Starting phenix.real_space_refine on Thu Sep 18 13:53:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz5_24751/09_2025/7rz5_24751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz5_24751/09_2025/7rz5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rz5_24751/09_2025/7rz5_24751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz5_24751/09_2025/7rz5_24751.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz5_24751/09_2025/7rz5_24751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz5_24751/09_2025/7rz5_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 179 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: 105 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: 142 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: 142 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: 3.13, per 1000 atoms: 0.19 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: 1.43 Conformation dependent library (CDL) restraints added in 646.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.60 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: 2.31 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: 10002 34.87 - 69.73: 245 69.73 - 104.60: 27 104.60 - 139.46: 8 139.46 - 174.33: 6 Dihedral angle restraints: 10288 sinusoidal: 4416 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 10285 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: 2.960 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.350 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 15.371 174.325 6526 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 aren 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 covalent geometry : bond 0.01025 (17102) covalent geometry : angle 1.19288 (22962) SS BOND : bond 0.00450 ( 6) SS BOND : angle 0.51745 ( 12) hydrogen bonds : bond 0.35376 ( 749) hydrogen bonds : angle 9.21013 ( 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 : 0.532 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: 0.8505 (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: 0.7653 (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: 0.1364 time to fit residues: 71.4644 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 : 0.434 ------------------------------------------------------------------------------- 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: 0.7980 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3597 r_free = 0.3597 target = 0.134375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.094180 restraints weight = 24134.546| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.98 r_work: 0.2863 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17108 Z= 0.138 Angle : 0.551 9.034 22974 Z= 0.289 Chirality : 0.041 0.157 2490 Planarity : 0.005 0.058 2772 Dihedral : 16.374 169.064 2832 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.62 % Allowed : 7.81 % Favored : 90.57 % 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 aren not related in a simple way. whole: -2.26 (0.15), residues: 2022 helix: -1.22 (0.13), residues: 1048 sheet: -0.16 (0.36), residues: 210 loop : -2.14 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.019 0.001 TYR C1032 PHE 0.018 0.002 PHE C1028 TRP 0.015 0.001 TRP C 766 HIS 0.008 0.002 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00301 (17102) covalent geometry : angle 0.55076 (22962) SS BOND : bond 0.00335 ( 6) SS BOND : angle 0.40137 ( 12) hydrogen bonds : bond 0.06572 ( 749) hydrogen bonds : angle 4.14213 ( 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 264 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.639 Fit side-chains REVERT: A 594 ARG cc_start: 0.8060 (ptp-110) cc_final: 0.7667 (ttp-110) REVERT: A 634 GLU cc_start: 0.8404 (pm20) cc_final: 0.8043 (pm20) REVERT: A 643 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 812 ILE cc_start: 0.7187 (pt) cc_final: 0.6978 (mt) REVERT: A 813 GLU cc_start: 0.6344 (mm-30) cc_final: 0.6139 (mm-30) REVERT: B 414 MET cc_start: 0.7911 (mmm) cc_final: 0.7671 (mmm) REVERT: B 515 PHE cc_start: 0.8671 (m-10) cc_final: 0.8351 (m-10) REVERT: B 805 LEU cc_start: 0.8770 (tt) cc_final: 0.8441 (tp) REVERT: C 581 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8994 (tp) REVERT: C 591 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7707 (pp) REVERT: C 643 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7981 (t) REVERT: C 684 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8478 (ttp-110) REVERT: C 811 LEU cc_start: 0.8041 (tt) cc_final: 0.7795 (mp) REVERT: C 813 GLU cc_start: 0.5104 (mm-30) cc_final: 0.4745 (tp30) REVERT: C 897 ARG cc_start: 0.7028 (ttt90) cc_final: 0.6715 (ttt-90) REVERT: C 933 LEU cc_start: 0.8262 (mt) cc_final: 0.8059 (mm) REVERT: C 955 ARG cc_start: 0.5755 (ttp80) cc_final: 0.4719 (ptp-110) REVERT: C 966 PHE cc_start: 0.8332 (m-10) cc_final: 0.8049 (m-10) REVERT: D 719 ASP cc_start: 0.7382 (t0) cc_final: 0.7084 (t0) outliers start: 28 outliers final: 10 residues processed: 254 average time/residue: 0.1322 time to fit residues: 49.9673 Evaluate side-chains 195 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 919 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 581 LEU 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: 0.0370 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094176 restraints weight = 24799.549| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.67 r_work: 0.2864 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3168 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= 0.127 Angle : 0.492 7.651 22974 Z= 0.257 Chirality : 0.040 0.160 2490 Planarity : 0.004 0.043 2772 Dihedral : 15.423 174.508 2830 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.56 % Allowed : 9.61 % Favored : 88.83 % 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 aren not related in a simple way. whole: -0.55 (0.18), residues: 2022 helix: 0.61 (0.16), residues: 1064 sheet: -0.00 (0.35), residues: 226 loop : -1.94 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 661 TYR 0.025 0.001 TYR C1032 PHE 0.016 0.001 PHE C 999 TRP 0.009 0.001 TRP A 460 HIS 0.007 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00284 (17102) covalent geometry : angle 0.49236 (22962) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.32371 ( 12) hydrogen bonds : bond 0.05720 ( 749) hydrogen bonds : angle 3.59873 ( 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 235 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.681 Fit side-chains REVERT: A 549 TYR cc_start: 0.5905 (m-10) cc_final: 0.5563 (m-80) REVERT: A 594 ARG cc_start: 0.8100 (ptp-110) cc_final: 0.7876 (mtp85) REVERT: A 634 GLU cc_start: 0.8405 (pm20) cc_final: 0.8053 (pm20) REVERT: A 684 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.8081 (mtp180) REVERT: B 515 PHE cc_start: 0.8809 (m-10) cc_final: 0.8555 (m-10) REVERT: B 805 LEU cc_start: 0.9031 (tt) cc_final: 0.8691 (tp) REVERT: C 581 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9054 (tp) REVERT: C 591 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7848 (pp) REVERT: C 634 GLU cc_start: 0.8410 (pm20) cc_final: 0.8044 (pm20) REVERT: C 684 ARG cc_start: 0.8667 (mtm180) cc_final: 0.8439 (ttp-110) REVERT: C 880 MET cc_start: 0.7032 (ppp) cc_final: 0.6794 (ppp) REVERT: C 897 ARG cc_start: 0.7183 (ttt90) cc_final: 0.6846 (ttt-90) REVERT: C 1012 ILE cc_start: 0.8263 (mt) cc_final: 0.7953 (mp) REVERT: D 814 PHE cc_start: 0.7769 (t80) cc_final: 0.7471 (t80) outliers start: 27 outliers final: 16 residues processed: 223 average time/residue: 0.1320 time to fit residues: 45.3288 Evaluate side-chains 206 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 1016 LEU Chi-restraints excluded: chain B residue 518 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 543 VAL Chi-restraints excluded: chain C residue 581 LEU 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 972 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS C 412 HIS C 874 GLN D 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.090173 restraints weight = 24837.497| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.53 r_work: 0.2840 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17108 Z= 0.181 Angle : 0.536 7.874 22974 Z= 0.279 Chirality : 0.043 0.162 2490 Planarity : 0.004 0.037 2772 Dihedral : 15.319 175.340 2830 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.14 % Allowed : 10.24 % Favored : 87.62 % 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 aren not related in a simple way. whole: -0.14 (0.18), residues: 2022 helix: 1.19 (0.16), residues: 1064 sheet: -0.47 (0.34), residues: 232 loop : -1.92 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.019 0.002 TYR C1032 PHE 0.014 0.002 PHE C 999 TRP 0.010 0.001 TRP C 460 HIS 0.008 0.002 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00438 (17102) covalent geometry : angle 0.53628 (22962) SS BOND : bond 0.00424 ( 6) SS BOND : angle 0.46284 ( 12) hydrogen bonds : bond 0.06363 ( 749) hydrogen bonds : angle 3.71219 ( 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 236 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.620 Fit side-chains REVERT: A 549 TYR cc_start: 0.5992 (m-10) cc_final: 0.5628 (m-80) REVERT: A 591 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8087 (pp) REVERT: A 634 GLU cc_start: 0.8342 (pm20) cc_final: 0.8108 (pm20) REVERT: B 678 GLU cc_start: 0.7805 (tp30) cc_final: 0.7594 (tp30) REVERT: B 805 LEU cc_start: 0.9103 (tt) cc_final: 0.8754 (tp) REVERT: C 581 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9094 (tp) REVERT: C 585 MET cc_start: 0.9322 (mmt) cc_final: 0.9107 (mmt) REVERT: C 591 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7959 (pp) REVERT: C 634 GLU cc_start: 0.8378 (pm20) cc_final: 0.7999 (pm20) REVERT: C 684 ARG cc_start: 0.8599 (mtm180) cc_final: 0.8369 (ttp-110) REVERT: C 811 LEU cc_start: 0.8132 (tt) cc_final: 0.7689 (mp) REVERT: C 880 MET cc_start: 0.7024 (ppp) cc_final: 0.6747 (ppp) REVERT: C 897 ARG cc_start: 0.7190 (ttt90) cc_final: 0.6669 (ttt180) REVERT: C 940 PHE cc_start: 0.8418 (t80) cc_final: 0.8213 (t80) REVERT: D 814 PHE cc_start: 0.7831 (t80) cc_final: 0.7609 (t80) outliers start: 37 outliers final: 26 residues processed: 225 average time/residue: 0.1268 time to fit residues: 44.1885 Evaluate side-chains 211 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 849 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 919 VAL 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 633 ILE 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 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 630 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 1023 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 196 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 67 optimal weight: 0.0670 chunk 164 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 overall best weight: 0.7528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS C 954 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091803 restraints weight = 24631.984| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.51 r_work: 0.2856 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17108 Z= 0.133 Angle : 0.485 8.973 22974 Z= 0.251 Chirality : 0.041 0.270 2490 Planarity : 0.003 0.034 2772 Dihedral : 14.877 179.745 2830 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 10.53 % Favored : 87.21 % 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 aren not related in a simple way. whole: 0.35 (0.19), residues: 2022 helix: 1.61 (0.16), residues: 1076 sheet: -0.04 (0.35), residues: 230 loop : -1.89 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 692 TYR 0.016 0.001 TYR C1032 PHE 0.014 0.001 PHE C 999 TRP 0.007 0.001 TRP A 460 HIS 0.007 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00312 (17102) covalent geometry : angle 0.48509 (22962) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.30820 ( 12) hydrogen bonds : bond 0.05360 ( 749) hydrogen bonds : angle 3.50405 ( 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 231 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.699 Fit side-chains REVERT: A 549 TYR cc_start: 0.5882 (m-10) cc_final: 0.5541 (m-80) REVERT: A 591 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8028 (pp) REVERT: A 634 GLU cc_start: 0.8318 (pm20) cc_final: 0.8056 (pm20) REVERT: B 678 GLU cc_start: 0.7841 (tp30) cc_final: 0.7303 (mm-30) REVERT: B 805 LEU cc_start: 0.9083 (tt) cc_final: 0.8724 (tp) REVERT: C 591 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8020 (pp) REVERT: C 634 GLU cc_start: 0.8378 (pm20) cc_final: 0.8082 (pm20) REVERT: C 684 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8346 (ttp-110) REVERT: C 880 MET cc_start: 0.7056 (ppp) cc_final: 0.6766 (ppp) REVERT: C 897 ARG cc_start: 0.7129 (ttt90) cc_final: 0.6568 (ttt180) outliers start: 39 outliers final: 30 residues processed: 218 average time/residue: 0.1288 time to fit residues: 43.5904 Evaluate side-chains 217 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 849 LEU Chi-restraints excluded: chain A residue 919 VAL 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 B residue 812 ILE 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 629 MET 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 C residue 1023 MET Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 633 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 139 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.089844 restraints weight = 24587.934| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.51 r_work: 0.2833 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17108 Z= 0.176 Angle : 0.522 8.009 22974 Z= 0.271 Chirality : 0.042 0.183 2490 Planarity : 0.004 0.034 2772 Dihedral : 14.971 178.557 2830 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.43 % Allowed : 10.59 % Favored : 86.98 % 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 aren not related in a simple way. whole: 0.43 (0.19), residues: 2022 helix: 1.63 (0.16), residues: 1092 sheet: 0.07 (0.35), residues: 230 loop : -1.90 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 628 TYR 0.016 0.001 TYR C1032 PHE 0.028 0.002 PHE A 814 TRP 0.009 0.001 TRP A 460 HIS 0.007 0.002 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00427 (17102) covalent geometry : angle 0.52234 (22962) SS BOND : bond 0.00401 ( 6) SS BOND : angle 0.45333 ( 12) hydrogen bonds : bond 0.06104 ( 749) hydrogen bonds : angle 3.63876 ( 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 229 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.718 Fit side-chains REVERT: A 549 TYR cc_start: 0.5685 (m-10) cc_final: 0.5429 (m-80) REVERT: A 591 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8105 (pp) REVERT: A 634 GLU cc_start: 0.8316 (pm20) cc_final: 0.8054 (pm20) REVERT: A 897 ARG cc_start: 0.7158 (ttt90) cc_final: 0.6561 (ttt-90) REVERT: B 684 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8284 (tpp80) REVERT: B 805 LEU cc_start: 0.9109 (tt) cc_final: 0.8745 (tp) REVERT: C 591 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8092 (pp) REVERT: C 634 GLU cc_start: 0.8345 (pm20) cc_final: 0.8050 (pm20) REVERT: C 684 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8370 (ttp-110) REVERT: C 880 MET cc_start: 0.7055 (ppp) cc_final: 0.6746 (ppp) REVERT: C 897 ARG cc_start: 0.7135 (ttt90) cc_final: 0.6638 (ttt-90) REVERT: C 940 PHE cc_start: 0.8704 (t80) cc_final: 0.8192 (t80) REVERT: D 684 ARG cc_start: 0.8440 (tpp80) cc_final: 0.8213 (tpp80) outliers start: 42 outliers final: 36 residues processed: 217 average time/residue: 0.1356 time to fit residues: 44.9136 Evaluate side-chains 221 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 857 SER Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 979 LEU 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 B residue 812 ILE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 630 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 C residue 1013 SER Chi-restraints excluded: chain C residue 1023 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 186 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.091467 restraints weight = 24596.615| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.51 r_work: 0.2853 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17108 Z= 0.134 Angle : 0.486 8.732 22974 Z= 0.250 Chirality : 0.041 0.176 2490 Planarity : 0.003 0.034 2772 Dihedral : 14.647 179.722 2830 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.20 % Allowed : 11.00 % Favored : 86.81 % 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 aren not related in a simple way. whole: 0.69 (0.19), residues: 2022 helix: 1.92 (0.16), residues: 1090 sheet: 0.04 (0.36), residues: 220 loop : -1.81 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 628 TYR 0.014 0.001 TYR C1032 PHE 0.027 0.001 PHE A 814 TRP 0.007 0.001 TRP B 766 HIS 0.008 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00316 (17102) covalent geometry : angle 0.48630 (22962) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.30824 ( 12) hydrogen bonds : bond 0.05308 ( 749) hydrogen bonds : angle 3.47881 ( 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 230 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.696 Fit side-chains REVERT: A 549 TYR cc_start: 0.5568 (m-10) cc_final: 0.5351 (m-80) REVERT: A 591 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8106 (pp) REVERT: A 634 GLU cc_start: 0.8305 (pm20) cc_final: 0.8029 (pm20) REVERT: A 897 ARG cc_start: 0.7181 (ttt90) cc_final: 0.6586 (ttt-90) REVERT: B 684 ARG cc_start: 0.8603 (tpp80) cc_final: 0.8272 (tpp80) REVERT: B 805 LEU cc_start: 0.9059 (tt) cc_final: 0.8687 (tp) REVERT: C 591 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8133 (pp) REVERT: C 634 GLU cc_start: 0.8369 (pm20) cc_final: 0.8032 (pm20) REVERT: C 638 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: C 684 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8379 (ttp-110) REVERT: C 880 MET cc_start: 0.7023 (ppp) cc_final: 0.6707 (ppp) REVERT: C 897 ARG cc_start: 0.7138 (ttt90) cc_final: 0.6617 (ttt-90) REVERT: D 684 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8232 (tpp80) outliers start: 38 outliers final: 31 residues processed: 219 average time/residue: 0.1295 time to fit residues: 44.0522 Evaluate side-chains 220 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 857 SER Chi-restraints excluded: chain A residue 919 VAL 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 629 MET Chi-restraints excluded: chain C residue 630 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 C residue 1013 SER Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 633 ILE 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: 0.6980 chunk 78 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 186 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 12 optimal weight: 0.0470 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092694 restraints weight = 24730.817| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.52 r_work: 0.2872 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.003 0.030 17108 Z= 0.113 Angle : 0.471 8.071 22974 Z= 0.241 Chirality : 0.041 0.278 2490 Planarity : 0.003 0.034 2772 Dihedral : 14.319 179.912 2830 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 11.63 % Favored : 86.34 % 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 aren not related in a simple way. whole: 0.95 (0.19), residues: 2022 helix: 2.15 (0.16), residues: 1086 sheet: 0.02 (0.35), residues: 236 loop : -1.71 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.013 0.001 TYR C1032 PHE 0.028 0.001 PHE A 814 TRP 0.007 0.001 TRP A1005 HIS 0.006 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00257 (17102) covalent geometry : angle 0.47072 (22962) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.26182 ( 12) hydrogen bonds : bond 0.04824 ( 749) hydrogen bonds : angle 3.39808 ( 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 228 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 549 TYR cc_start: 0.5589 (m-10) cc_final: 0.5372 (m-80) REVERT: A 591 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8090 (pp) REVERT: A 634 GLU cc_start: 0.8327 (pm20) cc_final: 0.8027 (pm20) REVERT: A 897 ARG cc_start: 0.7177 (ttt90) cc_final: 0.6576 (ttt-90) REVERT: B 684 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8260 (tpp80) REVERT: B 805 LEU cc_start: 0.9057 (tt) cc_final: 0.8696 (tp) REVERT: B 812 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6975 (mp) REVERT: C 591 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8143 (pp) REVERT: C 634 GLU cc_start: 0.8345 (pm20) cc_final: 0.7967 (pm20) REVERT: C 638 ASP cc_start: 0.8508 (m-30) cc_final: 0.8106 (m-30) REVERT: C 684 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8420 (ttp-110) REVERT: C 808 LEU cc_start: 0.8453 (mp) cc_final: 0.7971 (tt) REVERT: C 880 MET cc_start: 0.7024 (ppp) cc_final: 0.6700 (ppp) REVERT: C 897 ARG cc_start: 0.7141 (ttt90) cc_final: 0.6576 (ttt180) REVERT: D 684 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8186 (tpp80) outliers start: 35 outliers final: 26 residues processed: 218 average time/residue: 0.1277 time to fit residues: 43.2107 Evaluate side-chains 215 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 857 SER Chi-restraints excluded: chain A residue 919 VAL 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 B residue 812 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 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 979 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 633 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 131 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 chunk 146 optimal weight: 6.9990 chunk 88 optimal weight: 0.0010 chunk 191 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.094568 restraints weight = 24635.620| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.70 r_work: 0.2888 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4043 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= 0.112 Angle : 0.474 8.438 22974 Z= 0.241 Chirality : 0.041 0.279 2490 Planarity : 0.003 0.034 2772 Dihedral : 14.011 178.040 2830 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.97 % Allowed : 11.86 % Favored : 86.17 % 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 aren not related in a simple way. whole: 1.09 (0.19), residues: 2022 helix: 2.29 (0.16), residues: 1086 sheet: 0.04 (0.35), residues: 236 loop : -1.66 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 628 TYR 0.013 0.001 TYR C1032 PHE 0.029 0.001 PHE A 814 TRP 0.007 0.001 TRP B 766 HIS 0.005 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00256 (17102) covalent geometry : angle 0.47391 (22962) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.26179 ( 12) hydrogen bonds : bond 0.04712 ( 749) hydrogen bonds : angle 3.38736 ( 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 223 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (pp) REVERT: A 634 GLU cc_start: 0.8521 (pm20) cc_final: 0.8219 (pm20) REVERT: A 897 ARG cc_start: 0.7166 (ttt90) cc_final: 0.6516 (ttt180) REVERT: B 684 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8426 (tpp80) REVERT: B 805 LEU cc_start: 0.9075 (tt) cc_final: 0.8727 (tp) REVERT: B 812 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7070 (mp) REVERT: C 591 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8116 (pp) REVERT: C 634 GLU cc_start: 0.8547 (pm20) cc_final: 0.8164 (pm20) REVERT: C 638 ASP cc_start: 0.8628 (m-30) cc_final: 0.8260 (m-30) REVERT: C 684 ARG cc_start: 0.8805 (mtm180) cc_final: 0.8565 (ttp-110) REVERT: C 808 LEU cc_start: 0.8497 (mp) cc_final: 0.8019 (tt) REVERT: C 880 MET cc_start: 0.6989 (ppp) cc_final: 0.6601 (ppp) REVERT: C 897 ARG cc_start: 0.7132 (ttt90) cc_final: 0.6544 (ttt180) REVERT: D 684 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8419 (tpp80) REVERT: D 812 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7058 (mp) outliers start: 34 outliers final: 27 residues processed: 214 average time/residue: 0.1270 time to fit residues: 41.9859 Evaluate side-chains 217 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 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 B residue 812 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 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 C residue 1013 SER Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 633 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 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: 1.9990 chunk 193 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.091619 restraints weight = 24737.796| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.71 r_work: 0.2832 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17108 Z= 0.170 Angle : 0.529 8.757 22974 Z= 0.272 Chirality : 0.043 0.273 2490 Planarity : 0.003 0.033 2772 Dihedral : 14.282 176.850 2830 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.08 % Allowed : 11.75 % Favored : 86.17 % 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 aren not related in a simple way. whole: 0.83 (0.19), residues: 2022 helix: 2.06 (0.16), residues: 1092 sheet: -0.13 (0.34), residues: 240 loop : -1.76 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 628 TYR 0.013 0.001 TYR C1032 PHE 0.028 0.002 PHE A 814 TRP 0.008 0.001 TRP A 460 HIS 0.005 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00414 (17102) covalent geometry : angle 0.52882 (22962) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.43673 ( 12) hydrogen bonds : bond 0.05886 ( 749) hydrogen bonds : angle 3.63488 ( 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 223 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8077 (pp) REVERT: A 634 GLU cc_start: 0.8304 (pm20) cc_final: 0.8020 (pm20) REVERT: A 897 ARG cc_start: 0.7214 (ttt90) cc_final: 0.6581 (ttt-90) REVERT: B 684 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8296 (tpp80) REVERT: B 805 LEU cc_start: 0.9088 (tt) cc_final: 0.8732 (tp) REVERT: C 591 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8132 (pp) REVERT: C 634 GLU cc_start: 0.8325 (pm20) cc_final: 0.7988 (pm20) REVERT: C 638 ASP cc_start: 0.8579 (m-30) cc_final: 0.8294 (m-30) REVERT: C 684 ARG cc_start: 0.8596 (mtm180) cc_final: 0.8378 (ttp-110) REVERT: C 897 ARG cc_start: 0.7178 (ttt90) cc_final: 0.6591 (ttt180) outliers start: 36 outliers final: 30 residues processed: 214 average time/residue: 0.1276 time to fit residues: 42.4778 Evaluate side-chains 218 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 857 SER Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 979 LEU 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 B residue 812 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 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 979 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 633 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 194 optimal weight: 0.0980 chunk 134 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 164 optimal weight: 0.1980 chunk 155 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096172 restraints weight = 24655.771| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.73 r_work: 0.2908 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17108 Z= 0.097 Angle : 0.463 9.077 22974 Z= 0.235 Chirality : 0.040 0.286 2490 Planarity : 0.003 0.034 2772 Dihedral : 13.618 178.375 2830 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.45 % Allowed : 12.56 % Favored : 86.00 % 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 aren not related in a simple way. whole: 1.24 (0.19), residues: 2022 helix: 2.46 (0.16), residues: 1086 sheet: 0.00 (0.35), residues: 226 loop : -1.62 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.011 0.001 TYR C1032 PHE 0.028 0.001 PHE A 814 TRP 0.009 0.001 TRP A1005 HIS 0.006 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00209 (17102) covalent geometry : angle 0.46286 (22962) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.29809 ( 12) hydrogen bonds : bond 0.04114 ( 749) hydrogen bonds : angle 3.32398 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3948.22 seconds wall clock time: 68 minutes 21.80 seconds (4101.80 seconds total)