Starting phenix.real_space_refine on Sun Jan 26 08:52:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc0_45430/01_2025/9cc0_45430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc0_45430/01_2025/9cc0_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/cci-nas-00/data/ceres_data/9cc0_45430/01_2025/9cc0_45430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc0_45430/01_2025/9cc0_45430.map" model { file = "/net/cci-nas-00/data/ceres_data/9cc0_45430/01_2025/9cc0_45430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc0_45430/01_2025/9cc0_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 14.90, per 1000 atoms: 0.61 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: 5.95 Conformation dependent library (CDL) restraints added in 3.2 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: 3.26 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: 9.98 Time building geometry restraints manager: 6.72 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 56.020 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.140 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.030 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 3.013 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: 0.3766 time to fit residues: 132.8823 Evaluate side-chains 169 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 3.007 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076749 restraints weight = 47180.302| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.47 r_work: 0.2890 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 797 ASP cc_start: 0.8435 (t70) cc_final: 0.7989 (t0) REVERT: C 597 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7092 (ttm-80) REVERT: D 432 LYS cc_start: 0.8944 (tptp) cc_final: 0.8448 (tptp) REVERT: D 436 ASP cc_start: 0.8408 (m-30) cc_final: 0.7958 (m-30) REVERT: D 482 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8510 (ttt-90) REVERT: D 548 SER cc_start: 0.8806 (t) cc_final: 0.8464 (p) REVERT: D 770 TRP cc_start: 0.8718 (t60) cc_final: 0.8460 (t60) REVERT: D 869 MET cc_start: 0.8904 (mtp) cc_final: 0.8659 (mtp) REVERT: E 463 ASP cc_start: 0.8439 (m-30) cc_final: 0.8188 (m-30) REVERT: E 464 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7606 (m-90) REVERT: E 482 ARG cc_start: 0.8498 (tmm160) cc_final: 0.8284 (ttt180) REVERT: E 594 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8542 (mmmt) REVERT: E 826 MET cc_start: 0.8767 (tmm) cc_final: 0.8304 (ttm) REVERT: F 463 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: F 547 PHE cc_start: 0.6389 (t80) cc_final: 0.6040 (t80) REVERT: F 578 LYS cc_start: 0.7414 (tttm) cc_final: 0.6991 (mtpt) outliers start: 15 outliers final: 9 residues processed: 201 average time/residue: 0.3808 time to fit residues: 122.1818 Evaluate side-chains 173 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 3.020 ------------------------------------------------------------------------------- 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 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 144 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 chunk 298 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 616 ASN D 561 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077645 restraints weight = 46789.564| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.43 r_work: 0.2934 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25045 Z= 0.162 Angle : 0.500 7.884 33923 Z= 0.253 Chirality : 0.041 0.225 3899 Planarity : 0.004 0.047 4334 Dihedral : 7.229 88.971 3552 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.64 % Allowed : 6.25 % Favored : 93.11 % 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: 1.30 (0.15), residues: 3096 helix: 1.89 (0.14), residues: 1375 sheet: 0.62 (0.27), residues: 393 loop : -0.08 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 770 HIS 0.004 0.001 HIS F 622 PHE 0.014 0.001 PHE D 751 TYR 0.026 0.001 TYR F 834 ARG 0.005 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 197 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7271 (t80) cc_final: 0.7023 (t80) REVERT: A 632 LYS cc_start: 0.8969 (tppt) cc_final: 0.8592 (tppp) REVERT: B 756 MET cc_start: 0.9031 (ttm) cc_final: 0.8828 (ttm) REVERT: B 797 ASP cc_start: 0.8515 (t70) cc_final: 0.8119 (t0) REVERT: D 432 LYS cc_start: 0.8892 (tptp) cc_final: 0.8348 (tptp) REVERT: D 436 ASP cc_start: 0.8414 (m-30) cc_final: 0.7786 (m-30) REVERT: D 548 SER cc_start: 0.8675 (t) cc_final: 0.8363 (p) REVERT: D 869 MET cc_start: 0.8908 (mtp) cc_final: 0.8660 (mtp) REVERT: D 919 ASP cc_start: 0.8717 (m-30) cc_final: 0.8507 (m-30) REVERT: E 482 ARG cc_start: 0.8423 (tmm160) cc_final: 0.8146 (ttt180) REVERT: E 826 MET cc_start: 0.8794 (tmm) cc_final: 0.8399 (ttm) REVERT: F 547 PHE cc_start: 0.6459 (t80) cc_final: 0.6121 (t80) REVERT: F 578 LYS cc_start: 0.7403 (tttm) cc_final: 0.6992 (mtpt) outliers start: 17 outliers final: 15 residues processed: 190 average time/residue: 0.3775 time to fit residues: 114.5849 Evaluate side-chains 171 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 2.786 ------------------------------------------------------------------------------- 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 C residue 641 VAL 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 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 305 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN F 456 ASN F 934 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.072798 restraints weight = 48515.311| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.46 r_work: 0.2807 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.139 25045 Z= 0.572 Angle : 0.695 14.545 33923 Z= 0.354 Chirality : 0.048 0.278 3899 Planarity : 0.005 0.061 4334 Dihedral : 7.734 87.574 3552 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.39 % Allowed : 7.83 % Favored : 90.77 % 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: 0.68 (0.15), residues: 3096 helix: 1.39 (0.14), residues: 1366 sheet: 0.23 (0.26), residues: 395 loop : -0.40 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 770 HIS 0.006 0.001 HIS D 839 PHE 0.024 0.002 PHE E 820 TYR 0.036 0.002 TYR F 834 ARG 0.007 0.001 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 197 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 608 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8576 (mm) REVERT: B 647 GLU cc_start: 0.8692 (tp30) cc_final: 0.8431 (tp30) REVERT: B 797 ASP cc_start: 0.8416 (t70) cc_final: 0.8007 (t0) REVERT: C 482 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8030 (ttp80) REVERT: C 597 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7204 (ttm-80) REVERT: C 826 MET cc_start: 0.9031 (tmm) cc_final: 0.8614 (ttp) REVERT: D 432 LYS cc_start: 0.9056 (tptp) cc_final: 0.8496 (tptp) REVERT: D 436 ASP cc_start: 0.8528 (m-30) cc_final: 0.7880 (m-30) REVERT: D 548 SER cc_start: 0.8895 (t) cc_final: 0.8510 (p) REVERT: D 770 TRP cc_start: 0.8713 (t60) cc_final: 0.8268 (t60) REVERT: D 919 ASP cc_start: 0.8810 (m-30) cc_final: 0.8609 (m-30) REVERT: E 464 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7802 (m-90) REVERT: E 482 ARG cc_start: 0.8547 (tmm160) cc_final: 0.8279 (ttt180) REVERT: F 547 PHE cc_start: 0.6634 (t80) cc_final: 0.6040 (t80) REVERT: F 578 LYS cc_start: 0.7430 (tttm) cc_final: 0.6882 (mtpp) outliers start: 37 outliers final: 25 residues processed: 187 average time/residue: 0.3618 time to fit residues: 108.6653 Evaluate side-chains 175 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 2.847 ------------------------------------------------------------------------------- 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 434 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 430 VAL 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 463 ASP 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 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 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 246 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 221 optimal weight: 0.1980 chunk 157 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 257 optimal weight: 0.0170 chunk 176 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.101954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.075096 restraints weight = 47158.606| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.46 r_work: 0.2877 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1539 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= 0.183 Angle : 0.522 11.445 33923 Z= 0.265 Chirality : 0.041 0.289 3899 Planarity : 0.004 0.057 4334 Dihedral : 7.244 86.151 3552 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.24 % Allowed : 8.81 % Favored : 89.94 % 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: 1.01 (0.15), residues: 3096 helix: 1.74 (0.14), residues: 1376 sheet: 0.30 (0.26), residues: 395 loop : -0.29 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 470 HIS 0.004 0.001 HIS F 622 PHE 0.020 0.001 PHE D 751 TYR 0.032 0.001 TYR F 834 ARG 0.005 0.000 ARG C 597 *********************** 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 198 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 3.251 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7216 (t80) cc_final: 0.6977 (t80) REVERT: A 608 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8522 (mm) REVERT: B 797 ASP cc_start: 0.8395 (t70) cc_final: 0.8057 (t0) REVERT: C 597 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7200 (ttm-80) REVERT: D 432 LYS cc_start: 0.8908 (tptp) cc_final: 0.8326 (tptp) REVERT: D 436 ASP cc_start: 0.8494 (m-30) cc_final: 0.8023 (m-30) REVERT: D 488 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: D 548 SER cc_start: 0.8829 (t) cc_final: 0.8496 (p) REVERT: D 770 TRP cc_start: 0.8591 (t60) cc_final: 0.8183 (t60) REVERT: D 919 ASP cc_start: 0.8761 (m-30) cc_final: 0.8554 (m-30) REVERT: E 464 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.7721 (m-90) REVERT: E 482 ARG cc_start: 0.8474 (tmm160) cc_final: 0.8190 (ttt180) REVERT: E 826 MET cc_start: 0.8714 (tmm) cc_final: 0.8203 (ttm) REVERT: F 547 PHE cc_start: 0.6356 (t80) cc_final: 0.5943 (t80) outliers start: 33 outliers final: 21 residues processed: 193 average time/residue: 0.3758 time to fit residues: 116.2708 Evaluate side-chains 175 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 2.851 ------------------------------------------------------------------------------- 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 453 SER 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 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU 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 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 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 258 optimal weight: 0.0470 chunk 291 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 308 optimal weight: 0.2980 chunk 283 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- 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 = 0.102885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075707 restraints weight = 47258.818| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.49 r_work: 0.2886 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25045 Z= 0.198 Angle : 0.513 10.376 33923 Z= 0.259 Chirality : 0.041 0.249 3899 Planarity : 0.004 0.057 4334 Dihedral : 7.037 87.410 3552 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.17 % Allowed : 9.57 % Favored : 89.27 % 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: 1.14 (0.15), residues: 3096 helix: 1.89 (0.14), residues: 1370 sheet: 0.35 (0.26), residues: 395 loop : -0.28 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 470 HIS 0.003 0.001 HIS F 622 PHE 0.017 0.001 PHE D 751 TYR 0.030 0.001 TYR F 834 ARG 0.006 0.000 ARG D 459 *********************** 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 193 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 2.983 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7310 (t80) cc_final: 0.7070 (t80) REVERT: A 608 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8489 (mm) REVERT: B 797 ASP cc_start: 0.8403 (t70) cc_final: 0.8041 (t0) REVERT: C 597 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7152 (ttm-80) REVERT: C 808 GLU cc_start: 0.7877 (tp30) cc_final: 0.7668 (tp30) REVERT: D 432 LYS cc_start: 0.8956 (tptp) cc_final: 0.8383 (tptp) REVERT: D 436 ASP cc_start: 0.8499 (m-30) cc_final: 0.7974 (m-30) REVERT: D 488 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: D 548 SER cc_start: 0.8752 (t) cc_final: 0.8455 (p) REVERT: D 770 TRP cc_start: 0.8579 (t60) cc_final: 0.8191 (t60) REVERT: D 919 ASP cc_start: 0.8776 (m-30) cc_final: 0.8575 (m-30) REVERT: E 464 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.7726 (m-90) REVERT: E 826 MET cc_start: 0.8737 (tmm) cc_final: 0.8168 (ttm) REVERT: F 547 PHE cc_start: 0.6362 (t80) cc_final: 0.5965 (t80) outliers start: 31 outliers final: 22 residues processed: 187 average time/residue: 0.3530 time to fit residues: 107.6219 Evaluate side-chains 181 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 3.288 ------------------------------------------------------------------------------- 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 771 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS 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 488 GLU 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 464 TRP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 842 LEU Chi-restraints excluded: chain E residue 877 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 136 optimal weight: 0.0770 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075818 restraints weight = 47348.581| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.46 r_work: 0.2894 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1665 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= 0.189 Angle : 0.506 10.208 33923 Z= 0.255 Chirality : 0.041 0.256 3899 Planarity : 0.004 0.056 4334 Dihedral : 6.913 87.999 3552 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 1.20 (0.15), residues: 3096 helix: 1.94 (0.14), residues: 1375 sheet: 0.38 (0.26), residues: 395 loop : -0.24 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 470 HIS 0.003 0.001 HIS B 451 PHE 0.015 0.001 PHE D 751 TYR 0.028 0.001 TYR F 834 ARG 0.003 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 204 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 2.974 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7368 (t80) cc_final: 0.7105 (t80) REVERT: A 608 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 632 LYS cc_start: 0.9040 (tppt) cc_final: 0.8546 (tppp) REVERT: B 773 MET cc_start: 0.8989 (mmp) cc_final: 0.8779 (mmt) REVERT: B 797 ASP cc_start: 0.8388 (t70) cc_final: 0.8051 (t0) REVERT: C 808 GLU cc_start: 0.7834 (tp30) cc_final: 0.7621 (tp30) REVERT: D 432 LYS cc_start: 0.8955 (tptp) cc_final: 0.8395 (tptp) REVERT: D 436 ASP cc_start: 0.8495 (m-30) cc_final: 0.7957 (m-30) REVERT: D 488 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: D 548 SER cc_start: 0.8770 (t) cc_final: 0.8448 (p) REVERT: D 770 TRP cc_start: 0.8546 (t60) cc_final: 0.8179 (t60) REVERT: D 919 ASP cc_start: 0.8776 (m-30) cc_final: 0.8559 (m-30) REVERT: E 464 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.7775 (m-90) REVERT: E 482 ARG cc_start: 0.8477 (tmm160) cc_final: 0.8210 (ttt180) REVERT: E 562 ARG cc_start: 0.5755 (tpt170) cc_final: 0.5468 (tpt90) REVERT: E 826 MET cc_start: 0.8675 (tmm) cc_final: 0.8166 (ttm) REVERT: F 547 PHE cc_start: 0.6261 (t80) cc_final: 0.5941 (t80) REVERT: F 714 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7460 (mtmt) outliers start: 34 outliers final: 24 residues processed: 196 average time/residue: 0.3874 time to fit residues: 121.6101 Evaluate side-chains 185 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 2.979 ------------------------------------------------------------------------------- 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 590 ASP 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 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU 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 464 TRP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 842 LEU 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 292 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 242 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.075394 restraints weight = 47154.836| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.46 r_work: 0.2887 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25045 Z= 0.218 Angle : 0.523 10.986 33923 Z= 0.263 Chirality : 0.041 0.259 3899 Planarity : 0.004 0.056 4334 Dihedral : 6.894 88.831 3552 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.47 % Allowed : 10.32 % Favored : 88.21 % 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: 1.18 (0.15), residues: 3096 helix: 1.92 (0.14), residues: 1381 sheet: 0.36 (0.26), residues: 400 loop : -0.27 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 470 HIS 0.004 0.001 HIS F 622 PHE 0.013 0.001 PHE E 820 TYR 0.030 0.001 TYR F 834 ARG 0.007 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 202 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 3.032 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7362 (t80) cc_final: 0.7096 (t80) REVERT: A 608 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 632 LYS cc_start: 0.9047 (tppt) cc_final: 0.8600 (mmmm) REVERT: B 773 MET cc_start: 0.8993 (mmp) cc_final: 0.8763 (mmt) REVERT: B 797 ASP cc_start: 0.8385 (t70) cc_final: 0.8049 (t0) REVERT: C 808 GLU cc_start: 0.7867 (tp30) cc_final: 0.7656 (tp30) REVERT: C 826 MET cc_start: 0.8960 (tmm) cc_final: 0.8705 (ttp) REVERT: D 432 LYS cc_start: 0.8954 (tptp) cc_final: 0.8398 (tptp) REVERT: D 436 ASP cc_start: 0.8497 (m-30) cc_final: 0.7956 (m-30) REVERT: D 488 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: D 548 SER cc_start: 0.8701 (t) cc_final: 0.8366 (p) REVERT: D 770 TRP cc_start: 0.8557 (t60) cc_final: 0.8182 (t60) REVERT: D 919 ASP cc_start: 0.8771 (m-30) cc_final: 0.8551 (m-30) REVERT: E 464 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7771 (m-90) REVERT: E 482 ARG cc_start: 0.8500 (tmm160) cc_final: 0.8192 (ttt180) REVERT: E 826 MET cc_start: 0.8690 (tmm) cc_final: 0.8185 (ttm) REVERT: F 547 PHE cc_start: 0.6240 (t80) cc_final: 0.5917 (t80) REVERT: F 714 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7458 (mtmt) outliers start: 39 outliers final: 30 residues processed: 191 average time/residue: 0.3571 time to fit residues: 110.8625 Evaluate side-chains 190 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 653 MET Chi-restraints excluded: chain B residue 764 VAL 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 417 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU 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 E residue 833 ASP Chi-restraints excluded: chain E residue 842 LEU Chi-restraints excluded: chain E residue 877 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 228 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 141 optimal weight: 0.0870 chunk 66 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.104392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077421 restraints weight = 47413.618| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.45 r_work: 0.2898 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25045 Z= 0.184 Angle : 0.510 10.391 33923 Z= 0.256 Chirality : 0.041 0.257 3899 Planarity : 0.004 0.056 4334 Dihedral : 6.820 89.548 3552 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.36 % Allowed : 10.43 % Favored : 88.21 % 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: 1.23 (0.15), residues: 3096 helix: 1.97 (0.14), residues: 1384 sheet: 0.42 (0.27), residues: 395 loop : -0.26 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 470 HIS 0.006 0.001 HIS F 622 PHE 0.017 0.001 PHE D 751 TYR 0.029 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 204 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 3.035 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7341 (t80) cc_final: 0.7075 (t80) REVERT: A 608 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8426 (mm) REVERT: A 632 LYS cc_start: 0.9042 (tppt) cc_final: 0.8593 (mmmm) REVERT: B 773 MET cc_start: 0.8983 (mmp) cc_final: 0.8751 (mmt) REVERT: B 797 ASP cc_start: 0.8392 (t70) cc_final: 0.8062 (t0) REVERT: C 426 LYS cc_start: 0.8525 (ptpp) cc_final: 0.8191 (ptpp) REVERT: C 808 GLU cc_start: 0.7837 (tp30) cc_final: 0.7626 (tp30) REVERT: D 432 LYS cc_start: 0.8860 (tptp) cc_final: 0.8293 (tptp) REVERT: D 436 ASP cc_start: 0.8503 (m-30) cc_final: 0.7960 (m-30) REVERT: D 548 SER cc_start: 0.8666 (t) cc_final: 0.8325 (p) REVERT: D 770 TRP cc_start: 0.8541 (t60) cc_final: 0.8173 (t60) REVERT: D 919 ASP cc_start: 0.8769 (m-30) cc_final: 0.8551 (m-30) REVERT: E 421 PHE cc_start: 0.7067 (m-80) cc_final: 0.6778 (m-80) REVERT: E 464 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.7801 (m-90) REVERT: E 482 ARG cc_start: 0.8481 (tmm160) cc_final: 0.8180 (ttt180) REVERT: E 562 ARG cc_start: 0.5772 (tpt170) cc_final: 0.5527 (tpt-90) REVERT: E 826 MET cc_start: 0.8672 (tmm) cc_final: 0.8183 (ttm) REVERT: F 547 PHE cc_start: 0.6221 (t80) cc_final: 0.5938 (t80) REVERT: F 714 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7455 (mtmt) outliers start: 36 outliers final: 31 residues processed: 193 average time/residue: 0.3640 time to fit residues: 113.9483 Evaluate side-chains 193 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 2.968 ------------------------------------------------------------------------------- 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 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 417 ILE 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 E residue 842 LEU Chi-restraints excluded: chain E residue 877 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0355 > 50: distance: 32 - 58: 21.359 distance: 36 - 67: 28.245 distance: 46 - 77: 26.307 distance: 53 - 58: 19.479 distance: 58 - 59: 23.352 distance: 59 - 60: 42.908 distance: 59 - 62: 52.436 distance: 60 - 61: 47.306 distance: 60 - 67: 21.028 distance: 62 - 63: 38.989 distance: 63 - 64: 3.632 distance: 64 - 65: 54.560 distance: 64 - 66: 44.776 distance: 67 - 68: 49.644 distance: 68 - 69: 25.928 distance: 68 - 71: 55.981 distance: 69 - 70: 19.132 distance: 69 - 77: 39.862 distance: 71 - 72: 34.699 distance: 72 - 73: 4.216 distance: 72 - 74: 25.706 distance: 73 - 75: 17.077 distance: 74 - 76: 14.610 distance: 75 - 76: 27.397 distance: 77 - 78: 34.389 distance: 78 - 79: 44.376 distance: 78 - 81: 23.880 distance: 79 - 80: 57.943 distance: 79 - 82: 24.831 distance: 82 - 83: 18.315 distance: 83 - 84: 35.650 distance: 83 - 86: 41.370 distance: 84 - 85: 54.758 distance: 84 - 89: 7.086 distance: 86 - 87: 38.687 distance: 87 - 88: 38.891 distance: 89 - 90: 19.880 distance: 90 - 91: 21.577 distance: 90 - 93: 45.152 distance: 91 - 92: 29.518 distance: 91 - 94: 12.183 distance: 94 - 95: 15.281 distance: 95 - 96: 49.791 distance: 95 - 98: 25.606 distance: 96 - 97: 41.162 distance: 96 - 102: 32.859 distance: 98 - 99: 4.228 distance: 99 - 100: 20.055 distance: 99 - 101: 11.819 distance: 102 - 103: 6.361 distance: 103 - 104: 18.334 distance: 103 - 106: 32.036 distance: 104 - 105: 48.655 distance: 104 - 110: 19.941 distance: 106 - 107: 56.146 distance: 107 - 108: 36.636 distance: 107 - 109: 41.053 distance: 110 - 111: 40.470 distance: 111 - 112: 49.621 distance: 111 - 114: 37.998 distance: 112 - 113: 27.949 distance: 112 - 122: 40.246 distance: 113 - 144: 32.600 distance: 114 - 115: 32.390 distance: 115 - 116: 9.554 distance: 115 - 117: 23.067 distance: 116 - 118: 13.777 distance: 117 - 119: 9.922 distance: 118 - 120: 21.324 distance: 119 - 120: 18.228 distance: 120 - 121: 11.592 distance: 122 - 123: 41.096 distance: 123 - 124: 5.990 distance: 123 - 126: 13.473 distance: 124 - 130: 13.326 distance: 126 - 127: 28.667 distance: 127 - 129: 49.792 distance: 130 - 131: 23.694 distance: 131 - 132: 28.039 distance: 131 - 134: 16.295 distance: 132 - 133: 23.809 distance: 132 - 137: 16.431 distance: 134 - 135: 16.158 distance: 134 - 136: 40.629