Starting phenix.real_space_refine on Sat Jul 4 00:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz5_24751/07_2026/7rz5_24751.cif" } resolution = 3.3 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 106 5.16 5 C 10998 2.51 5 N 2606 2.21 5 O 3032 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16770 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4780 Classifications: {'peptide': 611} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 593} Chain breaks: 3 Chain: "B" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3211 Classifications: {'peptide': 412} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 4780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4780 Classifications: {'peptide': 611} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 593} Chain breaks: 3 Chain: "D" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3211 Classifications: {'peptide': 412} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 398} Chain breaks: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 210 Unusual residues: {'PCW': 7, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 184 Unusual residues: {'PCW': 5, 'ZK1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 197 Unusual residues: {'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 197 Unusual residues: {'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 3.39, per 1000 atoms: 0.20 Number of scatterers: 16770 At special positions: 0 Unit cell: (124.3, 130.9, 139.7, 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 106 16.00 P 16 15.00 F 12 9.00 O 3032 8.00 N 2606 7.00 C 10998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 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: 1.36 Conformation dependent library (CDL) restraints added in 791.7 milliseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 22 sheets defined 55.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.392A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.599A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.602A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.578A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.638A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.870A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.736A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 642' Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.703A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.651A pdb=" N LYS A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.682A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.501A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.701A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.521A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.545A pdb=" N SER A 780 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.942A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.519A pdb=" N PHE A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 917 through 928 removed outlier: 3.576A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 4.135A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 941 " --> pdb=" O PHE A 937 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 986 removed outlier: 4.403A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 964 " --> pdb=" O PHE A 960 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.528A pdb=" N ALA A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A1009 " --> pdb=" O TRP A1005 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A1034 " --> pdb=" O LYS A1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.149A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.524A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.514A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.522A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.864A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.600A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.829A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.598A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 609 " --> pdb=" O TRP B 605 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.977A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.744A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.652A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.666A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.515A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.604A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.521A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.894A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.392A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.599A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.602A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.578A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.637A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.870A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 630 " --> pdb=" O VAL C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.736A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 640 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 642' Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.702A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.651A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.682A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.500A pdb=" N GLU C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.701A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.521A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 781 removed outlier: 3.544A pdb=" N SER C 780 " --> pdb=" O ASP C 777 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 781 " --> pdb=" O SER C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.943A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 3.519A pdb=" N PHE C 844 " --> pdb=" O LEU C 840 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 917 through 928 removed outlier: 3.576A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 928 " --> pdb=" O MET C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 4.136A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 941 " --> pdb=" O PHE C 937 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 944 " --> pdb=" O PHE C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 986 removed outlier: 4.403A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 964 " --> pdb=" O PHE C 960 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 986 " --> pdb=" O SER C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.527A pdb=" N ALA C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C1009 " --> pdb=" O TRP C1005 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA C1034 " --> pdb=" O LYS C1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.149A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.525A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 3.513A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.521A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.864A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.600A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.831A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.598A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 609 " --> pdb=" O TRP D 605 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.978A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.744A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.652A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.666A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.515A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.604A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.520A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 820 removed outlier: 3.895A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 812 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.265A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.093A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.571A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 900 through 902 removed outlier: 4.045A pdb=" N SER A 875 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 866 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A 881 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 864 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A 883 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 862 " --> pdb=" O HIS A 883 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.795A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.795A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.619A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.842A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.265A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.094A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.570A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 900 through 902 removed outlier: 4.046A pdb=" N SER C 875 " --> pdb=" O LEU C 870 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU C 866 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C 881 " --> pdb=" O LEU C 864 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU C 864 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS C 883 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU C 862 " --> pdb=" O HIS C 883 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.796A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.796A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.619A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.842A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 757 hydrogen bonds defined for protein. 2217 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: 2.69 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2553 1.32 - 1.45: 4754 1.45 - 1.58: 9591 1.58 - 1.72: 24 1.72 - 1.85: 180 Bond restraints: 17102 Sorted by residual: bond pdb=" CAT ZK1 D1102 " pdb=" OAA ZK1 D1102 " ideal model delta sigma weight residual 1.214 1.396 -0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" CAT ZK1 B1101 " pdb=" OAA ZK1 B1101 " ideal model delta sigma weight residual 1.214 1.396 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" CAT ZK1 A1101 " pdb=" OAA ZK1 A1101 " ideal model delta sigma weight residual 1.214 1.394 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" CAU ZK1 D1102 " pdb=" OAB ZK1 D1102 " ideal model delta sigma weight residual 1.215 1.395 -0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" CAU ZK1 C1101 " pdb=" OAB ZK1 C1101 " ideal model delta sigma weight residual 1.215 1.395 -0.180 2.00e-02 2.50e+03 8.06e+01 ... (remaining 17097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 22338 2.89 - 5.78: 448 5.78 - 8.67: 116 8.67 - 11.56: 42 11.56 - 14.44: 18 Bond angle restraints: 22962 Sorted by residual: angle pdb=" N ASP A 519 " pdb=" CA ASP A 519 " pdb=" C ASP A 519 " ideal model delta sigma weight residual 113.57 120.04 -6.47 1.38e+00 5.25e-01 2.20e+01 angle pdb=" N ASP C 519 " pdb=" CA ASP C 519 " pdb=" C ASP C 519 " ideal model delta sigma weight residual 113.57 120.03 -6.46 1.38e+00 5.25e-01 2.19e+01 angle pdb=" O3P PCW A1102 " pdb=" P PCW A1102 " pdb=" O4P PCW A1102 " ideal model delta sigma weight residual 96.85 110.25 -13.40 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O3P PCW C1102 " pdb=" P PCW C1102 " pdb=" O4P PCW C1102 " ideal model delta sigma weight residual 96.85 110.24 -13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O3P PCW A1104 " pdb=" P PCW A1104 " pdb=" O4P PCW A1104 " ideal model delta sigma weight residual 96.85 110.04 -13.19 3.00e+00 1.11e-01 1.93e+01 ... (remaining 22957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 9904 34.87 - 69.73: 179 69.73 - 104.60: 15 104.60 - 139.46: 8 139.46 - 174.33: 6 Dihedral angle restraints: 10112 sinusoidal: 4240 harmonic: 5872 Sorted by residual: dihedral pdb=" C33 PCW C1104 " pdb=" C31 PCW C1104 " pdb=" C32 PCW C1104 " pdb=" O2 PCW C1104 " ideal model delta sinusoidal sigma weight residual -168.17 6.16 -174.33 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW D1105 " pdb=" C4 PCW D1105 " pdb=" C5 PCW D1105 " pdb=" O4P PCW D1105 " ideal model delta sinusoidal sigma weight residual 293.34 137.62 155.72 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" N PCW B1104 " pdb=" C4 PCW B1104 " pdb=" C5 PCW B1104 " pdb=" O4P PCW B1104 " ideal model delta sinusoidal sigma weight residual 293.34 137.93 155.41 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 10109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1846 0.049 - 0.098: 505 0.098 - 0.147: 105 0.147 - 0.197: 21 0.197 - 0.246: 13 Chirality restraints: 2490 Sorted by residual: chirality pdb=" C2 PCW C1103 " pdb=" C1 PCW C1103 " pdb=" C3 PCW C1103 " pdb=" O2 PCW C1103 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2 PCW A1103 " pdb=" C1 PCW A1103 " pdb=" C3 PCW A1103 " pdb=" O2 PCW A1103 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C2 PCW B1104 " pdb=" C1 PCW B1104 " pdb=" C3 PCW B1104 " pdb=" O2 PCW B1104 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2487 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 405 " -0.012 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR B 405 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 405 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 405 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 405 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 405 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 405 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 405 " -0.012 2.00e-02 2.50e+03 1.54e-02 4.72e+00 pdb=" CG TYR D 405 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR D 405 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 405 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR D 405 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 405 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 405 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 405 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 931 " -0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 932 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 932 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 932 " -0.031 5.00e-02 4.00e+02 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5657 2.87 - 3.38: 14402 3.38 - 3.89: 24638 3.89 - 4.39: 28443 4.39 - 4.90: 50435 Nonbonded interactions: 123575 Sorted by model distance: nonbonded pdb=" OG SER A 544 " pdb=" ND2 ASN A 569 " model vdw 2.368 3.120 nonbonded pdb=" OG SER C 544 " pdb=" ND2 ASN C 569 " model vdw 2.368 3.120 nonbonded pdb=" O2 PCW C1103 " pdb=" O3P PCW C1103 " model vdw 2.385 2.432 nonbonded pdb=" O2 PCW A1103 " pdb=" O3P PCW A1103 " model vdw 2.386 2.432 nonbonded pdb=" OD2 ASP D 651 " pdb=" NH2 ARG D 684 " model vdw 2.399 3.120 ... (remaining 123570 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 392 through 1106 or (resid 1107 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23)))) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 392 through 820 or resid 1103 through 1104 or (resid 1105 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19)) or resid 1106)) selection = (chain 'D' and (resid 392 through 820 or (resid 1103 and (name N or name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C5 or name C6 or name C7 or name C8 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) \ or (resid 1104 and (name N or name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C \ 42 or name C43 or name C44 or name C5 or name C6 or name C7 or name C8 or name O \ 11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 1105 and (name C13 or name C14 or name C15 or name C \ 16 or name C17 or name C18 or name C19)) or resid 1106)) } 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.620 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.182 17108 Z= 0.487 Angle : 1.193 14.445 22974 Z= 0.561 Chirality : 0.051 0.246 2490 Planarity : 0.006 0.054 2772 Dihedral : 14.267 174.325 6350 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.35 % Allowed : 4.51 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -5.41 (0.12), residues: 2022 helix: -4.47 (0.05), residues: 1064 sheet: -0.79 (0.38), residues: 184 loop : -2.66 (0.16), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 599 TYR 0.038 0.002 TYR B 405 PHE 0.020 0.002 PHE B 546 TRP 0.026 0.003 TRP C 861 HIS 0.004 0.002 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.01025 / 0.49 (17102) covalent geometry : angle 1.19288 / 0.56 (22962) SS BOND : bond 0.00450 / 0.19 ( 6) SS BOND : angle 0.51745 / 0.29 ( 12) hydrogen bonds : bond 0.35376 / 23.09 ( 749) hydrogen bonds : angle 9.21013 / 6.47 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 358 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7723 (pp) REVERT: A 634 GLU cc_start: 0.8096 (pm20) cc_final: 0.7856 (pm20) REVERT: A 669 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8300 (ttmm) REVERT: A 907 MET cc_start: 0.3497 (pp-130) cc_final: 0.2863 (ptp) REVERT: B 447 ASP cc_start: 0.7502 (m-30) cc_final: 0.7236 (t0) REVERT: B 473 ASP cc_start: 0.7837 (m-30) cc_final: 0.7463 (m-30) REVERT: B 527 MET cc_start: 0.7519 (ptp) cc_final: 0.7098 (ptt) REVERT: B 585 MET cc_start: 0.9094 (mmt) cc_final: 0.8338 (mmt) REVERT: B 674 MET cc_start: 0.8947 (mtp) cc_final: 0.8616 (mtp) REVERT: B 772 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8088 (mt-10) REVERT: C 591 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7654 (pp) REVERT: C 669 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8324 (ttmm) REVERT: C 684 ARG cc_start: 0.8251 (mtm180) cc_final: 0.8014 (ttp-110) REVERT: C 813 GLU cc_start: 0.4731 (mm-30) cc_final: 0.4065 (tp30) REVERT: C 897 ARG cc_start: 0.6996 (ttt90) cc_final: 0.6644 (ttt-90) REVERT: C 907 MET cc_start: 0.3275 (pp-130) cc_final: 0.2879 (ptp) REVERT: C 966 PHE cc_start: 0.8604 (m-10) cc_final: 0.8340 (m-10) REVERT: C 1005 TRP cc_start: 0.6574 (p-90) cc_final: 0.5949 (p90) REVERT: C 1027 LEU cc_start: 0.7668 (tp) cc_final: 0.7346 (tp) REVERT: D 511 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7609 (tptp) REVERT: D 591 ILE cc_start: 0.7945 (pt) cc_final: 0.6982 (pt) outliers start: 6 outliers final: 1 residues processed: 363 average time/residue: 0.1435 time to fit residues: 75.7120 Evaluate side-chains 234 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 882 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 874 GLN A 920 ASN A 954 HIS C 412 HIS C 587 GLN C 642 GLN C 873 ASN C 920 ASN D 575 ASN D 764 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.095909 restraints weight = 24145.408| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.66 r_work: 0.2877 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17108 Z= 0.137 Angle : 0.549 9.160 22974 Z= 0.289 Chirality : 0.041 0.157 2490 Planarity : 0.005 0.057 2772 Dihedral : 14.899 171.693 2656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.79 % Allowed : 7.87 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -2.30 (0.15), residues: 2022 helix: -1.27 (0.13), residues: 1048 sheet: -0.26 (0.35), residues: 220 loop : -2.11 (0.18), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.019 0.001 TYR C1032 PHE 0.019 0.002 PHE C1028 TRP 0.016 0.001 TRP C 766 HIS 0.008 0.002 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17102) covalent geometry : angle 0.54910 / 0.29 (22962) SS BOND : bond 0.00328 / 0.16 ( 6) SS BOND : angle 0.40120 / 0.21 ( 12) hydrogen bonds : bond 0.06072 / 3.98 ( 749) hydrogen bonds : angle 4.10888 / 3.00 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.644 Fit side-chains REVERT: A 594 ARG cc_start: 0.8082 (ptp-110) cc_final: 0.7656 (ttp-110) REVERT: A 634 GLU cc_start: 0.8401 (pm20) cc_final: 0.8011 (pm20) REVERT: A 643 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7913 (t) REVERT: A 880 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6771 (ppp) REVERT: B 414 MET cc_start: 0.7924 (mmm) cc_final: 0.7677 (mmm) REVERT: B 515 PHE cc_start: 0.8648 (m-10) cc_final: 0.8346 (m-10) REVERT: B 527 MET cc_start: 0.8328 (ptp) cc_final: 0.8127 (ptp) REVERT: B 805 LEU cc_start: 0.8655 (tt) cc_final: 0.8319 (tp) REVERT: C 591 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7659 (pp) REVERT: C 627 GLU cc_start: 0.8256 (tt0) cc_final: 0.8031 (tm-30) REVERT: C 643 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7993 (t) REVERT: C 684 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8437 (ttp-110) REVERT: C 813 GLU cc_start: 0.5050 (mm-30) cc_final: 0.4696 (tp30) REVERT: C 897 ARG cc_start: 0.7028 (ttt90) cc_final: 0.6710 (ttt-90) REVERT: C 955 ARG cc_start: 0.5797 (ttp80) cc_final: 0.4732 (ptp-110) REVERT: C 966 PHE cc_start: 0.8259 (m-10) cc_final: 0.8004 (m-10) REVERT: D 719 ASP cc_start: 0.7401 (t0) cc_final: 0.7092 (t0) outliers start: 31 outliers final: 12 residues processed: 255 average time/residue: 0.1366 time to fit residues: 51.9533 Evaluate side-chains 201 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 114 optimal weight: 0.0570 chunk 190 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094053 restraints weight = 24804.158| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.76 r_work: 0.2880 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17108 Z= 0.121 Angle : 0.486 7.717 22974 Z= 0.254 Chirality : 0.040 0.162 2490 Planarity : 0.004 0.042 2772 Dihedral : 14.006 169.227 2654 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.56 % Allowed : 9.78 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.52 (0.18), residues: 2022 helix: 0.63 (0.16), residues: 1064 sheet: -0.00 (0.35), residues: 226 loop : -1.92 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.026 0.001 TYR C1032 PHE 0.015 0.001 PHE C 999 TRP 0.008 0.001 TRP A1005 HIS 0.007 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (17102) covalent geometry : angle 0.48640 / 0.25 (22962) SS BOND : bond 0.00238 / 0.11 ( 6) SS BOND : angle 0.31103 / 0.16 ( 12) hydrogen bonds : bond 0.05572 / 3.66 ( 749) hydrogen bonds : angle 3.56260 / 2.61 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.598 Fit side-chains REVERT: A 549 TYR cc_start: 0.5895 (m-10) cc_final: 0.5569 (m-80) REVERT: A 594 ARG cc_start: 0.8101 (ptp-110) cc_final: 0.7883 (mtp85) REVERT: A 634 GLU cc_start: 0.8378 (pm20) cc_final: 0.8023 (pm20) REVERT: A 684 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.8109 (mtp180) REVERT: A 998 TYR cc_start: 0.7752 (p90) cc_final: 0.7480 (p90) REVERT: B 473 ASP cc_start: 0.8150 (m-30) cc_final: 0.7929 (m-30) REVERT: B 515 PHE cc_start: 0.8853 (m-10) cc_final: 0.8612 (m-10) REVERT: B 527 MET cc_start: 0.8373 (ptp) cc_final: 0.7970 (ptm) REVERT: B 805 LEU cc_start: 0.9042 (tt) cc_final: 0.8687 (tp) REVERT: C 585 MET cc_start: 0.9159 (mmt) cc_final: 0.8952 (mmt) REVERT: C 591 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7865 (pp) REVERT: C 634 GLU cc_start: 0.8385 (pm20) cc_final: 0.8027 (pm20) REVERT: C 684 ARG cc_start: 0.8644 (mtm180) cc_final: 0.8404 (ttp-110) REVERT: C 808 LEU cc_start: 0.8402 (mp) cc_final: 0.8128 (mp) REVERT: C 880 MET cc_start: 0.7021 (ppp) cc_final: 0.6783 (ppp) REVERT: C 897 ARG cc_start: 0.7154 (ttt90) cc_final: 0.6815 (ttt-90) REVERT: C 1012 ILE cc_start: 0.8252 (mt) cc_final: 0.7954 (mp) outliers start: 27 outliers final: 15 residues processed: 223 average time/residue: 0.1143 time to fit residues: 39.4284 Evaluate side-chains 200 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 0.0470 chunk 91 optimal weight: 0.0030 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.0010 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 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 = 0.3616 r_free = 0.3616 target = 0.134959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095658 restraints weight = 24838.294| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.53 r_work: 0.2924 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17108 Z= 0.098 Angle : 0.448 8.016 22974 Z= 0.232 Chirality : 0.039 0.163 2490 Planarity : 0.003 0.036 2772 Dihedral : 13.307 162.627 2654 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.68 % Allowed : 10.53 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 0.29 (0.18), residues: 2022 helix: 1.46 (0.16), residues: 1080 sheet: 0.15 (0.36), residues: 224 loop : -1.81 (0.19), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.018 0.001 TYR C1032 PHE 0.020 0.001 PHE D 814 TRP 0.007 0.001 TRP A1005 HIS 0.007 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (17102) covalent geometry : angle 0.44784 / 0.23 (22962) SS BOND : bond 0.00151 / 0.07 ( 6) SS BOND : angle 0.25256 / 0.13 ( 12) hydrogen bonds : bond 0.04405 / 2.89 ( 749) hydrogen bonds : angle 3.30893 / 2.44 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.647 Fit side-chains REVERT: A 549 TYR cc_start: 0.5830 (m-10) cc_final: 0.5493 (m-80) REVERT: A 591 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (pp) REVERT: A 634 GLU cc_start: 0.8361 (pm20) cc_final: 0.8016 (pm20) REVERT: A 684 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.8071 (mtp180) REVERT: A 987 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 998 TYR cc_start: 0.7752 (p90) cc_final: 0.7386 (p90) REVERT: B 473 ASP cc_start: 0.8083 (m-30) cc_final: 0.7860 (m-30) REVERT: B 515 PHE cc_start: 0.8853 (m-10) cc_final: 0.8653 (m-10) REVERT: B 527 MET cc_start: 0.8244 (ptp) cc_final: 0.7856 (ptm) REVERT: B 678 GLU cc_start: 0.7601 (tp30) cc_final: 0.7318 (mp0) REVERT: B 805 LEU cc_start: 0.9043 (tt) cc_final: 0.8654 (tp) REVERT: C 591 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7899 (pp) REVERT: C 634 GLU cc_start: 0.8389 (pm20) cc_final: 0.8059 (pm20) REVERT: C 684 ARG cc_start: 0.8586 (mtm180) cc_final: 0.8314 (ttp-110) REVERT: C 880 MET cc_start: 0.7100 (ppp) cc_final: 0.6820 (ppp) REVERT: C 897 ARG cc_start: 0.7098 (ttt90) cc_final: 0.6593 (ttt180) outliers start: 29 outliers final: 18 residues processed: 219 average time/residue: 0.1186 time to fit residues: 40.2942 Evaluate side-chains 202 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 196 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 164 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS C 412 HIS C 874 GLN C 954 HIS D 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092119 restraints weight = 24673.153| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.51 r_work: 0.2870 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17108 Z= 0.141 Angle : 0.485 8.788 22974 Z= 0.252 Chirality : 0.041 0.165 2490 Planarity : 0.003 0.034 2772 Dihedral : 13.430 165.915 2654 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.97 % Allowed : 10.94 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 0.55 (0.19), residues: 2022 helix: 1.77 (0.16), residues: 1080 sheet: 0.04 (0.35), residues: 226 loop : -1.79 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 628 TYR 0.016 0.001 TYR C1032 PHE 0.014 0.001 PHE C 999 TRP 0.008 0.001 TRP C 460 HIS 0.008 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17102) covalent geometry : angle 0.48509 / 0.25 (22962) SS BOND : bond 0.00328 / 0.16 ( 6) SS BOND : angle 0.35194 / 0.22 ( 12) hydrogen bonds : bond 0.05477 / 3.59 ( 749) hydrogen bonds : angle 3.46581 / 2.53 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.638 Fit side-chains REVERT: A 549 TYR cc_start: 0.5828 (m-10) cc_final: 0.5468 (m-80) REVERT: A 591 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8077 (pp) REVERT: A 634 GLU cc_start: 0.8336 (pm20) cc_final: 0.8061 (pm20) REVERT: B 473 ASP cc_start: 0.8089 (m-30) cc_final: 0.7876 (m-30) REVERT: B 527 MET cc_start: 0.8435 (ptp) cc_final: 0.8049 (ptm) REVERT: B 678 GLU cc_start: 0.7757 (tp30) cc_final: 0.7417 (mp0) REVERT: B 805 LEU cc_start: 0.9089 (tt) cc_final: 0.8726 (tp) REVERT: C 591 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7988 (pp) REVERT: C 634 GLU cc_start: 0.8418 (pm20) cc_final: 0.7995 (pm20) REVERT: C 684 ARG cc_start: 0.8582 (mtm180) cc_final: 0.8371 (ttp-110) REVERT: C 808 LEU cc_start: 0.8489 (mp) cc_final: 0.7978 (tt) REVERT: C 880 MET cc_start: 0.7092 (ppp) cc_final: 0.6785 (ppp) REVERT: C 897 ARG cc_start: 0.7125 (ttt90) cc_final: 0.6486 (ttt180) outliers start: 34 outliers final: 26 residues processed: 220 average time/residue: 0.1221 time to fit residues: 41.5877 Evaluate side-chains 212 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 812 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 139 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 0.0050 chunk 170 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.094824 restraints weight = 24561.908| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.52 r_work: 0.2901 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17108 Z= 0.100 Angle : 0.441 8.001 22974 Z= 0.230 Chirality : 0.039 0.211 2490 Planarity : 0.003 0.033 2772 Dihedral : 12.889 161.815 2654 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.97 % Allowed : 10.94 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 0.99 (0.19), residues: 2022 helix: 2.20 (0.16), residues: 1080 sheet: 0.09 (0.35), residues: 224 loop : -1.67 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.014 0.001 TYR C1032 PHE 0.029 0.001 PHE A 814 TRP 0.007 0.001 TRP A1005 HIS 0.006 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (17102) covalent geometry : angle 0.44134 / 0.23 (22962) SS BOND : bond 0.00178 / 0.08 ( 6) SS BOND : angle 0.26616 / 0.16 ( 12) hydrogen bonds : bond 0.04381 / 2.88 ( 749) hydrogen bonds : angle 3.28880 / 2.41 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 549 TYR cc_start: 0.5681 (m-10) cc_final: 0.5337 (m-80) REVERT: A 591 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8023 (pp) REVERT: A 634 GLU cc_start: 0.8355 (pm20) cc_final: 0.7997 (pm20) REVERT: A 813 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6203 (mm-30) REVERT: B 473 ASP cc_start: 0.8100 (m-30) cc_final: 0.7894 (m-30) REVERT: B 678 GLU cc_start: 0.7691 (tp30) cc_final: 0.7373 (mp0) REVERT: B 684 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8202 (tpp80) REVERT: B 805 LEU cc_start: 0.9012 (tt) cc_final: 0.8637 (tp) REVERT: C 585 MET cc_start: 0.9171 (mmt) cc_final: 0.8961 (mmt) REVERT: C 591 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8079 (pp) REVERT: C 634 GLU cc_start: 0.8446 (pm20) cc_final: 0.8069 (pm20) REVERT: C 638 ASP cc_start: 0.8511 (m-30) cc_final: 0.8234 (m-30) REVERT: C 684 ARG cc_start: 0.8645 (mtm180) cc_final: 0.8423 (ttp-110) REVERT: C 808 LEU cc_start: 0.8360 (mp) cc_final: 0.7827 (tt) REVERT: C 880 MET cc_start: 0.7099 (ppp) cc_final: 0.6778 (ppp) REVERT: C 897 ARG cc_start: 0.7077 (ttt90) cc_final: 0.6541 (ttt180) outliers start: 34 outliers final: 22 residues processed: 214 average time/residue: 0.1221 time to fit residues: 40.3356 Evaluate side-chains 207 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 186 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091633 restraints weight = 24609.490| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.51 r_work: 0.2861 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17108 Z= 0.144 Angle : 0.487 8.817 22974 Z= 0.253 Chirality : 0.041 0.164 2490 Planarity : 0.003 0.032 2772 Dihedral : 13.107 164.105 2654 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.97 % Allowed : 11.00 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 0.88 (0.19), residues: 2022 helix: 2.11 (0.16), residues: 1092 sheet: 0.00 (0.35), residues: 226 loop : -1.77 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 628 TYR 0.013 0.001 TYR C1032 PHE 0.027 0.001 PHE A 814 TRP 0.008 0.001 TRP C 460 HIS 0.009 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (17102) covalent geometry : angle 0.48677 / 0.25 (22962) SS BOND : bond 0.00313 / 0.15 ( 6) SS BOND : angle 0.37408 / 0.22 ( 12) hydrogen bonds : bond 0.05480 / 3.59 ( 749) hydrogen bonds : angle 3.46996 / 2.53 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 549 TYR cc_start: 0.5537 (m-10) cc_final: 0.5326 (m-80) REVERT: A 591 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8075 (pp) REVERT: A 634 GLU cc_start: 0.8361 (pm20) cc_final: 0.8079 (pm20) REVERT: B 678 GLU cc_start: 0.7763 (tp30) cc_final: 0.7439 (mp0) REVERT: B 684 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8230 (tpp80) REVERT: B 805 LEU cc_start: 0.9069 (tt) cc_final: 0.8716 (tp) REVERT: C 591 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8127 (pp) REVERT: C 634 GLU cc_start: 0.8409 (pm20) cc_final: 0.8069 (pm20) REVERT: C 638 ASP cc_start: 0.8539 (m-30) cc_final: 0.8255 (m-30) REVERT: C 684 ARG cc_start: 0.8587 (mtm180) cc_final: 0.8362 (ttp-110) REVERT: C 808 LEU cc_start: 0.8404 (mp) cc_final: 0.8052 (tt) REVERT: C 880 MET cc_start: 0.7073 (ppp) cc_final: 0.6736 (ppp) REVERT: C 897 ARG cc_start: 0.7122 (ttt90) cc_final: 0.6612 (ttt180) REVERT: C 940 PHE cc_start: 0.8494 (t80) cc_final: 0.8027 (t80) REVERT: D 684 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8144 (tpp80) outliers start: 34 outliers final: 26 residues processed: 210 average time/residue: 0.1231 time to fit residues: 40.4772 Evaluate side-chains 210 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 812 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 116 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 127 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094180 restraints weight = 24746.008| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.53 r_work: 0.2899 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17108 Z= 0.103 Angle : 0.445 8.045 22974 Z= 0.232 Chirality : 0.040 0.240 2490 Planarity : 0.003 0.034 2772 Dihedral : 12.646 160.093 2654 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.62 % Allowed : 11.63 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 1.14 (0.19), residues: 2022 helix: 2.34 (0.16), residues: 1094 sheet: 0.01 (0.35), residues: 226 loop : -1.65 (0.20), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.012 0.001 TYR C1032 PHE 0.028 0.001 PHE A 814 TRP 0.008 0.001 TRP A1005 HIS 0.008 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (17102) covalent geometry : angle 0.44482 / 0.23 (22962) SS BOND : bond 0.00182 / 0.09 ( 6) SS BOND : angle 0.24615 / 0.13 ( 12) hydrogen bonds : bond 0.04462 / 2.93 ( 749) hydrogen bonds : angle 3.31680 / 2.43 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 634 GLU cc_start: 0.8327 (pm20) cc_final: 0.8019 (pm20) REVERT: A 813 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6388 (mm-30) REVERT: B 678 GLU cc_start: 0.7719 (tp30) cc_final: 0.7427 (mp0) REVERT: B 684 ARG cc_start: 0.8520 (tpp80) cc_final: 0.8206 (tpp80) REVERT: B 805 LEU cc_start: 0.9037 (tt) cc_final: 0.8674 (tp) REVERT: C 585 MET cc_start: 0.9210 (mmt) cc_final: 0.8991 (mmt) REVERT: C 591 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8144 (pp) REVERT: C 634 GLU cc_start: 0.8400 (pm20) cc_final: 0.7991 (pm20) REVERT: C 638 ASP cc_start: 0.8481 (m-30) cc_final: 0.8057 (m-30) REVERT: C 684 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8344 (ttp-110) REVERT: C 808 LEU cc_start: 0.8390 (mp) cc_final: 0.8044 (tt) REVERT: C 880 MET cc_start: 0.7125 (ppp) cc_final: 0.6798 (ppp) REVERT: C 897 ARG cc_start: 0.7101 (ttt90) cc_final: 0.6542 (ttt180) REVERT: D 684 ARG cc_start: 0.8357 (tpp80) cc_final: 0.8126 (tpp80) outliers start: 28 outliers final: 20 residues processed: 210 average time/residue: 0.1253 time to fit residues: 41.2216 Evaluate side-chains 209 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 131 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 12 optimal weight: 0.0010 chunk 151 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 88 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.093744 restraints weight = 24625.209| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.51 r_work: 0.2893 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17108 Z= 0.110 Angle : 0.456 9.105 22974 Z= 0.235 Chirality : 0.040 0.201 2490 Planarity : 0.003 0.034 2772 Dihedral : 12.475 157.132 2654 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.62 % Allowed : 11.86 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 1.21 (0.19), residues: 2022 helix: 2.41 (0.16), residues: 1094 sheet: 0.01 (0.35), residues: 226 loop : -1.64 (0.20), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 628 TYR 0.012 0.001 TYR C1032 PHE 0.027 0.001 PHE A 814 TRP 0.006 0.001 TRP B 766 HIS 0.008 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17102) covalent geometry : angle 0.45574 / 0.24 (22962) SS BOND : bond 0.00210 / 0.10 ( 6) SS BOND : angle 0.24689 / 0.14 ( 12) hydrogen bonds : bond 0.04609 / 3.01 ( 749) hydrogen bonds : angle 3.34148 / 2.44 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 634 GLU cc_start: 0.8340 (pm20) cc_final: 0.7968 (pm20) REVERT: A 813 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6444 (mm-30) REVERT: B 678 GLU cc_start: 0.7696 (tp30) cc_final: 0.7399 (mp0) REVERT: B 684 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8213 (tpp80) REVERT: B 805 LEU cc_start: 0.9050 (tt) cc_final: 0.8699 (tp) REVERT: C 585 MET cc_start: 0.9287 (mmt) cc_final: 0.9073 (mmt) REVERT: C 591 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8177 (pp) REVERT: C 634 GLU cc_start: 0.8386 (pm20) cc_final: 0.7949 (pm20) REVERT: C 638 ASP cc_start: 0.8483 (m-30) cc_final: 0.8060 (m-30) REVERT: C 684 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8369 (ttp-110) REVERT: C 808 LEU cc_start: 0.8357 (mp) cc_final: 0.8027 (tt) REVERT: C 880 MET cc_start: 0.7155 (ppp) cc_final: 0.6820 (ppp) REVERT: C 897 ARG cc_start: 0.7111 (ttt90) cc_final: 0.6563 (ttt180) REVERT: D 684 ARG cc_start: 0.8376 (tpp80) cc_final: 0.8152 (tpp80) REVERT: D 805 LEU cc_start: 0.9129 (tt) cc_final: 0.8891 (tp) outliers start: 28 outliers final: 24 residues processed: 209 average time/residue: 0.1125 time to fit residues: 36.7620 Evaluate side-chains 211 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 181 optimal weight: 0.0770 chunk 166 optimal weight: 0.3980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093110 restraints weight = 24691.849| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.51 r_work: 0.2882 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17108 Z= 0.119 Angle : 0.461 8.001 22974 Z= 0.240 Chirality : 0.040 0.182 2490 Planarity : 0.003 0.034 2772 Dihedral : 12.342 154.538 2654 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.62 % Allowed : 11.86 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 1.20 (0.19), residues: 2022 helix: 2.40 (0.16), residues: 1096 sheet: -0.01 (0.35), residues: 226 loop : -1.66 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 628 TYR 0.012 0.001 TYR C1032 PHE 0.027 0.001 PHE A 814 TRP 0.006 0.001 TRP B 766 HIS 0.009 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17102) covalent geometry : angle 0.46074 / 0.24 (22962) SS BOND : bond 0.00235 / 0.11 ( 6) SS BOND : angle 0.27878 / 0.17 ( 12) hydrogen bonds : bond 0.04837 / 3.16 ( 749) hydrogen bonds : angle 3.35956 / 2.45 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.629 Fit side-chains REVERT: A 591 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8075 (pp) REVERT: A 634 GLU cc_start: 0.8354 (pm20) cc_final: 0.8049 (pm20) REVERT: A 813 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6404 (mm-30) REVERT: B 678 GLU cc_start: 0.7728 (tp30) cc_final: 0.7424 (mp0) REVERT: B 684 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8226 (tpp80) REVERT: B 805 LEU cc_start: 0.9068 (tt) cc_final: 0.8705 (tp) REVERT: C 585 MET cc_start: 0.9305 (mmt) cc_final: 0.9076 (mmt) REVERT: C 591 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8152 (pp) REVERT: C 634 GLU cc_start: 0.8395 (pm20) cc_final: 0.7966 (pm20) REVERT: C 638 ASP cc_start: 0.8493 (m-30) cc_final: 0.8098 (m-30) REVERT: C 684 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8381 (ttp-110) REVERT: C 808 LEU cc_start: 0.8350 (mp) cc_final: 0.8024 (tt) REVERT: C 880 MET cc_start: 0.7156 (ppp) cc_final: 0.6819 (ppp) REVERT: C 897 ARG cc_start: 0.7119 (ttt90) cc_final: 0.6565 (ttt180) REVERT: C 940 PHE cc_start: 0.8584 (t80) cc_final: 0.8355 (t80) REVERT: D 684 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8179 (tpp80) REVERT: D 805 LEU cc_start: 0.9112 (tt) cc_final: 0.8811 (tp) outliers start: 28 outliers final: 22 residues processed: 205 average time/residue: 0.1251 time to fit residues: 40.0523 Evaluate side-chains 208 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 969 SER Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 164 optimal weight: 0.0010 chunk 155 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093757 restraints weight = 24448.599| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.60 r_work: 0.2854 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17108 Z= 0.110 Angle : 0.463 8.564 22974 Z= 0.239 Chirality : 0.040 0.295 2490 Planarity : 0.003 0.034 2772 Dihedral : 12.125 151.112 2654 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.62 % Allowed : 12.15 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 1.28 (0.19), residues: 2022 helix: 2.49 (0.16), residues: 1094 sheet: -0.02 (0.35), residues: 226 loop : -1.62 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 628 TYR 0.012 0.001 TYR C1032 PHE 0.026 0.001 PHE A 814 TRP 0.006 0.001 TRP A1005 HIS 0.005 0.001 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17102) covalent geometry : angle 0.46330 / 0.24 (22962) SS BOND : bond 0.00208 / 0.10 ( 6) SS BOND : angle 0.23987 / 0.14 ( 12) hydrogen bonds : bond 0.04603 / 3.01 ( 749) hydrogen bonds : angle 3.33165 / 2.44 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.10 seconds wall clock time: 61 minutes 51.74 seconds (3711.74 seconds total)