Starting phenix.real_space_refine on Mon Sep 30 06:31:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cc0_45430/09_2024/9cc0_45430.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cc0_45430/09_2024/9cc0_45430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cc0_45430/09_2024/9cc0_45430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cc0_45430/09_2024/9cc0_45430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cc0_45430/09_2024/9cc0_45430.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cc0_45430/09_2024/9cc0_45430.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 118 5.16 5 C 15570 2.51 5 N 4224 2.21 5 O 4671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24603 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4097 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "B" Number of atoms: 4091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4091 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4099 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4047 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4039 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 494} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3988 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 486} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.51, per 1000 atoms: 0.63 Number of scatterers: 24603 At special positions: 0 Unit cell: (131.1, 138, 132.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 16 15.00 Mg 4 11.99 O 4671 8.00 N 4224 7.00 C 15570 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: 6.45 Conformation dependent library (CDL) restraints added in 2.9 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5838 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 32 sheets defined 52.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 417 through 425 removed outlier: 4.450A pdb=" N PHE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 431 through 448 removed outlier: 4.563A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.599A pdb=" N ASN A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.519A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.835A pdb=" N GLU A 557 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 592 through 595 removed outlier: 3.729A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 592 through 595' Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.102A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 4.041A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 removed outlier: 4.214A pdb=" N LYS A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.157A pdb=" N THR A 644 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.766A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.967A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 424 removed outlier: 3.767A pdb=" N PHE B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.884A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.545A pdb=" N ARG B 511 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 541 removed outlier: 3.777A pdb=" N ALA B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.559A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.908A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.617A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 747 removed outlier: 3.818A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.978A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.558A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 4.141A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.585A pdb=" N ALA C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.700A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 removed outlier: 3.981A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.703A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 683 removed outlier: 3.633A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL C 675 " --> pdb=" O GLU C 671 " (cutoff:3.500A) Proline residue: C 676 - end of helix Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 711 through 729 Processing helix chain 'C' and resid 741 through 747 removed outlier: 3.844A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 924 through 928 Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.946A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 removed outlier: 3.782A pdb=" N ARG D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.848A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.590A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 removed outlier: 3.517A pdb=" N ASP D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 570 through 581 removed outlier: 4.025A pdb=" N ILE D 574 " --> pdb=" O PRO D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 removed outlier: 4.016A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.630A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 4.383A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.801A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 removed outlier: 3.713A pdb=" N THR D 837 " --> pdb=" O ASP D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 906 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.760A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.818A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 424 Processing helix chain 'E' and resid 431 through 448 removed outlier: 4.431A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 removed outlier: 4.019A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 528 through 541 removed outlier: 3.549A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 603 through 612 Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.302A pdb=" N ALA E 617 " --> pdb=" O PRO E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 682 Processing helix chain 'E' and resid 692 through 702 Processing helix chain 'E' and resid 709 through 729 removed outlier: 3.592A pdb=" N LYS E 714 " --> pdb=" O ARG E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.530A pdb=" N GLN E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 838 Processing helix chain 'E' and resid 853 through 855 No H-bonds generated for 'chain 'E' and resid 853 through 855' Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.917A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.880A pdb=" N LEU F 425 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 452 through 466 Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 494 through 512 removed outlier: 3.827A pdb=" N LYS F 498 " --> pdb=" O MET F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 541 Processing helix chain 'F' and resid 571 through 580 Processing helix chain 'F' and resid 603 through 611 Processing helix chain 'F' and resid 612 through 617 removed outlier: 4.419A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 650 Processing helix chain 'F' and resid 662 through 673 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 704 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 742 through 747 Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 832 through 836 removed outlier: 4.425A pdb=" N LEU F 835 " --> pdb=" O ASN F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 906 Processing helix chain 'F' and resid 916 through 921 Processing helix chain 'F' and resid 924 through 929 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.919A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.927A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA3, first strand: chain 'A' and resid 765 through 770 removed outlier: 6.092A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.759A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA6, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.159A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 654 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 619 through 620 removed outlier: 3.503A pdb=" N PHE B 619 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 689 through 690 Processing sheet with id=AA9, first strand: chain 'B' and resid 764 through 770 removed outlier: 6.039A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.955A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB3, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.255A pdb=" N ILE C 587 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR C 638 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB5, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.901A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 764 through 770 removed outlier: 5.977A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.820A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB9, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.846A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 519 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA D 639 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE D 521 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 691 removed outlier: 7.009A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 764 through 769 removed outlier: 6.069A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 877 through 879 removed outlier: 3.521A pdb=" N ILE D 910 " --> pdb=" O GLU D 932 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC5, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.647A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.895A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 765 through 771 removed outlier: 5.991A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.825A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AD1, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.593A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.014A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 764 through 771 removed outlier: 6.205A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 877 through 879 Processing sheet with id=AD5, first strand: chain 'F' and resid 882 through 883 removed outlier: 3.506A pdb=" N GLU F 882 " --> pdb=" O LEU F 890 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3345 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: 8.44 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6821 1.33 - 1.45: 3948 1.45 - 1.58: 14056 1.58 - 1.70: 26 1.70 - 1.82: 194 Bond restraints: 25045 Sorted by residual: bond pdb=" N ASP F 463 " pdb=" CA ASP F 463 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.16e-02 7.43e+03 8.17e+00 bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.23e+00 bond pdb=" N TRP F 464 " pdb=" CA TRP F 464 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.33e+00 bond pdb=" N THR F 466 " pdb=" CA THR F 466 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.00e+00 bond pdb=" N LEU F 465 " pdb=" CA LEU F 465 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.52e+00 ... (remaining 25040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 33378 1.69 - 3.38: 441 3.38 - 5.06: 79 5.06 - 6.75: 18 6.75 - 8.44: 7 Bond angle restraints: 33923 Sorted by residual: angle pdb=" CA LEU F 462 " pdb=" C LEU F 462 " pdb=" O LEU F 462 " ideal model delta sigma weight residual 120.82 117.27 3.55 1.05e+00 9.07e-01 1.14e+01 angle pdb=" CA GLU D 781 " pdb=" C GLU D 781 " pdb=" O GLU D 781 " ideal model delta sigma weight residual 120.80 117.10 3.70 1.11e+00 8.12e-01 1.11e+01 angle pdb=" CA ASP F 463 " pdb=" C ASP F 463 " pdb=" O ASP F 463 " ideal model delta sigma weight residual 121.07 117.51 3.56 1.10e+00 8.26e-01 1.05e+01 angle pdb=" N ASN B 584 " pdb=" CA ASN B 584 " pdb=" C ASN B 584 " ideal model delta sigma weight residual 109.81 116.78 -6.97 2.21e+00 2.05e-01 9.94e+00 angle pdb=" CA TRP F 464 " pdb=" C TRP F 464 " pdb=" O TRP F 464 " ideal model delta sigma weight residual 121.07 117.74 3.33 1.10e+00 8.26e-01 9.14e+00 ... (remaining 33918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 14086 17.43 - 34.86: 944 34.86 - 52.29: 228 52.29 - 69.72: 50 69.72 - 87.15: 24 Dihedral angle restraints: 15332 sinusoidal: 6274 harmonic: 9058 Sorted by residual: dihedral pdb=" CA ASN B 584 " pdb=" C ASN B 584 " pdb=" N PRO B 585 " pdb=" CA PRO B 585 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASP F 833 " pdb=" C ASP F 833 " pdb=" N TYR F 834 " pdb=" CA TYR F 834 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA TYR D 492 " pdb=" C TYR D 492 " pdb=" N GLY D 493 " pdb=" CA GLY D 493 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 15329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2887 0.043 - 0.085: 767 0.085 - 0.128: 228 0.128 - 0.170: 11 0.170 - 0.213: 6 Chirality restraints: 3899 Sorted by residual: chirality pdb=" CA ASP F 463 " pdb=" N ASP F 463 " pdb=" C ASP F 463 " pdb=" CB ASP F 463 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB THR B 514 " pdb=" CA THR B 514 " pdb=" OG1 THR B 514 " pdb=" CG2 THR B 514 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE F 645 " pdb=" CA ILE F 645 " pdb=" CG1 ILE F 645 " pdb=" CG2 ILE F 645 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 3896 not shown) Planarity restraints: 4334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 461 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C TYR F 461 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR F 461 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU F 462 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 670 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ALA E 670 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA E 670 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU E 671 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 844 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 845 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 845 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 845 " 0.022 5.00e-02 4.00e+02 ... (remaining 4331 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 170 2.58 - 3.16: 20249 3.16 - 3.74: 38200 3.74 - 4.32: 53006 4.32 - 4.90: 88735 Nonbonded interactions: 200360 Sorted by model distance: nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1001 " model vdw 1.995 2.170 nonbonded pdb=" OG1 THR A 530 " pdb="MG MG A1001 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR C 530 " pdb="MG MG C1001 " model vdw 2.002 2.170 nonbonded pdb=" O1G ATP C1000 " pdb="MG MG C1001 " model vdw 2.025 2.170 nonbonded pdb=" O1G ATP A1000 " pdb="MG MG A1001 " model vdw 2.035 2.170 ... (remaining 200355 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 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 557 through 596 or resid 603 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or name \ CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 thro \ ugh 947)) selection = (chain 'B' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 557 through 596 or resid 603 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or name \ CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 thro \ ugh 947)) selection = (chain 'C' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 557 through 596 or resid 603 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or name \ CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 thro \ ugh 947)) selection = (chain 'D' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 557 through 631 or (resid 632 and (name N \ or name CA or name C or name O or name CB )) or resid 633 through 685 or (resid \ 686 and (name N or name CA or name C or name O or name CB )) or resid 687 throug \ h 947)) selection = (chain 'E' and (resid 420 through 550 or resid 557 through 596 or resid 603 thro \ ugh 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) o \ r resid 633 through 689 or (resid 690 and (name N or name CA or name C or name O \ or name CB )) or resid 691 through 772 or (resid 773 and (name N or name CA or \ name C or name O or name CB )) or resid 774 through 788 or resid 796 through 947 \ )) selection = (chain 'F' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 596 or resid 603 through 685 or (resid 686 and (name N \ or name CA or name C or name O or name CB )) or resid 687 through 689 or (resid \ 690 and (name N or name CA or name C or name O or name CB )) or resid 691 throug \ h 772 or (resid 773 and (name N or name CA or name C or name O or name CB )) or \ resid 774 through 788 or resid 796 through 947)) } 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 individual isotropic 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: 7.590 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.140 Set scattering table: 0.220 Process input model: 55.160 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.003 0.039 25045 Z= 0.195 Angle : 0.538 8.440 33923 Z= 0.281 Chirality : 0.042 0.213 3899 Planarity : 0.004 0.040 4334 Dihedral : 13.251 87.154 9494 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.08 % Allowed : 0.11 % Favored : 99.81 % 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: 1.17 (0.15), residues: 3096 helix: 1.61 (0.14), residues: 1347 sheet: 0.87 (0.27), residues: 401 loop : -0.02 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 464 HIS 0.003 0.001 HIS E 839 PHE 0.011 0.001 PHE E 820 TYR 0.015 0.001 TYR A 565 ARG 0.007 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 609 GLU cc_start: 0.8353 (tt0) cc_final: 0.8034 (tt0) REVERT: B 454 GLU cc_start: 0.7887 (tp30) cc_final: 0.7667 (tp30) REVERT: B 797 ASP cc_start: 0.8170 (t70) cc_final: 0.7762 (t0) REVERT: C 448 LEU cc_start: 0.8101 (mt) cc_final: 0.7594 (mt) REVERT: D 436 ASP cc_start: 0.7972 (m-30) cc_final: 0.7660 (m-30) REVERT: D 548 SER cc_start: 0.8537 (t) cc_final: 0.8185 (p) REVERT: E 463 ASP cc_start: 0.8369 (m-30) cc_final: 0.8117 (m-30) REVERT: E 482 ARG cc_start: 0.7774 (tmm160) cc_final: 0.7508 (tmm160) REVERT: E 554 ASP cc_start: 0.7572 (t0) cc_final: 0.7239 (m-30) REVERT: E 591 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7445 (tm-30) REVERT: E 594 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8411 (mmmt) REVERT: F 547 PHE cc_start: 0.6300 (t80) cc_final: 0.5917 (t80) REVERT: F 623 TYR cc_start: 0.4067 (t80) cc_final: 0.3823 (t80) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.3462 time to fit residues: 122.7464 Evaluate side-chains 169 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25045 Z= 0.268 Angle : 0.554 7.556 33923 Z= 0.284 Chirality : 0.043 0.199 3899 Planarity : 0.004 0.048 4334 Dihedral : 7.555 88.347 3552 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.56 % Allowed : 4.33 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.15 (0.15), residues: 3096 helix: 1.69 (0.14), residues: 1366 sheet: 0.61 (0.26), residues: 397 loop : -0.09 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 770 HIS 0.004 0.001 HIS C 843 PHE 0.014 0.001 PHE E 820 TYR 0.024 0.002 TYR F 834 ARG 0.005 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 797 ASP cc_start: 0.8129 (t70) cc_final: 0.7726 (t0) REVERT: C 569 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (mtm) REVERT: C 597 ARG cc_start: 0.7080 (mtp85) cc_final: 0.6594 (ttm-80) REVERT: D 432 LYS cc_start: 0.8815 (tptp) cc_final: 0.8277 (tptp) REVERT: D 436 ASP cc_start: 0.8058 (m-30) cc_final: 0.7499 (m-30) REVERT: D 548 SER cc_start: 0.8550 (t) cc_final: 0.8172 (p) REVERT: D 869 MET cc_start: 0.8502 (mtp) cc_final: 0.8239 (mtp) REVERT: E 464 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7654 (m-90) REVERT: E 554 ASP cc_start: 0.7719 (t0) cc_final: 0.7519 (t70) REVERT: E 591 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 594 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8475 (mmmt) REVERT: F 463 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: F 547 PHE cc_start: 0.6195 (t80) cc_final: 0.5915 (t80) REVERT: F 578 LYS cc_start: 0.7456 (tttm) cc_final: 0.7127 (mtpt) outliers start: 15 outliers final: 9 residues processed: 201 average time/residue: 0.3587 time to fit residues: 114.9370 Evaluate side-chains 173 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 463 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 589 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 251 optimal weight: 0.6980 chunk 280 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25045 Z= 0.155 Angle : 0.497 7.913 33923 Z= 0.252 Chirality : 0.041 0.229 3899 Planarity : 0.004 0.047 4334 Dihedral : 7.212 88.958 3552 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.64 % Allowed : 6.37 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.31 (0.15), residues: 3096 helix: 1.89 (0.14), residues: 1375 sheet: 0.62 (0.27), residues: 393 loop : -0.07 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 464 HIS 0.004 0.001 HIS F 622 PHE 0.014 0.001 PHE D 751 TYR 0.025 0.001 TYR F 834 ARG 0.004 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7485 (t80) cc_final: 0.7224 (t80) REVERT: A 632 LYS cc_start: 0.8867 (tppt) cc_final: 0.8538 (tppp) REVERT: B 797 ASP cc_start: 0.8188 (t70) cc_final: 0.7830 (t0) REVERT: C 569 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: D 432 LYS cc_start: 0.8747 (tptp) cc_final: 0.8187 (tptp) REVERT: D 436 ASP cc_start: 0.8049 (m-30) cc_final: 0.7305 (m-30) REVERT: D 548 SER cc_start: 0.8439 (t) cc_final: 0.8097 (p) REVERT: D 869 MET cc_start: 0.8534 (mtp) cc_final: 0.8275 (mtp) REVERT: D 919 ASP cc_start: 0.8298 (m-30) cc_final: 0.8065 (m-30) REVERT: E 464 TRP cc_start: 0.8068 (OUTLIER) cc_final: 0.7658 (m-90) REVERT: E 554 ASP cc_start: 0.7697 (t0) cc_final: 0.7493 (t70) REVERT: E 594 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8425 (mmmt) REVERT: F 547 PHE cc_start: 0.6272 (t80) cc_final: 0.5999 (t80) REVERT: F 578 LYS cc_start: 0.7460 (tttm) cc_final: 0.7129 (mtpt) outliers start: 17 outliers final: 13 residues processed: 191 average time/residue: 0.3545 time to fit residues: 109.0767 Evaluate side-chains 173 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN C 616 ASN D 561 HIS F 934 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25045 Z= 0.251 Angle : 0.526 9.147 33923 Z= 0.266 Chirality : 0.042 0.247 3899 Planarity : 0.004 0.052 4334 Dihedral : 7.173 89.094 3552 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.13 % Allowed : 7.57 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.26 (0.15), residues: 3096 helix: 1.87 (0.14), residues: 1380 sheet: 0.54 (0.27), residues: 395 loop : -0.13 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 770 HIS 0.005 0.001 HIS F 622 PHE 0.015 0.001 PHE E 820 TYR 0.029 0.001 TYR F 834 ARG 0.006 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7416 (t80) cc_final: 0.7146 (t80) REVERT: A 608 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8664 (mm) REVERT: A 632 LYS cc_start: 0.8846 (tppt) cc_final: 0.8500 (tppp) REVERT: B 797 ASP cc_start: 0.8079 (t70) cc_final: 0.7771 (t0) REVERT: C 569 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8465 (mtm) REVERT: D 432 LYS cc_start: 0.8773 (tptp) cc_final: 0.8119 (tptp) REVERT: D 436 ASP cc_start: 0.8116 (m-30) cc_final: 0.7326 (m-30) REVERT: D 548 SER cc_start: 0.8460 (t) cc_final: 0.8117 (p) REVERT: D 869 MET cc_start: 0.8574 (mtp) cc_final: 0.8307 (mtp) REVERT: D 919 ASP cc_start: 0.8372 (m-30) cc_final: 0.8142 (m-30) REVERT: F 547 PHE cc_start: 0.6296 (t80) cc_final: 0.6026 (t80) REVERT: F 578 LYS cc_start: 0.7416 (tttm) cc_final: 0.7026 (mtpt) outliers start: 30 outliers final: 19 residues processed: 190 average time/residue: 0.3527 time to fit residues: 108.3846 Evaluate side-chains 175 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25045 Z= 0.252 Angle : 0.519 9.980 33923 Z= 0.263 Chirality : 0.042 0.261 3899 Planarity : 0.004 0.054 4334 Dihedral : 7.099 88.000 3552 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.32 % Allowed : 8.51 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.25 (0.15), residues: 3096 helix: 1.89 (0.14), residues: 1374 sheet: 0.46 (0.26), residues: 397 loop : -0.13 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 770 HIS 0.005 0.001 HIS F 622 PHE 0.014 0.001 PHE E 820 TYR 0.028 0.001 TYR F 834 ARG 0.007 0.000 ARG C 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 2.739 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7461 (t80) cc_final: 0.7204 (t80) REVERT: A 608 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8637 (mm) REVERT: A 632 LYS cc_start: 0.8863 (tppt) cc_final: 0.8496 (tppp) REVERT: B 797 ASP cc_start: 0.8134 (t70) cc_final: 0.7799 (t0) REVERT: C 569 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8369 (mtm) REVERT: D 432 LYS cc_start: 0.8786 (tptp) cc_final: 0.8174 (tptp) REVERT: D 436 ASP cc_start: 0.8121 (m-30) cc_final: 0.7541 (m-30) REVERT: D 548 SER cc_start: 0.8512 (t) cc_final: 0.8157 (p) REVERT: D 869 MET cc_start: 0.8567 (mtp) cc_final: 0.8345 (mtp) REVERT: D 919 ASP cc_start: 0.8377 (m-30) cc_final: 0.8148 (m-30) REVERT: E 464 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7669 (m-90) REVERT: F 547 PHE cc_start: 0.6256 (t80) cc_final: 0.5896 (t80) REVERT: F 578 LYS cc_start: 0.7424 (tttm) cc_final: 0.6963 (mtpp) outliers start: 35 outliers final: 26 residues processed: 186 average time/residue: 0.3486 time to fit residues: 105.2498 Evaluate side-chains 182 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25045 Z= 0.208 Angle : 0.505 9.661 33923 Z= 0.256 Chirality : 0.041 0.265 3899 Planarity : 0.004 0.055 4334 Dihedral : 6.973 87.232 3552 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.32 % Allowed : 8.66 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.28 (0.15), residues: 3096 helix: 1.95 (0.14), residues: 1376 sheet: 0.47 (0.26), residues: 395 loop : -0.15 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 770 HIS 0.005 0.001 HIS F 622 PHE 0.014 0.001 PHE D 751 TYR 0.028 0.001 TYR F 834 ARG 0.007 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.730 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7572 (t80) cc_final: 0.7303 (t80) REVERT: A 608 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8582 (mm) REVERT: A 632 LYS cc_start: 0.8863 (tppt) cc_final: 0.8488 (tppp) REVERT: B 797 ASP cc_start: 0.8109 (t70) cc_final: 0.7773 (t0) REVERT: C 569 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: D 432 LYS cc_start: 0.8790 (tptp) cc_final: 0.8171 (tptp) REVERT: D 436 ASP cc_start: 0.8148 (m-30) cc_final: 0.7529 (m-30) REVERT: D 548 SER cc_start: 0.8501 (t) cc_final: 0.8148 (p) REVERT: D 919 ASP cc_start: 0.8368 (m-30) cc_final: 0.8121 (m-30) REVERT: E 464 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7699 (m-90) REVERT: F 463 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: F 547 PHE cc_start: 0.6224 (t80) cc_final: 0.5966 (t80) REVERT: F 588 LEU cc_start: 0.8592 (tp) cc_final: 0.8313 (tp) outliers start: 35 outliers final: 25 residues processed: 188 average time/residue: 0.3505 time to fit residues: 106.4444 Evaluate side-chains 182 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 463 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 253 optimal weight: 0.0980 chunk 168 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25045 Z= 0.187 Angle : 0.497 10.064 33923 Z= 0.252 Chirality : 0.041 0.267 3899 Planarity : 0.004 0.055 4334 Dihedral : 6.873 87.305 3552 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.36 % Allowed : 9.04 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.33 (0.15), residues: 3096 helix: 2.00 (0.14), residues: 1376 sheet: 0.47 (0.26), residues: 395 loop : -0.14 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 770 HIS 0.004 0.001 HIS F 622 PHE 0.013 0.001 PHE D 751 TYR 0.028 0.001 TYR F 834 ARG 0.007 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7574 (t80) cc_final: 0.7299 (t80) REVERT: A 608 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 632 LYS cc_start: 0.8861 (tppt) cc_final: 0.8485 (tppp) REVERT: B 773 MET cc_start: 0.8597 (mmp) cc_final: 0.8384 (mmt) REVERT: B 797 ASP cc_start: 0.8110 (t70) cc_final: 0.7784 (t0) REVERT: C 494 MET cc_start: 0.8287 (mtp) cc_final: 0.7869 (mtp) REVERT: C 569 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8315 (mtm) REVERT: D 432 LYS cc_start: 0.8767 (tptp) cc_final: 0.8150 (tptp) REVERT: D 436 ASP cc_start: 0.8154 (m-30) cc_final: 0.7526 (m-30) REVERT: D 548 SER cc_start: 0.8473 (t) cc_final: 0.8114 (p) REVERT: D 919 ASP cc_start: 0.8370 (m-30) cc_final: 0.8125 (m-30) REVERT: E 464 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7753 (m-90) REVERT: F 547 PHE cc_start: 0.6247 (t80) cc_final: 0.5998 (t80) REVERT: F 588 LEU cc_start: 0.8634 (tp) cc_final: 0.8380 (tp) REVERT: F 714 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7406 (mtmt) outliers start: 36 outliers final: 28 residues processed: 190 average time/residue: 0.3519 time to fit residues: 109.3358 Evaluate side-chains 190 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 272 optimal weight: 30.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25045 Z= 0.192 Angle : 0.511 12.528 33923 Z= 0.257 Chirality : 0.041 0.268 3899 Planarity : 0.004 0.055 4334 Dihedral : 6.819 86.888 3552 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.28 % Allowed : 9.60 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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 (0.15), residues: 3096 helix: 2.04 (0.14), residues: 1376 sheet: 0.43 (0.26), residues: 402 loop : -0.13 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 770 HIS 0.003 0.001 HIS F 622 PHE 0.014 0.001 PHE D 751 TYR 0.027 0.001 TYR F 834 ARG 0.006 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7577 (t80) cc_final: 0.7302 (t80) REVERT: A 608 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 632 LYS cc_start: 0.8871 (tppt) cc_final: 0.8475 (tppp) REVERT: B 773 MET cc_start: 0.8597 (mmp) cc_final: 0.8375 (mmt) REVERT: B 797 ASP cc_start: 0.8115 (t70) cc_final: 0.7800 (t0) REVERT: C 482 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7587 (ttp80) REVERT: C 569 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: D 432 LYS cc_start: 0.8788 (tptp) cc_final: 0.8196 (tptp) REVERT: D 436 ASP cc_start: 0.8130 (m-30) cc_final: 0.7489 (m-30) REVERT: D 548 SER cc_start: 0.8519 (t) cc_final: 0.8181 (p) REVERT: D 919 ASP cc_start: 0.8374 (m-30) cc_final: 0.8129 (m-30) REVERT: E 464 TRP cc_start: 0.8061 (OUTLIER) cc_final: 0.7733 (m-90) REVERT: F 547 PHE cc_start: 0.6240 (t80) cc_final: 0.5995 (t80) REVERT: F 714 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7403 (mtmt) outliers start: 34 outliers final: 28 residues processed: 188 average time/residue: 0.3458 time to fit residues: 105.6565 Evaluate side-chains 187 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 633 VAL Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 252 optimal weight: 0.4980 chunk 264 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25045 Z= 0.152 Angle : 0.496 11.121 33923 Z= 0.248 Chirality : 0.040 0.270 3899 Planarity : 0.004 0.055 4334 Dihedral : 6.698 87.687 3552 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.13 % Allowed : 9.83 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.45 (0.15), residues: 3096 helix: 2.13 (0.14), residues: 1375 sheet: 0.50 (0.26), residues: 402 loop : -0.10 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 770 HIS 0.003 0.001 HIS F 622 PHE 0.013 0.001 PHE B 547 TYR 0.026 0.001 TYR F 834 ARG 0.007 0.000 ARG C 597 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7574 (t80) cc_final: 0.7298 (t80) REVERT: A 608 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 632 LYS cc_start: 0.8858 (tppt) cc_final: 0.8471 (tppp) REVERT: B 797 ASP cc_start: 0.8120 (t70) cc_final: 0.7813 (t0) REVERT: C 423 GLU cc_start: 0.8048 (pp20) cc_final: 0.7785 (pp20) REVERT: C 494 MET cc_start: 0.7848 (mtp) cc_final: 0.7570 (mtp) REVERT: C 569 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8229 (mtm) REVERT: D 432 LYS cc_start: 0.8711 (tptp) cc_final: 0.8104 (tptp) REVERT: D 436 ASP cc_start: 0.8122 (m-30) cc_final: 0.7438 (m-30) REVERT: D 777 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8974 (t) REVERT: D 919 ASP cc_start: 0.8365 (m-30) cc_final: 0.8123 (m-30) REVERT: E 464 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: F 714 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7436 (mtmt) outliers start: 30 outliers final: 23 residues processed: 188 average time/residue: 0.3469 time to fit residues: 106.1127 Evaluate side-chains 185 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 7.9990 chunk 180 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 309 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25045 Z= 0.149 Angle : 0.503 12.685 33923 Z= 0.250 Chirality : 0.040 0.273 3899 Planarity : 0.004 0.054 4334 Dihedral : 6.636 88.803 3552 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.02 % Allowed : 10.17 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: 1.50 (0.15), residues: 3096 helix: 2.15 (0.14), residues: 1380 sheet: 0.57 (0.26), residues: 397 loop : -0.05 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 770 HIS 0.006 0.001 HIS F 622 PHE 0.020 0.001 PHE F 635 TYR 0.026 0.001 TYR F 834 ARG 0.007 0.000 ARG C 597 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 3.121 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7575 (t80) cc_final: 0.7313 (t80) REVERT: A 608 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 632 LYS cc_start: 0.8830 (tppt) cc_final: 0.8445 (tppp) REVERT: B 797 ASP cc_start: 0.8126 (t70) cc_final: 0.7820 (t0) REVERT: C 569 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8212 (mtm) REVERT: D 432 LYS cc_start: 0.8698 (tptp) cc_final: 0.8183 (tptp) REVERT: D 436 ASP cc_start: 0.8110 (m-30) cc_final: 0.7434 (m-30) REVERT: D 777 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8985 (t) REVERT: D 919 ASP cc_start: 0.8368 (m-30) cc_final: 0.8125 (m-30) REVERT: E 421 PHE cc_start: 0.7593 (m-80) cc_final: 0.7373 (m-80) REVERT: E 464 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: E 594 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8392 (mmtm) REVERT: F 714 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7430 (mtmt) outliers start: 27 outliers final: 21 residues processed: 180 average time/residue: 0.3605 time to fit residues: 105.4657 Evaluate side-chains 179 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075749 restraints weight = 47255.423| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.45 r_work: 0.2883 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25045 Z= 0.247 Angle : 0.532 10.457 33923 Z= 0.267 Chirality : 0.041 0.279 3899 Planarity : 0.004 0.059 4334 Dihedral : 6.802 89.811 3552 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.28 % Allowed : 9.87 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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 (0.15), residues: 3096 helix: 2.01 (0.14), residues: 1379 sheet: 0.56 (0.27), residues: 394 loop : -0.14 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 770 HIS 0.006 0.001 HIS F 622 PHE 0.016 0.001 PHE E 820 TYR 0.027 0.001 TYR F 834 ARG 0.007 0.000 ARG C 597 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.43 seconds wall clock time: 76 minutes 59.81 seconds (4619.81 seconds total)