Starting phenix.real_space_refine on Mon Aug 25 02:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc0_45430/08_2025/9cc0_45430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc0_45430/08_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_45430/08_2025/9cc0_45430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc0_45430/08_2025/9cc0_45430.map" model { file = "/net/cci-nas-00/data/ceres_data/9cc0_45430/08_2025/9cc0_45430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc0_45430/08_2025/9cc0_45430.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.52, per 1000 atoms: 0.27 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.01 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: 5.01 Time building geometry restraints manager: 2.91 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.650 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- 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= 0.136 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.007 0.000 ARG C 597 TYR 0.015 0.001 TYR A 565 PHE 0.011 0.001 PHE E 820 TRP 0.028 0.001 TRP E 464 HIS 0.003 0.001 HIS E 839 Details of bonding type rmsd covalent geometry : bond 0.00295 (25045) covalent geometry : angle 0.53770 (33923) hydrogen bonds : bond 0.15381 ( 1140) hydrogen bonds : angle 6.64656 ( 3345) *********************** 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 : 1.046 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: 0.7763 (t0) REVERT: C 448 LEU cc_start: 0.8101 (mt) cc_final: 0.7595 (mt) REVERT: D 436 ASP cc_start: 0.7972 (m-30) cc_final: 0.7661 (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 554 ASP cc_start: 0.7572 (t0) cc_final: 0.7238 (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: 0.5916 (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: 0.1720 time to fit residues: 60.8852 Evaluate side-chains 168 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0670 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 1.5322 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.104453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.077464 restraints weight = 47374.449| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.46 r_work: 0.2903 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25045 Z= 0.147 Angle : 0.543 7.334 33923 Z= 0.278 Chirality : 0.042 0.197 3899 Planarity : 0.004 0.047 4334 Dihedral : 7.506 88.205 3552 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.49 % Allowed : 4.44 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.15), residues: 3096 helix: 1.73 (0.14), residues: 1366 sheet: 0.63 (0.26), residues: 397 loop : -0.07 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 597 TYR 0.024 0.001 TYR F 834 PHE 0.014 0.001 PHE D 751 TRP 0.019 0.001 TRP D 770 HIS 0.004 0.001 HIS C 843 Details of bonding type rmsd covalent geometry : bond 0.00353 (25045) covalent geometry : angle 0.54277 (33923) hydrogen bonds : bond 0.03781 ( 1140) hydrogen bonds : angle 4.97784 ( 3345) *********************** 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 204 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 756 MET cc_start: 0.9069 (ttm) cc_final: 0.8822 (ttm) REVERT: B 797 ASP cc_start: 0.8477 (t70) cc_final: 0.8029 (t0) REVERT: C 597 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7069 (ttm-80) REVERT: D 432 LYS cc_start: 0.8940 (tptp) cc_final: 0.8442 (tptp) REVERT: D 436 ASP cc_start: 0.8396 (m-30) cc_final: 0.7941 (m-30) REVERT: D 548 SER cc_start: 0.8703 (t) cc_final: 0.8403 (p) REVERT: D 770 TRP cc_start: 0.8709 (t60) cc_final: 0.8458 (t60) REVERT: D 869 MET cc_start: 0.8896 (mtp) cc_final: 0.8641 (mtp) REVERT: E 463 ASP cc_start: 0.8424 (m-30) cc_final: 0.8171 (m-30) REVERT: E 464 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.7643 (m-90) REVERT: E 482 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8180 (ttt180) REVERT: E 594 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8535 (mmmt) REVERT: E 826 MET cc_start: 0.8747 (tmm) cc_final: 0.8357 (ttm) REVERT: F 463 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: F 547 PHE cc_start: 0.6392 (t80) cc_final: 0.6050 (t80) REVERT: F 578 LYS cc_start: 0.7405 (tttm) cc_final: 0.6981 (mtpt) outliers start: 13 outliers final: 7 residues processed: 200 average time/residue: 0.1736 time to fit residues: 56.1589 Evaluate side-chains 174 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 LEU 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 174 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 301 optimal weight: 0.6980 chunk 285 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 302 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 561 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078290 restraints weight = 47182.246| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.46 r_work: 0.2934 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25045 Z= 0.099 Angle : 0.492 7.668 33923 Z= 0.250 Chirality : 0.040 0.219 3899 Planarity : 0.004 0.045 4334 Dihedral : 7.191 89.403 3552 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.15), residues: 3096 helix: 1.96 (0.14), residues: 1368 sheet: 0.63 (0.26), residues: 395 loop : -0.04 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 597 TYR 0.024 0.001 TYR F 834 PHE 0.013 0.001 PHE D 751 TRP 0.011 0.001 TRP D 770 HIS 0.004 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00222 (25045) covalent geometry : angle 0.49241 (33923) hydrogen bonds : bond 0.03224 ( 1140) hydrogen bonds : angle 4.65568 ( 3345) *********************** 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 194 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7168 (t80) cc_final: 0.6893 (t80) REVERT: A 632 LYS cc_start: 0.8962 (tppt) cc_final: 0.8576 (tppp) REVERT: B 797 ASP cc_start: 0.8500 (t70) cc_final: 0.8113 (t0) REVERT: D 432 LYS cc_start: 0.8898 (tptp) cc_final: 0.8341 (tptp) REVERT: D 436 ASP cc_start: 0.8365 (m-30) cc_final: 0.7784 (m-30) REVERT: D 548 SER cc_start: 0.8692 (t) cc_final: 0.8357 (p) REVERT: D 770 TRP cc_start: 0.8696 (t60) cc_final: 0.8489 (t60) REVERT: D 869 MET cc_start: 0.8909 (mtp) cc_final: 0.8640 (mtp) REVERT: D 919 ASP cc_start: 0.8713 (m-30) cc_final: 0.8502 (m-30) REVERT: E 482 ARG cc_start: 0.8407 (ttm170) cc_final: 0.8073 (ttt180) REVERT: E 594 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8462 (mmmt) REVERT: E 826 MET cc_start: 0.8797 (tmm) cc_final: 0.8402 (ttm) REVERT: F 547 PHE cc_start: 0.6358 (t80) cc_final: 0.6042 (t80) REVERT: F 578 LYS cc_start: 0.7377 (tttm) cc_final: 0.6947 (mtpt) outliers start: 15 outliers final: 14 residues processed: 188 average time/residue: 0.1663 time to fit residues: 50.1786 Evaluate side-chains 175 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 641 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 467 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 270 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 275 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 308 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN C 616 ASN F 713 GLN F 934 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.076577 restraints weight = 47218.384| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.45 r_work: 0.2903 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25045 Z= 0.133 Angle : 0.503 8.503 33923 Z= 0.255 Chirality : 0.041 0.247 3899 Planarity : 0.004 0.050 4334 Dihedral : 7.084 89.250 3552 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.17 % Allowed : 7.31 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.15), residues: 3096 helix: 1.97 (0.14), residues: 1379 sheet: 0.60 (0.27), residues: 395 loop : -0.06 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 597 TYR 0.027 0.001 TYR F 834 PHE 0.014 0.001 PHE E 820 TRP 0.008 0.001 TRP D 770 HIS 0.006 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00320 (25045) covalent geometry : angle 0.50318 (33923) hydrogen bonds : bond 0.03303 ( 1140) hydrogen bonds : angle 4.53344 ( 3345) *********************** 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 203 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7141 (t80) cc_final: 0.6885 (t80) REVERT: A 608 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 632 LYS cc_start: 0.8936 (tppt) cc_final: 0.8553 (tppp) REVERT: B 797 ASP cc_start: 0.8457 (t70) cc_final: 0.8107 (t0) REVERT: C 826 MET cc_start: 0.9008 (tmm) cc_final: 0.8597 (ttp) REVERT: D 432 LYS cc_start: 0.8908 (tptp) cc_final: 0.8353 (tptp) REVERT: D 436 ASP cc_start: 0.8495 (m-30) cc_final: 0.7993 (m-30) REVERT: D 548 SER cc_start: 0.8736 (t) cc_final: 0.8406 (p) REVERT: D 869 MET cc_start: 0.8932 (mtp) cc_final: 0.8666 (mtp) REVERT: D 919 ASP cc_start: 0.8738 (m-30) cc_final: 0.8505 (m-30) REVERT: E 464 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7616 (m-90) REVERT: E 482 ARG cc_start: 0.8406 (ttm170) cc_final: 0.8013 (ttt180) REVERT: E 826 MET cc_start: 0.8799 (tmm) cc_final: 0.8405 (ttm) REVERT: F 547 PHE cc_start: 0.6463 (t80) cc_final: 0.6141 (t80) REVERT: F 578 LYS cc_start: 0.7373 (tttm) cc_final: 0.6918 (mtpt) outliers start: 31 outliers final: 18 residues processed: 195 average time/residue: 0.1608 time to fit residues: 50.5950 Evaluate side-chains 178 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 589 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 198 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 5 optimal weight: 0.0270 chunk 118 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.105282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078526 restraints weight = 46794.377| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.44 r_work: 0.2942 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25045 Z= 0.090 Angle : 0.476 7.707 33923 Z= 0.241 Chirality : 0.040 0.301 3899 Planarity : 0.004 0.050 4334 Dihedral : 6.828 88.123 3552 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.02 % Allowed : 8.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.15), residues: 3096 helix: 2.12 (0.14), residues: 1373 sheet: 0.66 (0.26), residues: 396 loop : -0.01 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 597 TYR 0.026 0.001 TYR F 834 PHE 0.013 0.001 PHE D 751 TRP 0.019 0.001 TRP D 770 HIS 0.006 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00203 (25045) covalent geometry : angle 0.47630 (33923) hydrogen bonds : bond 0.02900 ( 1140) hydrogen bonds : angle 4.38964 ( 3345) *********************** 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 211 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7134 (t80) cc_final: 0.6867 (t80) REVERT: A 608 LEU cc_start: 0.8877 (mm) cc_final: 0.8551 (mm) REVERT: A 632 LYS cc_start: 0.8887 (tppt) cc_final: 0.8493 (tppp) REVERT: B 647 GLU cc_start: 0.8486 (tp30) cc_final: 0.8176 (tp30) REVERT: B 797 ASP cc_start: 0.8429 (t70) cc_final: 0.8122 (t0) REVERT: D 432 LYS cc_start: 0.8884 (tptp) cc_final: 0.8340 (tptp) REVERT: D 436 ASP cc_start: 0.8472 (m-30) cc_final: 0.7967 (m-30) REVERT: D 609 GLU cc_start: 0.8470 (tp30) cc_final: 0.8161 (tp30) REVERT: D 869 MET cc_start: 0.8875 (mtp) cc_final: 0.8618 (mtp) REVERT: D 919 ASP cc_start: 0.8731 (m-30) cc_final: 0.8499 (m-30) REVERT: D 937 GLU cc_start: 0.8292 (tp30) cc_final: 0.8066 (tp30) REVERT: E 464 TRP cc_start: 0.8021 (OUTLIER) cc_final: 0.7633 (m-90) REVERT: E 482 ARG cc_start: 0.8328 (ttm170) cc_final: 0.7944 (ttt180) REVERT: F 463 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: F 547 PHE cc_start: 0.6326 (t80) cc_final: 0.6031 (t80) REVERT: F 714 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7398 (mtmt) outliers start: 27 outliers final: 17 residues processed: 205 average time/residue: 0.1729 time to fit residues: 57.5142 Evaluate side-chains 189 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 451 HIS 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 467 SER Chi-restraints excluded: chain D residue 611 LEU 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 F residue 463 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 286 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.104180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.077328 restraints weight = 46724.643| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.46 r_work: 0.2921 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1502 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= 0.116 Angle : 0.494 9.787 33923 Z= 0.249 Chirality : 0.040 0.262 3899 Planarity : 0.004 0.051 4334 Dihedral : 6.775 88.731 3552 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.24 % Allowed : 8.63 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.15), residues: 3096 helix: 2.11 (0.14), residues: 1379 sheet: 0.61 (0.26), residues: 400 loop : -0.01 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 597 TYR 0.028 0.001 TYR F 834 PHE 0.013 0.001 PHE D 751 TRP 0.019 0.001 TRP D 770 HIS 0.006 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00277 (25045) covalent geometry : angle 0.49414 (33923) hydrogen bonds : bond 0.03055 ( 1140) hydrogen bonds : angle 4.37668 ( 3345) *********************** 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 199 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7366 (t80) cc_final: 0.7124 (t80) REVERT: A 608 LEU cc_start: 0.8900 (mm) cc_final: 0.8569 (mm) REVERT: A 609 GLU cc_start: 0.8646 (tt0) cc_final: 0.8398 (tt0) REVERT: A 632 LYS cc_start: 0.8889 (tppt) cc_final: 0.8495 (tppp) REVERT: B 797 ASP cc_start: 0.8428 (t70) cc_final: 0.8115 (t0) REVERT: D 432 LYS cc_start: 0.8892 (tptp) cc_final: 0.8338 (tptp) REVERT: D 436 ASP cc_start: 0.8532 (m-30) cc_final: 0.7989 (m-30) REVERT: D 609 GLU cc_start: 0.8451 (tp30) cc_final: 0.8180 (tp30) REVERT: D 869 MET cc_start: 0.8890 (mtp) cc_final: 0.8639 (mtp) REVERT: D 919 ASP cc_start: 0.8751 (m-30) cc_final: 0.8517 (m-30) REVERT: D 937 GLU cc_start: 0.8329 (tp30) cc_final: 0.8091 (tp30) REVERT: E 454 GLU cc_start: 0.6600 (pm20) cc_final: 0.6384 (pm20) REVERT: E 464 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7723 (m-90) REVERT: E 482 ARG cc_start: 0.8377 (ttm170) cc_final: 0.7982 (ttt180) REVERT: E 826 MET cc_start: 0.8788 (tmm) cc_final: 0.8073 (ttm) REVERT: F 547 PHE cc_start: 0.6374 (t80) cc_final: 0.6082 (t80) REVERT: F 714 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7384 (mtmt) outliers start: 33 outliers final: 22 residues processed: 189 average time/residue: 0.1717 time to fit residues: 52.9311 Evaluate side-chains 184 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 756 MET 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 C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 70 optimal weight: 6.9990 chunk 228 optimal weight: 0.0050 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 299 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 182 optimal weight: 0.0270 chunk 63 optimal weight: 2.9990 overall best weight: 2.2058 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.103560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076360 restraints weight = 47855.059| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.49 r_work: 0.2872 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25045 Z= 0.186 Angle : 0.550 10.306 33923 Z= 0.277 Chirality : 0.042 0.271 3899 Planarity : 0.004 0.056 4334 Dihedral : 6.970 88.881 3552 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.24 % Allowed : 8.85 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.15), residues: 3096 helix: 1.91 (0.14), residues: 1388 sheet: 0.53 (0.26), residues: 395 loop : -0.18 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 597 TYR 0.032 0.002 TYR F 834 PHE 0.018 0.001 PHE E 820 TRP 0.022 0.001 TRP D 770 HIS 0.005 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00455 (25045) covalent geometry : angle 0.55032 (33923) hydrogen bonds : bond 0.03534 ( 1140) hydrogen bonds : angle 4.52694 ( 3345) *********************** 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 198 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7370 (t80) cc_final: 0.7130 (t80) REVERT: A 608 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 632 LYS cc_start: 0.8960 (tppt) cc_final: 0.8577 (tptm) REVERT: B 797 ASP cc_start: 0.8415 (t70) cc_final: 0.8062 (t0) REVERT: C 426 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8185 (ptpp) REVERT: C 494 MET cc_start: 0.8762 (mtp) cc_final: 0.8516 (mtp) REVERT: D 432 LYS cc_start: 0.8904 (tptp) cc_final: 0.8314 (tptp) REVERT: D 436 ASP cc_start: 0.8518 (m-30) cc_final: 0.7980 (m-30) REVERT: D 548 SER cc_start: 0.8775 (t) cc_final: 0.8435 (p) REVERT: D 609 GLU cc_start: 0.8481 (tp30) cc_final: 0.8191 (tp30) REVERT: D 777 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9215 (p) REVERT: D 919 ASP cc_start: 0.8771 (m-30) cc_final: 0.8540 (m-30) REVERT: E 464 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7723 (m-90) REVERT: E 482 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8050 (ttt180) REVERT: E 826 MET cc_start: 0.8755 (tmm) cc_final: 0.8012 (ttm) REVERT: F 547 PHE cc_start: 0.6460 (t80) cc_final: 0.6026 (t80) REVERT: F 588 LEU cc_start: 0.8701 (tp) cc_final: 0.8404 (tp) REVERT: F 714 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7442 (mtmt) outliers start: 33 outliers final: 26 residues processed: 188 average time/residue: 0.1640 time to fit residues: 49.7180 Evaluate side-chains 186 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 423 GLU 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 B residue 880 THR Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 833 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 112 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 294 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 238 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.104079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077192 restraints weight = 46953.609| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.47 r_work: 0.2915 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25045 Z= 0.099 Angle : 0.502 13.257 33923 Z= 0.250 Chirality : 0.040 0.266 3899 Planarity : 0.004 0.054 4334 Dihedral : 6.746 86.609 3552 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.05 % Allowed : 9.45 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.15), residues: 3096 helix: 2.10 (0.14), residues: 1380 sheet: 0.57 (0.26), residues: 397 loop : -0.13 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 597 TYR 0.029 0.001 TYR F 834 PHE 0.012 0.001 PHE D 751 TRP 0.022 0.001 TRP D 770 HIS 0.004 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00229 (25045) covalent geometry : angle 0.50249 (33923) hydrogen bonds : bond 0.02980 ( 1140) hydrogen bonds : angle 4.38224 ( 3345) *********************** 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 193 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7360 (t80) cc_final: 0.7099 (t80) REVERT: A 608 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8464 (mm) REVERT: A 632 LYS cc_start: 0.8935 (tppt) cc_final: 0.8487 (tppp) REVERT: B 797 ASP cc_start: 0.8430 (t70) cc_final: 0.8098 (t0) REVERT: C 426 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8177 (ptpp) REVERT: C 494 MET cc_start: 0.8545 (mtp) cc_final: 0.8178 (mtp) REVERT: D 432 LYS cc_start: 0.8881 (tptp) cc_final: 0.8285 (tptp) REVERT: D 436 ASP cc_start: 0.8481 (m-30) cc_final: 0.7895 (m-30) REVERT: D 609 GLU cc_start: 0.8444 (tp30) cc_final: 0.8169 (tp30) REVERT: D 777 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9126 (t) REVERT: D 919 ASP cc_start: 0.8742 (m-30) cc_final: 0.8511 (m-30) REVERT: E 421 PHE cc_start: 0.7123 (m-80) cc_final: 0.6823 (m-80) REVERT: E 464 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.7786 (m-90) REVERT: E 482 ARG cc_start: 0.8328 (ttm170) cc_final: 0.8001 (ttt180) REVERT: E 826 MET cc_start: 0.8762 (tmm) cc_final: 0.8040 (ttm) REVERT: F 547 PHE cc_start: 0.6347 (t80) cc_final: 0.6056 (t80) REVERT: F 588 LEU cc_start: 0.8652 (tp) cc_final: 0.8402 (tp) REVERT: F 714 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7413 (mtmt) outliers start: 28 outliers final: 22 residues processed: 184 average time/residue: 0.1744 time to fit residues: 51.6034 Evaluate side-chains 184 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 423 GLU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 227 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 307 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 456 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 = 0.3504 r_free = 0.3504 target = 0.105717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078680 restraints weight = 47078.871| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.47 r_work: 0.2925 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25045 Z= 0.102 Angle : 0.505 12.723 33923 Z= 0.250 Chirality : 0.040 0.270 3899 Planarity : 0.004 0.054 4334 Dihedral : 6.641 88.935 3552 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.05 % Allowed : 9.45 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.15), residues: 3096 helix: 2.14 (0.14), residues: 1387 sheet: 0.60 (0.26), residues: 397 loop : -0.09 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 597 TYR 0.029 0.001 TYR F 834 PHE 0.013 0.001 PHE B 547 TRP 0.020 0.001 TRP D 770 HIS 0.004 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00237 (25045) covalent geometry : angle 0.50519 (33923) hydrogen bonds : bond 0.02938 ( 1140) hydrogen bonds : angle 4.34355 ( 3345) *********************** 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 200 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7315 (t80) cc_final: 0.7068 (t80) REVERT: A 608 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 632 LYS cc_start: 0.8944 (tppt) cc_final: 0.8503 (tppp) REVERT: B 797 ASP cc_start: 0.8474 (t70) cc_final: 0.8138 (t0) REVERT: C 426 LYS cc_start: 0.8471 (ptpp) cc_final: 0.8154 (ptpp) REVERT: C 826 MET cc_start: 0.8929 (tmm) cc_final: 0.8659 (ttp) REVERT: C 869 MET cc_start: 0.9360 (mtp) cc_final: 0.9127 (mtp) REVERT: D 432 LYS cc_start: 0.8871 (tptp) cc_final: 0.8339 (tptp) REVERT: D 436 ASP cc_start: 0.8488 (m-30) cc_final: 0.7911 (m-30) REVERT: D 609 GLU cc_start: 0.8445 (tp30) cc_final: 0.8181 (tp30) REVERT: D 777 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9113 (t) REVERT: D 919 ASP cc_start: 0.8749 (m-30) cc_final: 0.8520 (m-30) REVERT: E 421 PHE cc_start: 0.7027 (m-80) cc_final: 0.6728 (m-80) REVERT: E 464 TRP cc_start: 0.8112 (OUTLIER) cc_final: 0.7790 (m-90) REVERT: E 482 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8042 (ttt180) REVERT: E 826 MET cc_start: 0.8750 (tmm) cc_final: 0.8057 (ttm) REVERT: F 547 PHE cc_start: 0.6344 (t80) cc_final: 0.6040 (t80) REVERT: F 588 LEU cc_start: 0.8397 (tp) cc_final: 0.8103 (tp) REVERT: F 714 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7423 (mtmt) outliers start: 28 outliers final: 24 residues processed: 190 average time/residue: 0.1766 time to fit residues: 53.6557 Evaluate side-chains 189 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 423 GLU 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 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 171 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 209 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 289 optimal weight: 0.8980 overall best weight: 1.1202 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.103880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076941 restraints weight = 46877.955| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.43 r_work: 0.2926 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25045 Z= 0.117 Angle : 0.517 13.233 33923 Z= 0.256 Chirality : 0.041 0.270 3899 Planarity : 0.004 0.054 4334 Dihedral : 6.664 88.989 3552 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.13 % Allowed : 9.49 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.15), residues: 3096 helix: 2.12 (0.14), residues: 1383 sheet: 0.60 (0.26), residues: 397 loop : -0.08 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 597 TYR 0.029 0.001 TYR F 834 PHE 0.014 0.001 PHE D 751 TRP 0.020 0.001 TRP D 770 HIS 0.004 0.001 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00279 (25045) covalent geometry : angle 0.51700 (33923) hydrogen bonds : bond 0.03038 ( 1140) hydrogen bonds : angle 4.34691 ( 3345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 455 PHE cc_start: 0.7387 (t80) cc_final: 0.7135 (t80) REVERT: A 608 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 632 LYS cc_start: 0.8931 (tppt) cc_final: 0.8500 (tppp) REVERT: B 797 ASP cc_start: 0.8459 (t70) cc_final: 0.8115 (t0) REVERT: C 826 MET cc_start: 0.8918 (tmm) cc_final: 0.8660 (ttp) REVERT: D 432 LYS cc_start: 0.8830 (tptp) cc_final: 0.8239 (tptp) REVERT: D 436 ASP cc_start: 0.8510 (m-30) cc_final: 0.7917 (m-30) REVERT: D 548 SER cc_start: 0.8717 (t) cc_final: 0.8385 (p) REVERT: D 609 GLU cc_start: 0.8448 (tp30) cc_final: 0.8208 (tp30) REVERT: D 777 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9123 (t) REVERT: D 919 ASP cc_start: 0.8747 (m-30) cc_final: 0.8518 (m-30) REVERT: E 421 PHE cc_start: 0.7094 (m-80) cc_final: 0.6808 (m-80) REVERT: E 464 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.7830 (m-90) REVERT: E 482 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7955 (ttt180) REVERT: E 826 MET cc_start: 0.8711 (tmm) cc_final: 0.8048 (ttm) REVERT: F 547 PHE cc_start: 0.6364 (t80) cc_final: 0.6071 (t80) REVERT: F 588 LEU cc_start: 0.8419 (tp) cc_final: 0.8134 (tp) REVERT: F 714 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7445 (mtmt) outliers start: 30 outliers final: 26 residues processed: 186 average time/residue: 0.1728 time to fit residues: 52.3740 Evaluate side-chains 191 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 423 GLU 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 B residue 880 THR Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain E residue 464 TRP Chi-restraints excluded: chain E residue 620 LEU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 253 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 264 optimal weight: 10.0000 chunk 49 optimal weight: 0.0020 chunk 231 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 832 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078492 restraints weight = 47209.052| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.50 r_work: 0.2933 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25045 Z= 0.094 Angle : 0.502 13.195 33923 Z= 0.248 Chirality : 0.040 0.273 3899 Planarity : 0.004 0.055 4334 Dihedral : 6.573 89.154 3552 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.09 % Allowed : 9.60 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.15), residues: 3096 helix: 2.18 (0.14), residues: 1388 sheet: 0.65 (0.27), residues: 387 loop : -0.07 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 597 TYR 0.028 0.001 TYR F 834 PHE 0.013 0.001 PHE B 547 TRP 0.020 0.001 TRP D 770 HIS 0.004 0.000 HIS F 622 Details of bonding type rmsd covalent geometry : bond 0.00212 (25045) covalent geometry : angle 0.50223 (33923) hydrogen bonds : bond 0.02838 ( 1140) hydrogen bonds : angle 4.29916 ( 3345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6398.96 seconds wall clock time: 110 minutes 41.84 seconds (6641.84 seconds total)