 " --> pdb=" O ASP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 388 Processing helix chain 'G' and resid 390 through 400 removed outlier: 3.649A pdb=" N LYS G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 411 Processing helix chain 'G' and resid 414 through 430 Processing helix chain 'G' and resid 431 through 433 No H-bonds generated for 'chain 'G' and resid 431 through 433' Processing helix chain 'G' and resid 434 through 442 Processing helix chain 'G' and resid 442 through 453 removed outlier: 3.819A pdb=" N LEU G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU G 448 " --> pdb=" O MET G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 455 through 468 removed outlier: 3.513A pdb=" N ARG G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 462 " --> pdb=" O THR G 458 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR G 466 " --> pdb=" O ASP G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 479 Processing helix chain 'G' and resid 480 through 483 Processing helix chain 'G' and resid 487 through 508 Processing helix chain 'G' and resid 511 through 517 removed outlier: 4.103A pdb=" N GLN G 515 " --> pdb=" O LEU G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 529 removed outlier: 3.969A pdb=" N ALA G 522 " --> pdb=" O GLY G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 546 removed outlier: 3.574A pdb=" N GLY G 546 " --> pdb=" O LEU G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 561 through 572 Processing helix chain 'G' and resid 574 through 576 No H-bonds generated for 'chain 'G' and resid 574 through 576' Processing helix chain 'G' and resid 577 through 584 Processing helix chain 'G' and resid 587 through 594 Processing helix chain 'G' and resid 595 through 602 Processing helix chain 'G' and resid 607 through 625 Processing helix chain 'G' and resid 634 through 643 Processing helix chain 'G' and resid 644 through 648 Processing helix chain 'G' and resid 649 through 656 Processing helix chain 'G' and resid 661 through 666 removed outlier: 4.116A pdb=" N SER G 664 " --> pdb=" O SER G 661 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 666 " --> pdb=" O LEU G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 667 through 674 Processing helix chain 'G' and resid 679 through 694 removed outlier: 4.113A pdb=" N LYS G 694 " --> pdb=" O PHE G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 719 through 731 Processing helix chain 'G' and resid 751 through 760 removed outlier: 4.369A pdb=" N ILE G 757 " --> pdb=" O LEU G 753 " (cutoff:3.500A) Processing helix chain 'G' and resid 772 through 776 Processing helix chain 'G' and resid 783 through 795 Processing helix chain 'G' and resid 812 through 816 Processing helix chain 'G' and resid 820 through 826 Processing helix chain 'G' and resid 832 through 834 No H-bonds generated for 'chain 'G' and resid 832 through 834' Processing helix chain 'G' and resid 835 through 849 Processing helix chain 'H' and resid 195 through 225 Processing helix chain 'H' and resid 228 through 248 Processing helix chain 'H' and resid 252 through 267 Processing helix chain 'H' and resid 268 through 279 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 285 through 300 removed outlier: 3.790A pdb=" N ARG H 289 " --> pdb=" O CYS H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 313 through 324 Processing helix chain 'H' and resid 327 through 342 Processing helix chain 'H' and resid 345 through 354 removed outlier: 3.600A pdb=" N GLU H 354 " --> pdb=" O LEU H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 368 removed outlier: 3.597A pdb=" N HIS H 360 " --> pdb=" O ASP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 388 Processing helix chain 'H' and resid 390 through 400 removed outlier: 3.629A pdb=" N LYS H 400 " --> pdb=" O LYS H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 412 Processing helix chain 'H' and resid 414 through 430 Processing helix chain 'H' and resid 431 through 433 No H-bonds generated for 'chain 'H' and resid 431 through 433' Processing helix chain 'H' and resid 434 through 441 Processing helix chain 'H' and resid 443 through 445 No H-bonds generated for 'chain 'H' and resid 443 through 445' Processing helix chain 'H' and resid 446 through 453 removed outlier: 3.670A pdb=" N VAL H 453 " --> pdb=" O PRO H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 468 removed outlier: 5.995A pdb=" N LYS H 465 " --> pdb=" O ARG H 461 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR H 466 " --> pdb=" O ASP H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 479 Processing helix chain 'H' and resid 480 through 483 Processing helix chain 'H' and resid 487 through 508 Processing helix chain 'H' and resid 511 through 517 removed outlier: 4.095A pdb=" N GLN H 515 " --> pdb=" O LEU H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 529 removed outlier: 3.985A pdb=" N ALA H 522 " --> pdb=" O GLY H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 546 removed outlier: 3.561A pdb=" N GLY H 546 " --> pdb=" O LEU H 542 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 560 Processing helix chain 'H' and resid 561 through 572 Processing helix chain 'H' and resid 574 through 584 removed outlier: 3.593A pdb=" N VAL H 578 " --> pdb=" O PHE H 574 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU H 579 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS H 580 " --> pdb=" O GLU H 576 " (cutoff:3.500A) Processing helix chain 'H' and resid 587 through 594 Processing helix chain 'H' and resid 595 through 602 Processing helix chain 'H' and resid 607 through 625 Processing helix chain 'H' and resid 634 through 643 Processing helix chain 'H' and resid 644 through 648 Processing helix chain 'H' and resid 649 through 656 Processing helix chain 'H' and resid 661 through 666 removed outlier: 4.125A pdb=" N SER H 664 " --> pdb=" O SER H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 675 Processing helix chain 'H' and resid 679 through 694 removed outlier: 4.158A pdb=" N LYS H 694 " --> pdb=" O PHE H 690 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 733 Processing helix chain 'H' and resid 750 through 760 removed outlier: 4.242A pdb=" N LEU H 754 " --> pdb=" O ASP H 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 772 through 776 Processing helix chain 'H' and resid 783 through 795 Processing helix chain 'H' and resid 812 through 816 Processing helix chain 'H' and resid 820 through 826 Processing helix chain 'H' and resid 832 through 834 No H-bonds generated for 'chain 'H' and resid 832 through 834' Processing helix chain 'H' and resid 835 through 849 Processing helix chain 'I' and resid 195 through 226 Processing helix chain 'I' and resid 228 through 248 Processing helix chain 'I' and resid 252 through 267 Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 280 through 284 Processing helix chain 'I' and resid 285 through 299 removed outlier: 3.748A pdb=" N ARG I 289 " --> pdb=" O CYS I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 327 through 342 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 356 through 368 removed outlier: 3.777A pdb=" N HIS I 360 " --> pdb=" O ASP I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 388 Processing helix chain 'I' and resid 390 through 400 Processing helix chain 'I' and resid 401 through 412 Processing helix chain 'I' and resid 414 through 430 Processing helix chain 'I' and resid 431 through 433 No H-bonds generated for 'chain 'I' and resid 431 through 433' Processing helix chain 'I' and resid 434 through 442 Processing helix chain 'I' and resid 443 through 453 removed outlier: 4.130A pdb=" N GLU I 448 " --> pdb=" O MET I 444 " (cutoff:3.500A) Proline residue: I 449 - end of helix Processing helix chain 'I' and resid 455 through 468 removed outlier: 5.593A pdb=" N LYS I 465 " --> pdb=" O ARG I 461 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR I 466 " --> pdb=" O ASP I 462 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN I 468 " --> pdb=" O HIS I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 471 through 479 Processing helix chain 'I' and resid 480 through 483 Processing helix chain 'I' and resid 487 through 508 Processing helix chain 'I' and resid 511 through 517 removed outlier: 4.106A pdb=" N GLN I 515 " --> pdb=" O LEU I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 529 removed outlier: 3.978A pdb=" N ALA I 522 " --> pdb=" O GLY I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 546 removed outlier: 4.052A pdb=" N GLY I 546 " --> pdb=" O LEU I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 560 Processing helix chain 'I' and resid 561 through 572 Processing helix chain 'I' and resid 574 through 576 No H-bonds generated for 'chain 'I' and resid 574 through 576' Processing helix chain 'I' and resid 577 through 584 Processing helix chain 'I' and resid 589 through 594 removed outlier: 3.532A pdb=" N GLN I 593 " --> pdb=" O ASP I 589 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 594 " --> pdb=" O LEU I 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 589 through 594' Processing helix chain 'I' and resid 595 through 602 Processing helix chain 'I' and resid 607 through 625 Processing helix chain 'I' and resid 634 through 643 Processing helix chain 'I' and resid 644 through 648 Processing helix chain 'I' and resid 649 through 656 Processing helix chain 'I' and resid 661 through 666 removed outlier: 4.131A pdb=" N SER I 664 " --> pdb=" O SER I 661 " (cutoff:3.500A) Processing helix chain 'I' and resid 667 through 674 Processing helix chain 'I' and resid 679 through 693 Processing helix chain 'I' and resid 719 through 733 Processing helix chain 'I' and resid 751 through 760 Processing helix chain 'I' and resid 772 through 776 Processing helix chain 'I' and resid 783 through 795 Processing helix chain 'I' and resid 812 through 816 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 832 through 834 No H-bonds generated for 'chain 'I' and resid 832 through 834' Processing helix chain 'I' and resid 835 through 849 Processing sheet with id=AA1, first strand: chain 'A' and resid 737 through 739 removed outlier: 6.361A pdb=" N VAL A 710 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 763 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE A 802 " --> pdb=" O PHE A 763 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 765 " --> pdb=" O ILE A 802 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 737 through 738 removed outlier: 3.747A pdb=" N PHE B 738 " --> pdb=" O VAL B 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 737 through 739 removed outlier: 6.723A pdb=" N VAL C 710 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 829 " --> pdb=" O ILE C 799 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 737 through 739 removed outlier: 7.732A pdb=" N PHE D 738 " --> pdb=" O ILE D 708 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 710 " --> pdb=" O PHE D 738 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP D 709 " --> pdb=" O ALA D 760 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LYS D 761 " --> pdb=" O ASN D 798 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ILE D 800 " --> pdb=" O LYS D 761 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE D 763 " --> pdb=" O ILE D 800 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 802 " --> pdb=" O PHE D 763 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 765 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL D 829 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 737 through 739 removed outlier: 7.888A pdb=" N PHE E 738 " --> pdb=" O ILE E 708 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 710 " --> pdb=" O PHE E 738 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP E 709 " --> pdb=" O ALA E 760 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS E 761 " --> pdb=" O ASN E 798 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE E 800 " --> pdb=" O LYS E 761 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE E 763 " --> pdb=" O ILE E 800 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE E 802 " --> pdb=" O PHE E 763 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU E 765 " --> pdb=" O ILE E 802 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 737 through 739 removed outlier: 6.595A pdb=" N VAL F 710 " --> pdb=" O PHE F 738 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE F 763 " --> pdb=" O ILE F 800 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE F 802 " --> pdb=" O PHE F 763 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 765 " --> pdb=" O ILE F 802 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 737 through 739 removed outlier: 6.433A pdb=" N VAL G 710 " --> pdb=" O PHE G 738 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE G 763 " --> pdb=" O ASN G 798 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL G 829 " --> pdb=" O ILE G 799 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 737 through 739 removed outlier: 6.388A pdb=" N VAL H 710 " --> pdb=" O PHE H 738 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE H 763 " --> pdb=" O ASN H 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 737 through 739 removed outlier: 5.912A pdb=" N VAL I 710 " --> pdb=" O PHE I 738 " (cutoff:3.500A) 2998 hydrogen bonds defined for protein. 8541 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: 17.01 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.28: 7708 1.28 - 1.44: 12027 1.44 - 1.60: 27346 1.60 - 1.77: 13 1.77 - 1.93: 475 Bond restraints: 47569 Sorted by residual: bond pdb=" C TRP E 831 " pdb=" O TRP E 831 " ideal model delta sigma weight residual 1.234 1.143 0.092 1.22e-02 6.72e+03 5.63e+01 bond pdb=" C MET C 840 " pdb=" O MET C 840 " ideal model delta sigma weight residual 1.236 1.152 0.085 1.18e-02 7.18e+03 5.16e+01 bond pdb=" CD GLU F 501 " pdb=" OE2 GLU F 501 " ideal model delta sigma weight residual 1.249 1.115 0.134 1.90e-02 2.77e+03 4.95e+01 bond pdb=" CE1 HIS G 360 " pdb=" NE2 HIS G 360 " ideal model delta sigma weight residual 1.321 1.387 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" CG ASN A 679 " pdb=" OD1 ASN A 679 " ideal model delta sigma weight residual 1.231 1.116 0.115 1.90e-02 2.77e+03 3.67e+01 ... (remaining 47564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.07: 64158 9.07 - 18.13: 73 18.13 - 27.20: 1 27.20 - 36.26: 2 36.26 - 45.33: 1 Bond angle restraints: 64235 Sorted by residual: angle pdb=" CG GLU F 501 " pdb=" CD GLU F 501 " pdb=" OE1 GLU F 501 " ideal model delta sigma weight residual 118.40 163.73 -45.33 2.30e+00 1.89e-01 3.88e+02 angle pdb=" CG GLU F 501 " pdb=" CD GLU F 501 " pdb=" OE2 GLU F 501 " ideal model delta sigma weight residual 118.40 84.76 33.64 2.30e+00 1.89e-01 2.14e+02 angle pdb=" OE1 GLU F 501 " pdb=" CD GLU F 501 " pdb=" OE2 GLU F 501 " ideal model delta sigma weight residual 122.90 93.02 29.88 2.40e+00 1.74e-01 1.55e+02 angle pdb=" C GLN D 836 " pdb=" CA GLN D 836 " pdb=" CB GLN D 836 " ideal model delta sigma weight residual 110.31 133.00 -22.69 2.09e+00 2.29e-01 1.18e+02 angle pdb=" CA ASP C 455 " pdb=" CB ASP C 455 " pdb=" CG ASP C 455 " ideal model delta sigma weight residual 112.60 122.88 -10.28 1.00e+00 1.00e+00 1.06e+02 ... (remaining 64230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.34: 26550 18.34 - 36.69: 2177 36.69 - 55.03: 369 55.03 - 73.37: 59 73.37 - 91.72: 17 Dihedral angle restraints: 29172 sinusoidal: 11903 harmonic: 17269 Sorted by residual: dihedral pdb=" C GLN D 836 " pdb=" N GLN D 836 " pdb=" CA GLN D 836 " pdb=" CB GLN D 836 " ideal model delta harmonic sigma weight residual -122.60 -155.34 32.74 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" N GLN D 836 " pdb=" C GLN D 836 " pdb=" CA GLN D 836 " pdb=" CB GLN D 836 " ideal model delta harmonic sigma weight residual 122.80 147.71 -24.91 0 2.50e+00 1.60e-01 9.93e+01 dihedral pdb=" C ASP G 742 " pdb=" N ASP G 742 " pdb=" CA ASP G 742 " pdb=" CB ASP G 742 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 ... (remaining 29169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 6833 0.249 - 0.499: 484 0.499 - 0.748: 31 0.748 - 0.998: 3 0.998 - 1.247: 2 Chirality restraints: 7353 Sorted by residual: chirality pdb=" CA GLN D 836 " pdb=" N GLN D 836 " pdb=" C GLN D 836 " pdb=" CB GLN D 836 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.89e+01 chirality pdb=" CB VAL I 544 " pdb=" CA VAL I 544 " pdb=" CG1 VAL I 544 " pdb=" CG2 VAL I 544 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CB VAL A 565 " pdb=" CA VAL A 565 " pdb=" CG1 VAL A 565 " pdb=" CG2 VAL A 565 " both_signs ideal model delta sigma weight residual False -2.63 -1.68 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 7350 not shown) Planarity restraints: 8131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 714 " -0.184 2.00e-02 2.50e+03 1.03e-01 2.14e+02 pdb=" CG TYR I 714 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR I 714 " 0.140 2.00e-02 2.50e+03 pdb=" CD2 TYR I 714 " 0.108 2.00e-02 2.50e+03 pdb=" CE1 TYR I 714 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR I 714 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR I 714 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 714 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 463 " -0.134 2.00e-02 2.50e+03 7.15e-02 1.02e+02 pdb=" CG TYR B 463 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 463 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR B 463 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR B 463 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 463 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B 463 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 463 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 567 " -0.129 2.00e-02 2.50e+03 6.94e-02 9.63e+01 pdb=" CG TYR A 567 " 0.126 2.00e-02 2.50e+03 pdb=" CD1 TYR A 567 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 567 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 567 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 567 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 567 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 567 " -0.037 2.00e-02 2.50e+03 ... (remaining 8128 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1277 2.73 - 3.27: 51689 3.27 - 3.82: 82051 3.82 - 4.36: 108332 4.36 - 4.90: 168531 Nonbonded interactions: 411880 Sorted by model distance: nonbonded pdb=" OE1 GLN E 688 " pdb=" OE1 GLU E 691 " model vdw 2.190 3.040 nonbonded pdb=" OG SER H 724 " pdb=" CE1 HIS I 833 " model vdw 2.193 3.260 nonbonded pdb=" OE1 GLN G 688 " pdb=" OE1 GLU G 691 " model vdw 2.329 3.040 nonbonded pdb=" OE2 GLU A 354 " pdb=" OD1 ASN I 310 " model vdw 2.355 3.040 nonbonded pdb=" O TYR C 835 " pdb=" OH TYR E 835 " model vdw 2.375 3.040 ... (remaining 411875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 194 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 695 or resid 707 through 849)) \ selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.220 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: 0.050 Extract box with map and model: 2.050 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 81.260 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.134 47569 Z= 0.757 Angle : 1.847 45.330 64235 Z= 1.197 Chirality : 0.139 1.247 7353 Planarity : 0.013 0.103 8131 Dihedral : 13.835 91.716 17894 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 4.32 % Favored : 93.78 % Cbeta Deviations : 1.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.10), residues: 5785 helix: -1.26 (0.07), residues: 4166 sheet: -2.16 (0.31), residues: 164 loop : 0.12 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.019 TRP A 560 HIS 0.052 0.011 HIS B 695 PHE 0.117 0.020 PHE C 638 TYR 0.184 0.021 TYR I 714 ARG 0.078 0.007 ARG E 821 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 587 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.2433 (ttp) cc_final: 0.1030 (mtt) REVERT: A 216 MET cc_start: 0.5531 (mtp) cc_final: 0.5101 (ttt) REVERT: A 243 MET cc_start: 0.9051 (mmm) cc_final: 0.8502 (tpp) REVERT: A 471 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.8327 (p) REVERT: A 793 PHE cc_start: 0.9193 (m-80) cc_final: 0.8892 (m-80) REVERT: A 795 HIS cc_start: 0.8464 (m90) cc_final: 0.8076 (m-70) REVERT: A 816 ILE cc_start: 0.9243 (mt) cc_final: 0.8997 (mm) REVERT: A 817 PRO cc_start: 0.4593 (Cg_exo) cc_final: 0.4086 (Cg_endo) REVERT: B 444 MET cc_start: 0.7627 (mtm) cc_final: 0.7272 (mtp) REVERT: B 738 PHE cc_start: 0.7500 (m-80) cc_final: 0.7276 (m-80) REVERT: C 194 MET cc_start: 0.8523 (ttp) cc_final: 0.8020 (tmm) REVERT: C 299 CYS cc_start: 0.9649 (m) cc_final: 0.9098 (t) REVERT: C 605 MET cc_start: 0.9320 (tmm) cc_final: 0.8224 (tmm) REVERT: C 721 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6496 (mp10) REVERT: C 826 TYR cc_start: 0.4332 (OUTLIER) cc_final: 0.3802 (m-80) REVERT: D 217 MET cc_start: 0.9557 (ttm) cc_final: 0.9304 (ttm) REVERT: D 605 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8175 (tpt) REVERT: D 721 GLN cc_start: -0.0065 (OUTLIER) cc_final: -0.1286 (mm-40) REVERT: D 836 GLN cc_start: 0.2525 (OUTLIER) cc_final: 0.1649 (pt0) REVERT: D 840 MET cc_start: 0.8041 (tpp) cc_final: 0.7496 (ptt) REVERT: E 194 MET cc_start: 0.8124 (ttp) cc_final: 0.7430 (tmm) REVERT: E 581 PHE cc_start: 0.9034 (m-80) cc_final: 0.8807 (m-80) REVERT: E 694 LYS cc_start: 0.8787 (pttm) cc_final: 0.8513 (mmtm) REVERT: E 784 TRP cc_start: 0.6204 (m100) cc_final: 0.5641 (p-90) REVERT: E 831 TRP cc_start: 0.8075 (t-100) cc_final: 0.7747 (t-100) REVERT: F 194 MET cc_start: 0.8981 (ttp) cc_final: 0.8754 (tmm) REVERT: F 551 TYR cc_start: 0.9498 (m-80) cc_final: 0.9295 (m-80) REVERT: F 773 ASP cc_start: 0.8912 (t0) cc_final: 0.8553 (m-30) REVERT: G 243 MET cc_start: 0.9524 (mmm) cc_final: 0.8977 (mmm) REVERT: G 251 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.8915 (ptmm) REVERT: G 273 LEU cc_start: 0.9837 (mt) cc_final: 0.9623 (tp) REVERT: G 581 PHE cc_start: 0.9044 (m-80) cc_final: 0.8735 (m-80) REVERT: G 826 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.3669 (m-10) REVERT: H 277 PHE cc_start: 0.9736 (t80) cc_final: 0.9165 (t80) REVERT: H 419 TYR cc_start: 0.8971 (t80) cc_final: 0.8628 (t80) REVERT: I 194 MET cc_start: 0.6979 (ttp) cc_final: 0.6226 (tmm) REVERT: I 253 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8420 (t) REVERT: I 594 LEU cc_start: 0.9436 (mt) cc_final: 0.9227 (mt) REVERT: I 826 TYR cc_start: 0.1544 (OUTLIER) cc_final: 0.0487 (t80) outliers start: 98 outliers final: 20 residues processed: 666 average time/residue: 0.5354 time to fit residues: 566.1251 Evaluate side-chains 398 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 368 time to evaluate : 4.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 826 TYR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 826 TYR Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain D residue 836 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 675 CYS Chi-restraints excluded: chain E residue 774 ARG Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain G residue 251 LYS Chi-restraints excluded: chain G residue 497 HIS Chi-restraints excluded: chain G residue 826 TYR Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 686 LEU Chi-restraints excluded: chain I residue 774 ARG Chi-restraints excluded: chain I residue 826 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 487 optimal weight: 6.9990 chunk 437 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 452 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 336 optimal weight: 20.0000 chunk 523 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 601 HIS B 695 HIS ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN E 231 ASN E 468 GLN E 508 GLN E 695 HIS F 468 GLN ** F 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN F 756 ASN G 497 HIS G 508 GLN H 231 ASN ** I 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 47569 Z= 0.232 Angle : 0.680 12.461 64235 Z= 0.363 Chirality : 0.043 0.205 7353 Planarity : 0.004 0.038 8131 Dihedral : 6.228 86.119 6303 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 1.59 % Allowed : 8.18 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 5785 helix: 0.75 (0.08), residues: 4229 sheet: -2.00 (0.34), residues: 167 loop : 0.81 (0.19), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 474 HIS 0.009 0.002 HIS I 377 PHE 0.030 0.002 PHE I 690 TYR 0.024 0.002 TYR I 419 ARG 0.008 0.001 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 379 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.1672 (ttp) cc_final: 0.1410 (ttm) REVERT: A 202 MET cc_start: -0.1590 (ttt) cc_final: -0.2422 (tpt) REVERT: A 203 MET cc_start: 0.7932 (tpt) cc_final: 0.7323 (mmt) REVERT: A 216 MET cc_start: 0.5682 (mtp) cc_final: 0.5267 (ttt) REVERT: A 474 TRP cc_start: 0.9206 (t60) cc_final: 0.8827 (t60) REVERT: A 581 PHE cc_start: 0.8625 (m-80) cc_final: 0.8342 (m-80) REVERT: B 217 MET cc_start: 0.9617 (ttm) cc_final: 0.9068 (ptm) REVERT: B 318 MET cc_start: 0.7583 (tmm) cc_final: 0.7359 (ppp) REVERT: B 444 MET cc_start: 0.7552 (mtm) cc_final: 0.7167 (mtt) REVERT: B 840 MET cc_start: 0.8712 (mmt) cc_final: 0.8163 (mmp) REVERT: C 213 TYR cc_start: 0.9832 (m-10) cc_final: 0.9455 (m-80) REVERT: C 299 CYS cc_start: 0.9603 (m) cc_final: 0.9056 (t) REVERT: C 318 MET cc_start: 0.7673 (ttm) cc_final: 0.7317 (ptm) REVERT: C 322 MET cc_start: 0.8964 (tmm) cc_final: 0.8744 (ttm) REVERT: C 551 TYR cc_start: 0.9573 (m-80) cc_final: 0.9347 (m-80) REVERT: C 677 ILE cc_start: 0.9392 (mt) cc_final: 0.9144 (tt) REVERT: C 822 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7265 (pmm) REVERT: C 826 TYR cc_start: 0.4017 (OUTLIER) cc_final: 0.3627 (m-80) REVERT: D 194 MET cc_start: 0.5667 (mtt) cc_final: 0.3093 (ttt) REVERT: D 322 MET cc_start: 0.7552 (mtp) cc_final: 0.7041 (mtt) REVERT: D 605 MET cc_start: 0.9089 (mmm) cc_final: 0.8171 (tpt) REVERT: D 640 MET cc_start: 0.8916 (mmm) cc_final: 0.8637 (mmp) REVERT: D 822 MET cc_start: 0.2425 (mmp) cc_final: 0.1987 (pmm) REVERT: D 840 MET cc_start: 0.8051 (tpp) cc_final: 0.7583 (ptt) REVERT: E 194 MET cc_start: 0.7668 (ttp) cc_final: 0.6550 (tmm) REVERT: E 216 MET cc_start: 0.9278 (ttp) cc_final: 0.8835 (ttt) REVERT: E 219 LYS cc_start: 0.9584 (mttt) cc_final: 0.9362 (ptpt) REVERT: E 222 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9070 (tm-30) REVERT: E 243 MET cc_start: 0.8512 (tpp) cc_final: 0.8306 (tpp) REVERT: E 581 PHE cc_start: 0.9059 (m-80) cc_final: 0.8729 (m-80) REVERT: E 745 TYR cc_start: -0.0904 (OUTLIER) cc_final: -0.2393 (p90) REVERT: E 784 TRP cc_start: 0.6045 (m100) cc_final: 0.5771 (p-90) REVERT: F 551 TYR cc_start: 0.9494 (m-80) cc_final: 0.9239 (m-80) REVERT: F 831 TRP cc_start: 0.8845 (t-100) cc_final: 0.8562 (t-100) REVERT: G 243 MET cc_start: 0.9585 (mmm) cc_final: 0.9048 (mmm) REVERT: G 318 MET cc_start: 0.6403 (ttm) cc_final: 0.5855 (ptm) REVERT: G 745 TYR cc_start: 0.9301 (m-80) cc_final: 0.8857 (m-80) REVERT: H 217 MET cc_start: 0.9656 (OUTLIER) cc_final: 0.9431 (ptm) REVERT: H 277 PHE cc_start: 0.9723 (t80) cc_final: 0.9186 (t80) REVERT: H 343 LYS cc_start: 0.9141 (mtmm) cc_final: 0.8763 (mmmm) REVERT: H 419 TYR cc_start: 0.8931 (t80) cc_final: 0.8658 (t80) REVERT: I 551 TYR cc_start: 0.9289 (m-80) cc_final: 0.9072 (m-80) REVERT: I 640 MET cc_start: 0.9146 (mmm) cc_final: 0.8919 (mmm) REVERT: I 822 MET cc_start: 0.7049 (ttp) cc_final: 0.6299 (tpp) REVERT: I 826 TYR cc_start: 0.1067 (OUTLIER) cc_final: 0.0221 (t80) outliers start: 82 outliers final: 37 residues processed: 446 average time/residue: 0.5019 time to fit residues: 367.1191 Evaluate side-chains 354 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 826 TYR Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 745 TYR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 340 ASN Chi-restraints excluded: chain F residue 506 LYS Chi-restraints excluded: chain F residue 571 LYS Chi-restraints excluded: chain F residue 721 GLN Chi-restraints excluded: chain G residue 354 GLU Chi-restraints excluded: chain G residue 497 HIS Chi-restraints excluded: chain G residue 507 GLU Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 618 LEU Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 314 THR Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 291 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 436 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 524 optimal weight: 10.0000 chunk 567 optimal weight: 1.9990 chunk 467 optimal weight: 20.0000 chunk 520 optimal weight: 20.0000 chunk 178 optimal weight: 0.8980 chunk 421 optimal weight: 0.8980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 HIS E 707 GLN E 836 GLN ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 HIS F 509 ASN F 656 ASN G 695 HIS ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 468 GLN ** I 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47569 Z= 0.206 Angle : 0.627 12.355 64235 Z= 0.330 Chirality : 0.041 0.172 7353 Planarity : 0.004 0.061 8131 Dihedral : 5.561 80.718 6269 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.26 % Allowed : 9.38 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 5785 helix: 1.20 (0.08), residues: 4230 sheet: -2.04 (0.35), residues: 167 loop : 1.11 (0.20), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 474 HIS 0.009 0.001 HIS B 377 PHE 0.027 0.002 PHE I 365 TYR 0.022 0.002 TYR E 835 ARG 0.008 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 346 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.7976 (tpt) cc_final: 0.7338 (mmt) REVERT: A 216 MET cc_start: 0.5570 (mtp) cc_final: 0.5135 (ttt) REVERT: A 217 MET cc_start: 0.7437 (ptm) cc_final: 0.6833 (ptp) REVERT: A 243 MET cc_start: 0.9314 (mmm) cc_final: 0.8638 (tpp) REVERT: A 789 LEU cc_start: 0.9557 (tp) cc_final: 0.9161 (pp) REVERT: B 194 MET cc_start: 0.3030 (ttm) cc_final: 0.2546 (ttt) REVERT: B 290 MET cc_start: 0.8830 (mtt) cc_final: 0.8268 (mmm) REVERT: B 444 MET cc_start: 0.7454 (mtm) cc_final: 0.6936 (mtt) REVERT: B 822 MET cc_start: 0.4502 (pmm) cc_final: 0.4245 (pmm) REVERT: C 194 MET cc_start: 0.8584 (ttp) cc_final: 0.8055 (tmm) REVERT: C 299 CYS cc_start: 0.9563 (m) cc_final: 0.8951 (t) REVERT: C 318 MET cc_start: 0.7755 (ttm) cc_final: 0.7341 (ptm) REVERT: C 677 ILE cc_start: 0.9424 (mt) cc_final: 0.9168 (tt) REVERT: C 822 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7210 (pmm) REVERT: D 243 MET cc_start: 0.9591 (ttm) cc_final: 0.9230 (ppp) REVERT: D 605 MET cc_start: 0.9056 (mmm) cc_final: 0.8148 (tpt) REVERT: D 640 MET cc_start: 0.8936 (mmm) cc_final: 0.8669 (mmp) REVERT: D 721 GLN cc_start: 0.0071 (OUTLIER) cc_final: -0.0380 (pm20) REVERT: D 822 MET cc_start: 0.2981 (mmp) cc_final: 0.2569 (pmm) REVERT: D 840 MET cc_start: 0.8155 (tpp) cc_final: 0.7734 (ptt) REVERT: E 194 MET cc_start: 0.7761 (ttp) cc_final: 0.6359 (tmm) REVERT: E 217 MET cc_start: 0.8821 (ptm) cc_final: 0.8381 (ppp) REVERT: E 222 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9136 (tm-30) REVERT: E 322 MET cc_start: 0.9012 (mtt) cc_final: 0.8779 (mmt) REVERT: E 581 PHE cc_start: 0.9117 (m-80) cc_final: 0.8779 (m-80) REVERT: E 784 TRP cc_start: 0.6003 (m100) cc_final: 0.5756 (p-90) REVERT: F 194 MET cc_start: 0.9469 (tmm) cc_final: 0.9057 (tmm) REVERT: F 203 MET cc_start: 0.9640 (mtt) cc_final: 0.9332 (mtt) REVERT: F 551 TYR cc_start: 0.9537 (m-80) cc_final: 0.9281 (m-80) REVERT: G 194 MET cc_start: 0.5984 (ttm) cc_final: 0.5100 (ttm) REVERT: G 243 MET cc_start: 0.9617 (mmm) cc_final: 0.9054 (mmm) REVERT: G 318 MET cc_start: 0.6463 (ttm) cc_final: 0.5977 (ptm) REVERT: G 322 MET cc_start: 0.9617 (tmm) cc_final: 0.9218 (ttm) REVERT: G 745 TYR cc_start: 0.9268 (m-80) cc_final: 0.8798 (m-80) REVERT: I 194 MET cc_start: 0.6433 (ttt) cc_final: 0.4386 (tmm) REVERT: I 217 MET cc_start: 0.9736 (ptm) cc_final: 0.9503 (ppp) REVERT: I 551 TYR cc_start: 0.9341 (m-80) cc_final: 0.9079 (m-80) REVERT: I 640 MET cc_start: 0.9146 (mmm) cc_final: 0.8930 (mmm) REVERT: I 826 TYR cc_start: 0.1135 (OUTLIER) cc_final: 0.0548 (t80) outliers start: 65 outliers final: 30 residues processed: 401 average time/residue: 0.4902 time to fit residues: 330.0648 Evaluate side-chains 329 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 296 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 340 ASN Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 506 LYS Chi-restraints excluded: chain G residue 507 GLU Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 618 LEU Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 518 optimal weight: 0.9990 chunk 394 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 chunk 526 optimal weight: 4.9990 chunk 557 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 499 optimal weight: 0.0970 chunk 150 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 798 ASN E 248 ASN ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47569 Z= 0.182 Angle : 0.614 16.058 64235 Z= 0.315 Chirality : 0.040 0.277 7353 Planarity : 0.004 0.058 8131 Dihedral : 5.164 76.086 6263 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.26 % Allowed : 10.09 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.11), residues: 5785 helix: 1.31 (0.08), residues: 4226 sheet: -2.07 (0.36), residues: 166 loop : 1.28 (0.20), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 474 HIS 0.008 0.001 HIS B 377 PHE 0.027 0.002 PHE B 365 TYR 0.019 0.002 TYR H 419 ARG 0.010 0.000 ARG I 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 339 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.1623 (ttt) cc_final: -0.2450 (tpt) REVERT: A 203 MET cc_start: 0.7942 (tpt) cc_final: 0.7292 (mmt) REVERT: A 216 MET cc_start: 0.5540 (mtp) cc_final: 0.5129 (ttt) REVERT: A 217 MET cc_start: 0.7126 (ptm) cc_final: 0.6838 (ptm) REVERT: A 581 PHE cc_start: 0.8661 (m-80) cc_final: 0.8439 (m-80) REVERT: A 789 LEU cc_start: 0.9540 (tp) cc_final: 0.9180 (pp) REVERT: A 840 MET cc_start: 0.8283 (tpt) cc_final: 0.7852 (ttt) REVERT: B 194 MET cc_start: 0.2655 (ttm) cc_final: 0.1992 (ttt) REVERT: B 217 MET cc_start: 0.9591 (ttm) cc_final: 0.9304 (ptm) REVERT: B 318 MET cc_start: 0.7227 (tmm) cc_final: 0.6849 (ppp) REVERT: B 322 MET cc_start: 0.7950 (mmm) cc_final: 0.7734 (mmt) REVERT: B 444 MET cc_start: 0.7371 (mtm) cc_final: 0.6879 (mtt) REVERT: B 822 MET cc_start: 0.4296 (pmm) cc_final: 0.3958 (pmm) REVERT: C 194 MET cc_start: 0.8532 (ttp) cc_final: 0.7968 (tmm) REVERT: C 299 CYS cc_start: 0.9595 (m) cc_final: 0.8964 (t) REVERT: C 318 MET cc_start: 0.7780 (ttm) cc_final: 0.7407 (ptm) REVERT: C 322 MET cc_start: 0.8999 (tmm) cc_final: 0.8648 (ptp) REVERT: C 822 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7301 (pmm) REVERT: D 217 MET cc_start: 0.9444 (ptm) cc_final: 0.9144 (ppp) REVERT: D 243 MET cc_start: 0.9530 (ttm) cc_final: 0.9156 (ppp) REVERT: D 318 MET cc_start: 0.9199 (ppp) cc_final: 0.8975 (ppp) REVERT: D 605 MET cc_start: 0.8968 (mmm) cc_final: 0.8063 (tpt) REVERT: D 640 MET cc_start: 0.8991 (mmm) cc_final: 0.8728 (mmp) REVERT: D 721 GLN cc_start: -0.0072 (OUTLIER) cc_final: -0.0435 (pm20) REVERT: D 840 MET cc_start: 0.8187 (tpp) cc_final: 0.7792 (ptt) REVERT: E 194 MET cc_start: 0.7547 (ttp) cc_final: 0.5785 (tmm) REVERT: E 216 MET cc_start: 0.9309 (ttp) cc_final: 0.8948 (ttt) REVERT: E 217 MET cc_start: 0.8760 (ptm) cc_final: 0.8210 (ppp) REVERT: E 322 MET cc_start: 0.9019 (mtt) cc_final: 0.8710 (mmt) REVERT: E 581 PHE cc_start: 0.9112 (m-80) cc_final: 0.8765 (m-80) REVERT: E 730 LEU cc_start: 0.8773 (mt) cc_final: 0.8571 (tp) REVERT: E 745 TYR cc_start: -0.0640 (OUTLIER) cc_final: -0.1960 (p90) REVERT: E 784 TRP cc_start: 0.6089 (m100) cc_final: 0.5817 (p-90) REVERT: F 217 MET cc_start: 0.9766 (ptm) cc_final: 0.9495 (ppp) REVERT: F 290 MET cc_start: 0.9139 (ptp) cc_final: 0.8800 (ppp) REVERT: F 318 MET cc_start: 0.8492 (ppp) cc_final: 0.8197 (ppp) REVERT: F 551 TYR cc_start: 0.9554 (m-80) cc_final: 0.9247 (m-80) REVERT: G 194 MET cc_start: 0.6003 (ttm) cc_final: 0.5211 (ttm) REVERT: G 243 MET cc_start: 0.9638 (mmm) cc_final: 0.9051 (mmm) REVERT: G 276 MET cc_start: 0.9270 (mpp) cc_final: 0.8975 (mpp) REVERT: G 318 MET cc_start: 0.6415 (ttm) cc_final: 0.5720 (ptm) REVERT: G 322 MET cc_start: 0.9614 (tmm) cc_final: 0.9213 (ttm) REVERT: G 444 MET cc_start: 0.7011 (mtt) cc_final: 0.6315 (mpp) REVERT: G 640 MET cc_start: 0.9195 (mmm) cc_final: 0.8686 (mmm) REVERT: G 745 TYR cc_start: 0.9234 (m-80) cc_final: 0.8752 (m-80) REVERT: G 798 ASN cc_start: 0.8024 (m-40) cc_final: 0.7765 (t0) REVERT: I 505 LYS cc_start: 0.9826 (mmmt) cc_final: 0.9610 (mmtm) REVERT: I 551 TYR cc_start: 0.9346 (m-80) cc_final: 0.9068 (m-80) REVERT: I 640 MET cc_start: 0.9150 (mmm) cc_final: 0.8934 (mmm) REVERT: I 822 MET cc_start: 0.5966 (ptm) cc_final: 0.5121 (pmm) REVERT: I 826 TYR cc_start: 0.1210 (OUTLIER) cc_final: 0.0202 (t80) outliers start: 65 outliers final: 33 residues processed: 395 average time/residue: 0.4564 time to fit residues: 303.8844 Evaluate side-chains 345 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 308 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 745 TYR Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 506 LYS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 314 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 591 LEU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 464 optimal weight: 8.9990 chunk 316 optimal weight: 40.0000 chunk 8 optimal weight: 8.9990 chunk 415 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 475 optimal weight: 50.0000 chunk 385 optimal weight: 20.0000 chunk 0 optimal weight: 90.0000 chunk 284 optimal weight: 5.9990 chunk 500 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN ** C 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN E 196 ASN E 566 GLN F 248 ASN F 597 ASN H 340 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN I 566 GLN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 47569 Z= 0.297 Angle : 0.682 13.452 64235 Z= 0.358 Chirality : 0.041 0.194 7353 Planarity : 0.005 0.047 8131 Dihedral : 5.209 67.143 6260 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.32 % Allowed : 11.60 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.11), residues: 5785 helix: 1.09 (0.08), residues: 4219 sheet: -2.12 (0.37), residues: 169 loop : 1.13 (0.19), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 474 HIS 0.008 0.001 HIS H 610 PHE 0.030 0.002 PHE B 365 TYR 0.026 0.002 TYR B 463 ARG 0.013 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 302 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8034 (tpt) cc_final: 0.7360 (mmt) REVERT: A 216 MET cc_start: 0.5546 (mtp) cc_final: 0.5125 (ttt) REVERT: A 217 MET cc_start: 0.7287 (ptm) cc_final: 0.7030 (ptm) REVERT: A 481 MET cc_start: 0.9364 (mmm) cc_final: 0.9153 (mmp) REVERT: A 789 LEU cc_start: 0.9585 (tp) cc_final: 0.9238 (pp) REVERT: B 194 MET cc_start: 0.2994 (ttm) cc_final: 0.1891 (ttp) REVERT: B 290 MET cc_start: 0.8745 (ttt) cc_final: 0.8325 (mmm) REVERT: B 318 MET cc_start: 0.7214 (tmm) cc_final: 0.6880 (ppp) REVERT: B 322 MET cc_start: 0.8011 (mmm) cc_final: 0.7793 (mmt) REVERT: B 444 MET cc_start: 0.7447 (mtm) cc_final: 0.7160 (mtt) REVERT: B 822 MET cc_start: 0.4369 (pmm) cc_final: 0.4038 (pmm) REVERT: C 194 MET cc_start: 0.8675 (ttp) cc_final: 0.8418 (tmm) REVERT: C 299 CYS cc_start: 0.9541 (m) cc_final: 0.8827 (t) REVERT: C 318 MET cc_start: 0.7954 (ttm) cc_final: 0.7562 (ptm) REVERT: C 322 MET cc_start: 0.8983 (tmm) cc_final: 0.8777 (ttm) REVERT: C 653 MET cc_start: 0.8904 (ptm) cc_final: 0.8694 (tmm) REVERT: C 721 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: C 822 MET cc_start: 0.7725 (pmt) cc_final: 0.7266 (pmm) REVERT: D 523 LEU cc_start: 0.9620 (mm) cc_final: 0.9377 (tp) REVERT: D 605 MET cc_start: 0.9102 (mmm) cc_final: 0.8159 (tpt) REVERT: D 640 MET cc_start: 0.9055 (mmm) cc_final: 0.8817 (mmp) REVERT: D 721 GLN cc_start: -0.0462 (OUTLIER) cc_final: -0.0776 (pm20) REVERT: D 822 MET cc_start: 0.3012 (mmp) cc_final: 0.2699 (pmm) REVERT: D 840 MET cc_start: 0.8174 (tpp) cc_final: 0.7704 (ptt) REVERT: E 194 MET cc_start: 0.7577 (ttp) cc_final: 0.4563 (tmm) REVERT: E 216 MET cc_start: 0.9185 (ttp) cc_final: 0.8829 (ttt) REVERT: E 217 MET cc_start: 0.8809 (ptm) cc_final: 0.7939 (ppp) REVERT: E 322 MET cc_start: 0.9073 (mtt) cc_final: 0.8761 (mmt) REVERT: E 481 MET cc_start: 0.8767 (ptm) cc_final: 0.8564 (tmm) REVERT: E 784 TRP cc_start: 0.6242 (m100) cc_final: 0.5838 (p-90) REVERT: E 822 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7216 (tpt) REVERT: F 217 MET cc_start: 0.9768 (ptm) cc_final: 0.9231 (ppp) REVERT: F 243 MET cc_start: 0.9127 (ttm) cc_final: 0.8726 (ppp) REVERT: F 322 MET cc_start: 0.9501 (tmm) cc_final: 0.8901 (ptm) REVERT: F 551 TYR cc_start: 0.9561 (m-80) cc_final: 0.9241 (m-80) REVERT: G 243 MET cc_start: 0.9650 (mmm) cc_final: 0.9370 (mmm) REVERT: G 276 MET cc_start: 0.9345 (mpp) cc_final: 0.9054 (mpp) REVERT: G 318 MET cc_start: 0.6442 (ttm) cc_final: 0.5895 (ptm) REVERT: G 322 MET cc_start: 0.9605 (tmm) cc_final: 0.9209 (ttt) REVERT: H 194 MET cc_start: 0.7783 (ttt) cc_final: 0.7113 (tmm) REVERT: H 217 MET cc_start: 0.9619 (ppp) cc_final: 0.9374 (ppp) REVERT: H 822 MET cc_start: 0.8814 (pmm) cc_final: 0.8384 (ptp) REVERT: I 194 MET cc_start: 0.6267 (ttt) cc_final: 0.4652 (tmm) REVERT: I 276 MET cc_start: 0.9174 (mtm) cc_final: 0.8876 (ptp) REVERT: I 551 TYR cc_start: 0.9366 (m-80) cc_final: 0.9061 (m-80) REVERT: I 822 MET cc_start: 0.6292 (ptm) cc_final: 0.5395 (pmm) REVERT: I 826 TYR cc_start: 0.1187 (OUTLIER) cc_final: 0.0130 (t80) outliers start: 68 outliers final: 46 residues processed: 365 average time/residue: 0.4542 time to fit residues: 281.1826 Evaluate side-chains 332 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 282 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 593 GLN Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 721 GLN Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 835 TYR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 497 HIS Chi-restraints excluded: chain F residue 836 GLN Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 408 PHE Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 355 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 408 PHE Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 187 optimal weight: 7.9990 chunk 502 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 558 optimal weight: 1.9990 chunk 463 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 184 optimal weight: 30.0000 chunk 293 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 777 ASN E 196 ASN G 652 GLN H 196 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47569 Z= 0.209 Angle : 0.639 13.157 64235 Z= 0.330 Chirality : 0.041 0.305 7353 Planarity : 0.004 0.073 8131 Dihedral : 5.017 59.768 6257 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.41 % Allowed : 12.13 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.11), residues: 5785 helix: 1.17 (0.08), residues: 4219 sheet: -2.13 (0.38), residues: 168 loop : 1.18 (0.19), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 784 HIS 0.008 0.001 HIS A 497 PHE 0.028 0.002 PHE B 365 TYR 0.030 0.002 TYR G 745 ARG 0.008 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 306 time to evaluate : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.1604 (ttt) cc_final: -0.2563 (tpt) REVERT: A 203 MET cc_start: 0.8041 (tpt) cc_final: 0.7352 (mmt) REVERT: A 216 MET cc_start: 0.5487 (mtp) cc_final: 0.5069 (ttt) REVERT: A 217 MET cc_start: 0.7356 (ptm) cc_final: 0.7102 (ptm) REVERT: A 444 MET cc_start: 0.9371 (mtp) cc_final: 0.9122 (mtm) REVERT: A 789 LEU cc_start: 0.9582 (tp) cc_final: 0.9240 (pp) REVERT: A 840 MET cc_start: 0.8577 (tpt) cc_final: 0.8294 (tpt) REVERT: B 194 MET cc_start: 0.2881 (ttm) cc_final: 0.2325 (ttt) REVERT: B 318 MET cc_start: 0.7245 (tmm) cc_final: 0.6947 (ppp) REVERT: B 322 MET cc_start: 0.8067 (mmm) cc_final: 0.7824 (mmt) REVERT: B 822 MET cc_start: 0.4406 (pmm) cc_final: 0.3955 (pmm) REVERT: C 194 MET cc_start: 0.8620 (ttp) cc_final: 0.7926 (tmm) REVERT: C 217 MET cc_start: 0.9399 (ptt) cc_final: 0.8868 (ppp) REVERT: C 299 CYS cc_start: 0.9482 (m) cc_final: 0.8741 (t) REVERT: C 318 MET cc_start: 0.7844 (ttm) cc_final: 0.7540 (ptm) REVERT: C 322 MET cc_start: 0.9000 (tmm) cc_final: 0.8695 (ptm) REVERT: C 822 MET cc_start: 0.7789 (pmt) cc_final: 0.7360 (pmm) REVERT: D 194 MET cc_start: 0.5070 (mtm) cc_final: 0.4617 (mtm) REVERT: D 243 MET cc_start: 0.9590 (ttm) cc_final: 0.9244 (ppp) REVERT: D 523 LEU cc_start: 0.9612 (mm) cc_final: 0.9390 (tp) REVERT: D 605 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8013 (tpt) REVERT: D 640 MET cc_start: 0.9067 (mmm) cc_final: 0.8825 (mmp) REVERT: D 840 MET cc_start: 0.8171 (tpp) cc_final: 0.7660 (ptt) REVERT: E 194 MET cc_start: 0.7078 (ttp) cc_final: 0.5437 (tmm) REVERT: E 217 MET cc_start: 0.8824 (ptm) cc_final: 0.8311 (ppp) REVERT: E 322 MET cc_start: 0.9140 (mtt) cc_final: 0.8854 (mmt) REVERT: E 745 TYR cc_start: -0.0572 (OUTLIER) cc_final: -0.1856 (p90) REVERT: E 784 TRP cc_start: 0.6321 (m100) cc_final: 0.5792 (p-90) REVERT: E 822 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7186 (tpt) REVERT: F 217 MET cc_start: 0.9764 (ptm) cc_final: 0.9259 (ppp) REVERT: F 322 MET cc_start: 0.9531 (tmm) cc_final: 0.8928 (ptm) REVERT: F 551 TYR cc_start: 0.9597 (m-80) cc_final: 0.9311 (m-80) REVERT: G 194 MET cc_start: 0.6270 (mtm) cc_final: 0.6032 (mtt) REVERT: G 243 MET cc_start: 0.9641 (mmm) cc_final: 0.9349 (mmm) REVERT: G 276 MET cc_start: 0.9327 (mpp) cc_final: 0.9103 (mpp) REVERT: G 318 MET cc_start: 0.6387 (ttm) cc_final: 0.5823 (ptm) REVERT: G 322 MET cc_start: 0.9618 (tmm) cc_final: 0.9254 (ttt) REVERT: G 444 MET cc_start: 0.6937 (mtt) cc_final: 0.6199 (mpp) REVERT: H 194 MET cc_start: 0.6841 (ttt) cc_final: 0.5156 (tmm) REVERT: H 217 MET cc_start: 0.9627 (ppp) cc_final: 0.9394 (ppp) REVERT: H 602 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8649 (t0) REVERT: I 276 MET cc_start: 0.9217 (mtm) cc_final: 0.8918 (ptp) REVERT: I 318 MET cc_start: 0.4538 (ptm) cc_final: 0.4102 (ptm) REVERT: I 344 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7815 (t-90) REVERT: I 551 TYR cc_start: 0.9383 (m-80) cc_final: 0.9070 (m-80) REVERT: I 822 MET cc_start: 0.6555 (ptm) cc_final: 0.5688 (pmm) REVERT: I 826 TYR cc_start: 0.1176 (OUTLIER) cc_final: 0.0087 (t80) outliers start: 73 outliers final: 45 residues processed: 371 average time/residue: 0.4519 time to fit residues: 285.3268 Evaluate side-chains 334 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 283 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 826 TYR Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 745 TYR Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 835 TYR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 497 HIS Chi-restraints excluded: chain F residue 836 GLN Chi-restraints excluded: chain G residue 354 GLU Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 602 ASP Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 314 THR Chi-restraints excluded: chain I residue 344 HIS Chi-restraints excluded: chain I residue 355 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 397 ILE Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 538 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 318 optimal weight: 40.0000 chunk 407 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 469 optimal weight: 9.9990 chunk 311 optimal weight: 1.9990 chunk 556 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 HIS D 196 ASN E 196 ASN H 196 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 695 HIS I 196 ASN ** I 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 707 GLN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 47569 Z= 0.255 Angle : 0.682 12.613 64235 Z= 0.354 Chirality : 0.041 0.248 7353 Planarity : 0.004 0.047 8131 Dihedral : 4.979 55.518 6254 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.43 % Allowed : 13.02 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.11), residues: 5785 helix: 1.07 (0.08), residues: 4213 sheet: -2.20 (0.38), residues: 170 loop : 1.12 (0.19), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 784 HIS 0.008 0.001 HIS A 497 PHE 0.029 0.002 PHE B 365 TYR 0.017 0.002 TYR A 567 ARG 0.015 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 293 time to evaluate : 4.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8108 (tpt) cc_final: 0.7406 (mmt) REVERT: A 216 MET cc_start: 0.5600 (mtp) cc_final: 0.5169 (ttt) REVERT: A 217 MET cc_start: 0.7290 (ptm) cc_final: 0.7039 (ptm) REVERT: A 306 GLU cc_start: 0.9787 (tp30) cc_final: 0.9440 (mm-30) REVERT: A 444 MET cc_start: 0.9376 (mtp) cc_final: 0.9124 (mtm) REVERT: A 481 MET cc_start: 0.9579 (mmp) cc_final: 0.9135 (mmm) REVERT: A 789 LEU cc_start: 0.9604 (tp) cc_final: 0.9267 (pp) REVERT: B 194 MET cc_start: 0.2826 (ttm) cc_final: 0.2230 (ttt) REVERT: B 290 MET cc_start: 0.8807 (ttt) cc_final: 0.8392 (mmm) REVERT: B 318 MET cc_start: 0.7246 (tmm) cc_final: 0.6927 (ppp) REVERT: B 322 MET cc_start: 0.8034 (mmm) cc_final: 0.7668 (mmm) REVERT: B 640 MET cc_start: 0.9238 (tpp) cc_final: 0.8959 (tpp) REVERT: B 822 MET cc_start: 0.4600 (pmm) cc_final: 0.4320 (pmm) REVERT: C 194 MET cc_start: 0.8672 (ttp) cc_final: 0.7354 (tmm) REVERT: C 203 MET cc_start: 0.9743 (tpp) cc_final: 0.9501 (tpp) REVERT: C 217 MET cc_start: 0.9405 (ptt) cc_final: 0.8587 (tmm) REVERT: C 299 CYS cc_start: 0.9469 (m) cc_final: 0.8716 (t) REVERT: C 318 MET cc_start: 0.7923 (ttm) cc_final: 0.7574 (ptm) REVERT: C 822 MET cc_start: 0.7797 (pmt) cc_final: 0.7346 (pmm) REVERT: D 194 MET cc_start: 0.5425 (mtm) cc_final: 0.4375 (mtm) REVERT: D 243 MET cc_start: 0.9585 (ttm) cc_final: 0.9254 (ppp) REVERT: D 523 LEU cc_start: 0.9634 (mm) cc_final: 0.9414 (tp) REVERT: D 605 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8114 (tpt) REVERT: D 640 MET cc_start: 0.9105 (mmm) cc_final: 0.8847 (mmp) REVERT: D 822 MET cc_start: 0.3222 (mmp) cc_final: 0.2972 (pmm) REVERT: D 840 MET cc_start: 0.8199 (tpp) cc_final: 0.7709 (ptt) REVERT: E 194 MET cc_start: 0.7351 (ttp) cc_final: 0.5735 (tmm) REVERT: E 216 MET cc_start: 0.9268 (ttp) cc_final: 0.8807 (ttt) REVERT: E 217 MET cc_start: 0.8876 (ptm) cc_final: 0.8263 (ppp) REVERT: E 322 MET cc_start: 0.9200 (mtt) cc_final: 0.8923 (mmt) REVERT: E 784 TRP cc_start: 0.6455 (m100) cc_final: 0.5893 (p-90) REVERT: E 822 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7214 (tpt) REVERT: F 217 MET cc_start: 0.9765 (ptm) cc_final: 0.9256 (ppp) REVERT: F 243 MET cc_start: 0.9180 (ttm) cc_final: 0.8692 (ppp) REVERT: F 322 MET cc_start: 0.9533 (tmm) cc_final: 0.8941 (ptm) REVERT: F 551 TYR cc_start: 0.9577 (m-80) cc_final: 0.9268 (m-80) REVERT: G 194 MET cc_start: 0.6611 (mtm) cc_final: 0.6230 (mtt) REVERT: G 243 MET cc_start: 0.9649 (mmm) cc_final: 0.9344 (mmm) REVERT: G 276 MET cc_start: 0.9348 (mpp) cc_final: 0.9108 (mpp) REVERT: G 318 MET cc_start: 0.6454 (ttm) cc_final: 0.5668 (ptm) REVERT: G 322 MET cc_start: 0.9613 (tmm) cc_final: 0.9250 (ttt) REVERT: G 358 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8446 (tt) REVERT: G 444 MET cc_start: 0.6970 (mtt) cc_final: 0.6182 (mpp) REVERT: G 640 MET cc_start: 0.9190 (mmm) cc_final: 0.8693 (mmm) REVERT: G 745 TYR cc_start: 0.9106 (m-80) cc_final: 0.8701 (m-80) REVERT: H 194 MET cc_start: 0.6622 (ttt) cc_final: 0.3763 (tmm) REVERT: H 217 MET cc_start: 0.9648 (ppp) cc_final: 0.9417 (ppp) REVERT: H 640 MET cc_start: 0.8942 (mmm) cc_final: 0.8488 (mmm) REVERT: H 822 MET cc_start: 0.8729 (pmm) cc_final: 0.8311 (ptp) REVERT: I 276 MET cc_start: 0.9225 (mtm) cc_final: 0.8910 (ptp) REVERT: I 318 MET cc_start: 0.4782 (ptm) cc_final: 0.4222 (ptm) REVERT: I 344 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7960 (t-90) REVERT: I 551 TYR cc_start: 0.9384 (m-80) cc_final: 0.9068 (m-80) REVERT: I 822 MET cc_start: 0.6688 (ptm) cc_final: 0.5815 (pmm) REVERT: I 826 TYR cc_start: 0.0908 (OUTLIER) cc_final: -0.0137 (t80) outliers start: 74 outliers final: 50 residues processed: 358 average time/residue: 0.4549 time to fit residues: 278.8338 Evaluate side-chains 342 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 287 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 835 TYR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 497 HIS Chi-restraints excluded: chain F residue 670 MET Chi-restraints excluded: chain F residue 836 GLN Chi-restraints excluded: chain G residue 354 GLU Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 408 PHE Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain H residue 373 ASP Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 408 PHE Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 314 THR Chi-restraints excluded: chain I residue 344 HIS Chi-restraints excluded: chain I residue 355 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 408 PHE Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 344 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 378 optimal weight: 5.9990 chunk 274 optimal weight: 0.0050 chunk 51 optimal weight: 7.9990 chunk 437 optimal weight: 2.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN D 196 ASN H 196 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN I 509 ASN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47569 Z= 0.192 Angle : 0.669 13.200 64235 Z= 0.341 Chirality : 0.041 0.312 7353 Planarity : 0.004 0.049 8131 Dihedral : 4.847 54.298 6254 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 1.38 % Allowed : 13.68 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.12), residues: 5785 helix: 1.16 (0.08), residues: 4221 sheet: -2.20 (0.38), residues: 170 loop : 1.20 (0.19), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 405 HIS 0.008 0.001 HIS A 497 PHE 0.027 0.002 PHE B 365 TYR 0.016 0.001 TYR B 463 ARG 0.014 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 300 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.1626 (ttt) cc_final: -0.2625 (tpt) REVERT: A 203 MET cc_start: 0.8095 (tpt) cc_final: 0.7383 (mmt) REVERT: A 216 MET cc_start: 0.5613 (mtp) cc_final: 0.5191 (ttt) REVERT: A 217 MET cc_start: 0.7323 (ptm) cc_final: 0.7058 (ptm) REVERT: A 306 GLU cc_start: 0.9794 (tp30) cc_final: 0.9421 (mm-30) REVERT: A 316 LYS cc_start: 0.9670 (mttt) cc_final: 0.9409 (tptm) REVERT: A 444 MET cc_start: 0.9373 (mtp) cc_final: 0.9126 (mtm) REVERT: A 481 MET cc_start: 0.9564 (mmp) cc_final: 0.9042 (mmm) REVERT: A 789 LEU cc_start: 0.9605 (tp) cc_final: 0.9263 (pp) REVERT: A 840 MET cc_start: 0.8727 (tpt) cc_final: 0.8499 (tpt) REVERT: B 194 MET cc_start: 0.2688 (ttm) cc_final: 0.2090 (ttt) REVERT: B 217 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8987 (ppp) REVERT: B 318 MET cc_start: 0.7294 (tmm) cc_final: 0.6999 (ppp) REVERT: B 322 MET cc_start: 0.8078 (mmm) cc_final: 0.7819 (mmt) REVERT: B 822 MET cc_start: 0.4718 (pmm) cc_final: 0.4505 (pmm) REVERT: C 194 MET cc_start: 0.7950 (ttp) cc_final: 0.7144 (tmm) REVERT: C 217 MET cc_start: 0.9405 (ptt) cc_final: 0.8917 (ppp) REVERT: C 299 CYS cc_start: 0.9473 (m) cc_final: 0.8746 (t) REVERT: C 318 MET cc_start: 0.7885 (ttm) cc_final: 0.7664 (ptm) REVERT: C 322 MET cc_start: 0.9021 (tmm) cc_final: 0.8768 (ptm) REVERT: C 640 MET cc_start: 0.9302 (tpp) cc_final: 0.8809 (tpt) REVERT: C 822 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7335 (pmm) REVERT: D 194 MET cc_start: 0.5018 (mtm) cc_final: 0.3213 (mtm) REVERT: D 198 GLU cc_start: 0.9733 (mm-30) cc_final: 0.9526 (mp0) REVERT: D 203 MET cc_start: 0.9805 (tpp) cc_final: 0.9596 (tpp) REVERT: D 243 MET cc_start: 0.9583 (ttm) cc_final: 0.9255 (ppp) REVERT: D 640 MET cc_start: 0.9099 (mmm) cc_final: 0.8831 (mmp) REVERT: D 840 MET cc_start: 0.8165 (tpp) cc_final: 0.7719 (ptt) REVERT: E 194 MET cc_start: 0.7465 (ttp) cc_final: 0.5643 (tmm) REVERT: E 216 MET cc_start: 0.9349 (ttp) cc_final: 0.8952 (ttt) REVERT: E 217 MET cc_start: 0.8966 (ptm) cc_final: 0.8395 (ppp) REVERT: E 322 MET cc_start: 0.9244 (mtt) cc_final: 0.8966 (mmt) REVERT: E 670 MET cc_start: 0.9592 (ptp) cc_final: 0.9390 (ptp) REVERT: E 745 TYR cc_start: -0.0500 (OUTLIER) cc_final: -0.1766 (p90) REVERT: E 784 TRP cc_start: 0.6420 (m100) cc_final: 0.5854 (p-90) REVERT: E 822 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7244 (tpt) REVERT: F 217 MET cc_start: 0.9757 (ptm) cc_final: 0.9346 (ppp) REVERT: F 243 MET cc_start: 0.9124 (ttm) cc_final: 0.8641 (ppp) REVERT: F 322 MET cc_start: 0.9549 (tmm) cc_final: 0.8975 (ptm) REVERT: F 551 TYR cc_start: 0.9587 (m-80) cc_final: 0.9286 (m-80) REVERT: G 194 MET cc_start: 0.5509 (mtm) cc_final: 0.4595 (ttm) REVERT: G 243 MET cc_start: 0.9662 (mmm) cc_final: 0.9424 (mmm) REVERT: G 276 MET cc_start: 0.9365 (mpp) cc_final: 0.9128 (mpp) REVERT: G 318 MET cc_start: 0.6381 (ttm) cc_final: 0.5883 (ptm) REVERT: G 322 MET cc_start: 0.9624 (tmm) cc_final: 0.9286 (ttt) REVERT: G 444 MET cc_start: 0.6900 (mtt) cc_final: 0.6056 (mpp) REVERT: G 640 MET cc_start: 0.9189 (mmm) cc_final: 0.8689 (mmm) REVERT: G 745 TYR cc_start: 0.9089 (m-80) cc_final: 0.8669 (m-80) REVERT: H 194 MET cc_start: 0.5432 (ttt) cc_final: 0.2869 (tmm) REVERT: H 217 MET cc_start: 0.9654 (ppp) cc_final: 0.9411 (ppp) REVERT: H 419 TYR cc_start: 0.9365 (t80) cc_final: 0.8821 (m-80) REVERT: H 822 MET cc_start: 0.8673 (pmm) cc_final: 0.8248 (ptp) REVERT: I 276 MET cc_start: 0.9232 (mtm) cc_final: 0.8904 (ptp) REVERT: I 318 MET cc_start: 0.4783 (ptm) cc_final: 0.4292 (ptm) REVERT: I 344 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7908 (t-90) REVERT: I 551 TYR cc_start: 0.9382 (m-80) cc_final: 0.9069 (m-80) REVERT: I 822 MET cc_start: 0.6735 (ptm) cc_final: 0.5937 (pmm) REVERT: I 826 TYR cc_start: 0.0824 (OUTLIER) cc_final: -0.0257 (t80) outliers start: 71 outliers final: 48 residues processed: 363 average time/residue: 0.4571 time to fit residues: 283.2011 Evaluate side-chains 337 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 283 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 497 HIS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 745 TYR Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 835 TYR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 497 HIS Chi-restraints excluded: chain F residue 667 THR Chi-restraints excluded: chain F residue 836 GLN Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 408 PHE Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain G residue 780 ASN Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain H residue 653 MET Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 314 THR Chi-restraints excluded: chain I residue 344 HIS Chi-restraints excluded: chain I residue 355 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 408 PHE Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 691 GLU Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 505 optimal weight: 9.9990 chunk 532 optimal weight: 8.9990 chunk 486 optimal weight: 0.0770 chunk 518 optimal weight: 4.9990 chunk 311 optimal weight: 0.0060 chunk 225 optimal weight: 5.9990 chunk 406 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 468 optimal weight: 6.9990 chunk 490 optimal weight: 3.9990 chunk 516 optimal weight: 8.9990 overall best weight: 3.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN D 196 ASN F 619 GLN H 196 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 47569 Z= 0.185 Angle : 0.683 14.326 64235 Z= 0.346 Chirality : 0.042 0.343 7353 Planarity : 0.004 0.049 8131 Dihedral : 4.770 53.030 6254 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 1.10 % Allowed : 14.20 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.12), residues: 5785 helix: 1.22 (0.08), residues: 4217 sheet: -2.13 (0.39), residues: 168 loop : 1.25 (0.20), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 474 HIS 0.010 0.001 HIS I 497 PHE 0.026 0.001 PHE B 365 TYR 0.015 0.001 TYR E 835 ARG 0.018 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 297 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.1692 (ttt) cc_final: -0.2716 (tpt) REVERT: A 203 MET cc_start: 0.8070 (tpt) cc_final: 0.7366 (mmt) REVERT: A 216 MET cc_start: 0.5637 (mtp) cc_final: 0.5216 (ttt) REVERT: A 217 MET cc_start: 0.7224 (ptm) cc_final: 0.6970 (ptm) REVERT: A 306 GLU cc_start: 0.9797 (tp30) cc_final: 0.9452 (mm-30) REVERT: A 316 LYS cc_start: 0.9680 (mttt) cc_final: 0.9434 (tptm) REVERT: A 444 MET cc_start: 0.9375 (mtp) cc_final: 0.9131 (mtm) REVERT: A 481 MET cc_start: 0.9570 (mmp) cc_final: 0.9048 (mmm) REVERT: A 736 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8516 (ptt90) REVERT: A 789 LEU cc_start: 0.9592 (tp) cc_final: 0.9255 (pp) REVERT: B 194 MET cc_start: 0.2750 (ttm) cc_final: 0.2137 (ttt) REVERT: B 217 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9000 (ppp) REVERT: B 318 MET cc_start: 0.7278 (tmm) cc_final: 0.7015 (ppp) REVERT: B 322 MET cc_start: 0.8056 (mmm) cc_final: 0.7806 (mmt) REVERT: B 822 MET cc_start: 0.4626 (pmm) cc_final: 0.4422 (pmm) REVERT: B 840 MET cc_start: 0.8475 (mmp) cc_final: 0.7517 (ppp) REVERT: C 194 MET cc_start: 0.8202 (ttp) cc_final: 0.7370 (tmm) REVERT: C 217 MET cc_start: 0.9396 (ptt) cc_final: 0.8916 (ppp) REVERT: C 276 MET cc_start: 0.9409 (mpp) cc_final: 0.8867 (ppp) REVERT: C 299 CYS cc_start: 0.9458 (m) cc_final: 0.8721 (t) REVERT: C 318 MET cc_start: 0.7833 (ttm) cc_final: 0.7609 (ptm) REVERT: C 322 MET cc_start: 0.9038 (tmm) cc_final: 0.8791 (ptm) REVERT: C 822 MET cc_start: 0.7763 (pmt) cc_final: 0.7331 (pmm) REVERT: D 194 MET cc_start: 0.5000 (mtm) cc_final: 0.3453 (mtm) REVERT: D 203 MET cc_start: 0.9799 (tpp) cc_final: 0.9588 (tpp) REVERT: D 243 MET cc_start: 0.9552 (ttm) cc_final: 0.9269 (ppp) REVERT: D 605 MET cc_start: 0.9066 (tpt) cc_final: 0.8209 (tpt) REVERT: D 640 MET cc_start: 0.9075 (mmm) cc_final: 0.8800 (mmp) REVERT: D 840 MET cc_start: 0.8155 (tpp) cc_final: 0.7732 (ptt) REVERT: E 194 MET cc_start: 0.7459 (ttp) cc_final: 0.5605 (tmm) REVERT: E 217 MET cc_start: 0.9064 (ptm) cc_final: 0.8746 (ppp) REVERT: E 322 MET cc_start: 0.9266 (mtt) cc_final: 0.8980 (mmt) REVERT: E 640 MET cc_start: 0.9523 (ptp) cc_final: 0.9253 (ptp) REVERT: E 745 TYR cc_start: -0.0403 (OUTLIER) cc_final: -0.1691 (p90) REVERT: E 784 TRP cc_start: 0.6467 (m100) cc_final: 0.5894 (p-90) REVERT: E 822 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7273 (tpt) REVERT: F 217 MET cc_start: 0.9759 (ptm) cc_final: 0.9354 (ppp) REVERT: F 243 MET cc_start: 0.9137 (ttm) cc_final: 0.8695 (ppp) REVERT: F 551 TYR cc_start: 0.9582 (m-80) cc_final: 0.9282 (m-80) REVERT: G 194 MET cc_start: 0.5134 (mtm) cc_final: 0.4150 (mtp) REVERT: G 243 MET cc_start: 0.9667 (mmm) cc_final: 0.9434 (mmm) REVERT: G 276 MET cc_start: 0.9297 (mpp) cc_final: 0.9053 (mpp) REVERT: G 318 MET cc_start: 0.6359 (ttm) cc_final: 0.5826 (ptm) REVERT: G 322 MET cc_start: 0.9624 (tmm) cc_final: 0.9302 (ttt) REVERT: G 444 MET cc_start: 0.6780 (mtt) cc_final: 0.5989 (mpp) REVERT: G 594 LEU cc_start: 0.8753 (mm) cc_final: 0.8346 (mm) REVERT: G 640 MET cc_start: 0.9216 (mmm) cc_final: 0.8741 (mmm) REVERT: G 745 TYR cc_start: 0.9083 (m-80) cc_final: 0.8660 (m-80) REVERT: H 194 MET cc_start: 0.5145 (ttt) cc_final: 0.3156 (tmm) REVERT: H 217 MET cc_start: 0.9663 (ppp) cc_final: 0.9441 (ppp) REVERT: H 640 MET cc_start: 0.8824 (mmm) cc_final: 0.8338 (mmm) REVERT: H 822 MET cc_start: 0.8652 (pmm) cc_final: 0.8239 (ptp) REVERT: I 276 MET cc_start: 0.9236 (mtm) cc_final: 0.8906 (ptp) REVERT: I 318 MET cc_start: 0.4845 (ptm) cc_final: 0.4387 (ptm) REVERT: I 551 TYR cc_start: 0.9376 (m-80) cc_final: 0.9076 (m-80) REVERT: I 822 MET cc_start: 0.6735 (ptm) cc_final: 0.5947 (pmm) REVERT: I 826 TYR cc_start: 0.0547 (OUTLIER) cc_final: -0.0502 (t80) outliers start: 57 outliers final: 42 residues processed: 347 average time/residue: 0.4590 time to fit residues: 272.1144 Evaluate side-chains 333 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 287 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 780 ASN Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 745 TYR Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 835 TYR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 497 HIS Chi-restraints excluded: chain F residue 667 THR Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 408 PHE Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain G residue 780 ASN Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain H residue 653 MET Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 355 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 408 PHE Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 565 VAL Chi-restraints excluded: chain I residue 667 THR Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 340 optimal weight: 6.9990 chunk 548 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 380 optimal weight: 5.9990 chunk 574 optimal weight: 9.9990 chunk 529 optimal weight: 0.8980 chunk 457 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 353 optimal weight: 8.9990 chunk 280 optimal weight: 50.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN C 780 ASN D 196 ASN H 196 ASN H 360 HIS ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 47569 Z= 0.236 Angle : 0.722 14.451 64235 Z= 0.369 Chirality : 0.043 0.335 7353 Planarity : 0.004 0.048 8131 Dihedral : 4.824 51.705 6254 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 1.01 % Allowed : 14.51 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 5785 helix: 1.12 (0.08), residues: 4223 sheet: -2.19 (0.39), residues: 170 loop : 1.20 (0.19), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 474 HIS 0.008 0.001 HIS A 497 PHE 0.028 0.002 PHE I 342 TYR 0.015 0.001 TYR E 835 ARG 0.019 0.000 ARG A 845 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 289 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.1675 (ttt) cc_final: -0.2707 (tpt) REVERT: A 203 MET cc_start: 0.8128 (tpt) cc_final: 0.7427 (mmt) REVERT: A 216 MET cc_start: 0.5643 (mtp) cc_final: 0.5233 (ttt) REVERT: A 217 MET cc_start: 0.7270 (ptm) cc_final: 0.7019 (ptm) REVERT: A 306 GLU cc_start: 0.9790 (tp30) cc_final: 0.9452 (mm-30) REVERT: A 316 LYS cc_start: 0.9673 (mttt) cc_final: 0.9407 (tptm) REVERT: A 444 MET cc_start: 0.9388 (mtp) cc_final: 0.9146 (mtm) REVERT: A 481 MET cc_start: 0.9585 (mmp) cc_final: 0.9073 (mmm) REVERT: A 789 LEU cc_start: 0.9606 (tp) cc_final: 0.9276 (pp) REVERT: B 194 MET cc_start: 0.2751 (ttm) cc_final: 0.2101 (ttt) REVERT: B 217 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9097 (ppp) REVERT: B 322 MET cc_start: 0.8227 (mmm) cc_final: 0.7878 (mmm) REVERT: B 822 MET cc_start: 0.4596 (pmm) cc_final: 0.4347 (pmm) REVERT: C 194 MET cc_start: 0.8369 (ttp) cc_final: 0.7629 (tmm) REVERT: C 217 MET cc_start: 0.9412 (ptt) cc_final: 0.8916 (ppp) REVERT: C 276 MET cc_start: 0.9416 (mpp) cc_final: 0.8856 (ppp) REVERT: C 299 CYS cc_start: 0.9440 (m) cc_final: 0.8718 (t) REVERT: C 318 MET cc_start: 0.7890 (ttm) cc_final: 0.7555 (ptm) REVERT: C 780 ASN cc_start: 0.5373 (OUTLIER) cc_final: 0.5035 (p0) REVERT: C 822 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7352 (pmm) REVERT: C 833 HIS cc_start: 0.3793 (OUTLIER) cc_final: 0.3408 (t-170) REVERT: D 194 MET cc_start: 0.4618 (mtm) cc_final: 0.0429 (tmm) REVERT: D 198 GLU cc_start: 0.9755 (mp0) cc_final: 0.9479 (mp0) REVERT: D 203 MET cc_start: 0.9803 (tpp) cc_final: 0.9595 (tpp) REVERT: D 243 MET cc_start: 0.9558 (ttm) cc_final: 0.9298 (ppp) REVERT: D 605 MET cc_start: 0.9256 (tpt) cc_final: 0.8512 (tpt) REVERT: D 640 MET cc_start: 0.9091 (mmm) cc_final: 0.8815 (mmp) REVERT: D 840 MET cc_start: 0.8165 (tpp) cc_final: 0.7754 (ptt) REVERT: E 194 MET cc_start: 0.7626 (ttp) cc_final: 0.5649 (tmm) REVERT: E 216 MET cc_start: 0.9493 (ttp) cc_final: 0.9154 (ttt) REVERT: E 217 MET cc_start: 0.9152 (ptm) cc_final: 0.8594 (ppp) REVERT: E 322 MET cc_start: 0.9282 (mtt) cc_final: 0.9000 (mmt) REVERT: E 640 MET cc_start: 0.9535 (ptp) cc_final: 0.9299 (ptp) REVERT: E 745 TYR cc_start: -0.0299 (OUTLIER) cc_final: -0.1648 (p90) REVERT: E 784 TRP cc_start: 0.6464 (m100) cc_final: 0.5867 (p-90) REVERT: E 822 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7227 (tpt) REVERT: F 217 MET cc_start: 0.9755 (ptm) cc_final: 0.9550 (ppp) REVERT: F 322 MET cc_start: 0.9527 (tmm) cc_final: 0.8911 (ptm) REVERT: F 551 TYR cc_start: 0.9585 (m-80) cc_final: 0.9252 (m-80) REVERT: G 194 MET cc_start: 0.5364 (mtm) cc_final: 0.4381 (mtp) REVERT: G 243 MET cc_start: 0.9660 (mmm) cc_final: 0.9359 (mmm) REVERT: G 276 MET cc_start: 0.9319 (mpp) cc_final: 0.9075 (mpp) REVERT: G 318 MET cc_start: 0.6452 (ttm) cc_final: 0.5653 (ptm) REVERT: G 322 MET cc_start: 0.9612 (tmm) cc_final: 0.9262 (ttt) REVERT: G 444 MET cc_start: 0.6845 (mtt) cc_final: 0.6079 (mpp) REVERT: G 745 TYR cc_start: 0.9086 (m-80) cc_final: 0.8671 (m-80) REVERT: H 194 MET cc_start: 0.5300 (ttt) cc_final: 0.3652 (tmm) REVERT: H 217 MET cc_start: 0.9675 (ppp) cc_final: 0.9439 (ppp) REVERT: H 640 MET cc_start: 0.8836 (mmm) cc_final: 0.8375 (mmm) REVERT: H 822 MET cc_start: 0.8568 (pmm) cc_final: 0.8173 (ptp) REVERT: I 276 MET cc_start: 0.9246 (mtm) cc_final: 0.8907 (ptp) REVERT: I 318 MET cc_start: 0.4894 (ptm) cc_final: 0.4317 (ptm) REVERT: I 551 TYR cc_start: 0.9369 (m-80) cc_final: 0.9051 (m-80) REVERT: I 822 MET cc_start: 0.6782 (ptm) cc_final: 0.5975 (pmm) REVERT: I 826 TYR cc_start: 0.0619 (OUTLIER) cc_final: -0.0379 (t80) outliers start: 52 outliers final: 42 residues processed: 330 average time/residue: 0.4555 time to fit residues: 256.8584 Evaluate side-chains 332 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 283 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 780 ASN Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain C residue 833 HIS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 365 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 665 SER Chi-restraints excluded: chain E residue 745 TYR Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain E residue 835 TYR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 397 ILE Chi-restraints excluded: chain F residue 497 HIS Chi-restraints excluded: chain F residue 667 THR Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 408 PHE Chi-restraints excluded: chain G residue 493 VAL Chi-restraints excluded: chain G residue 551 TYR Chi-restraints excluded: chain G residue 780 ASN Chi-restraints excluded: chain H residue 401 LYS Chi-restraints excluded: chain H residue 565 VAL Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain H residue 653 MET Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 355 THR Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 408 PHE Chi-restraints excluded: chain I residue 481 MET Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 667 THR Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 363 optimal weight: 0.9980 chunk 487 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 422 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 458 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 470 optimal weight: 7.9990 chunk 58 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 ASN C 827 ASN E 196 ASN F 652 GLN H 196 ASN ** H 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.102070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.084599 restraints weight = 397688.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.084325 restraints weight = 166333.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.084596 restraints weight = 90244.788| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47569 Z= 0.202 Angle : 0.725 14.637 64235 Z= 0.366 Chirality : 0.043 0.377 7353 Planarity : 0.004 0.048 8131 Dihedral : 4.756 50.862 6253 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.03 % Rotamer: Outliers : 0.99 % Allowed : 14.61 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.12), residues: 5785 helix: 1.16 (0.08), residues: 4217 sheet: -2.06 (0.41), residues: 159 loop : 1.17 (0.19), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 474 HIS 0.008 0.001 HIS A 497 PHE 0.027 0.001 PHE B 365 TYR 0.016 0.001 TYR E 835 ARG 0.020 0.000 ARG A 845 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7708.49 seconds wall clock time: 137 minutes 14.64 seconds (8234.64 seconds total)