Starting phenix.real_space_refine on Sat Jul 4 10:30:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ss7_40746/07_2026/8ss7_40746.cif" } resolution = 2.76 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= 0.007 sd= 0.172 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 S 130 5.16 5 Na 1 4.78 5 C 12985 2.51 5 N 2903 2.21 5 O 3382 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 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19437 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "C" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4639 Classifications: {'peptide': 592} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 574} Chain breaks: 4 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3134 Classifications: {'peptide': 401} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 387} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 387 Unusual residues: {' NA': 1, '6ZP': 1, 'CLR': 2, 'PCW': 6, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 325 Unusual residues: {'6ZP': 1, 'CLR': 2, 'PCW': 5, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 376 Unusual residues: {'6ZP': 1, 'CLR': 2, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 325 Unusual residues: {'6ZP': 1, 'CLR': 2, 'PCW': 5, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.86, per 1000 atoms: 0.20 Number of scatterers: 19437 At special positions: 0 Unit cell: (115.625, 134.125, 137.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 130 16.00 P 24 15.00 Na 1 11.00 F 12 9.00 O 3382 8.00 N 2903 7.00 C 12985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS D 589 " distance=2.01 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 589 " - pdb=" SG CYS C 589 " distance=2.06 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: 1.76 Conformation dependent library (CDL) restraints added in 686.5 milliseconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 26 sheets defined 58.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.129A 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 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.591A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 4.092A pdb=" N PHE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 627 removed outlier: 3.706A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.531A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.633A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.769A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.605A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.861A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 816 " --> pdb=" O ILE A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.670A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 925 Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.829A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.133A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1033 removed outlier: 3.722A pdb=" N PHE A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.527A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.616A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 removed outlier: 3.513A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 817 removed outlier: 3.861A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.129A 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 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.591A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 removed outlier: 4.092A pdb=" N PHE C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 627 removed outlier: 3.705A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.530A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.633A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.769A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.605A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.862A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 816 " --> pdb=" O ILE C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.670A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 843 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.829A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 988 removed outlier: 4.132A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1033 removed outlier: 3.723A pdb=" N PHE C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C1017 " --> pdb=" O SER C1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.526A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.615A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 675 removed outlier: 3.514A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 817 removed outlier: 3.860A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.806A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.570A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 85 removed outlier: 3.824A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 107 Proline residue: E 96 - end of helix removed outlier: 3.540A pdb=" N TYR E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG E 104 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR E 105 " --> pdb=" O HIS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 159 removed outlier: 3.528A pdb=" N TYR E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 removed outlier: 3.806A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.570A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 85 removed outlier: 3.824A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Proline residue: F 96 - end of helix removed outlier: 3.540A pdb=" N TYR F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 104 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 159 removed outlier: 3.528A pdb=" N TYR F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 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 452 through 454 removed outlier: 3.620A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 459 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.620A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 480 removed outlier: 7.620A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.492A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AA8, first strand: chain 'A' and resid 868 through 869 Processing sheet with id=AA9, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.352A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.335A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.335A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.628A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.619A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.620A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.620A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.492A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 882 through 884 Processing sheet with id=AC3, first strand: chain 'C' and resid 868 through 869 Processing sheet with id=AC4, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.352A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.335A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.335A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.628A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2844 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: 3.23 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.18: 29 1.18 - 1.35: 5515 1.35 - 1.52: 10035 1.52 - 1.70: 4058 1.70 - 1.87: 230 Bond restraints: 19867 Sorted by residual: bond pdb=" C4 CLR D1109 " pdb=" C5 CLR D1109 " ideal model delta sigma weight residual 1.506 1.005 0.501 2.00e-02 2.50e+03 6.27e+02 bond pdb=" C4 CLR D1108 " pdb=" C5 CLR D1108 " ideal model delta sigma weight residual 1.506 1.006 0.500 2.00e-02 2.50e+03 6.24e+02 bond pdb=" C4 CLR A1107 " pdb=" C5 CLR A1107 " ideal model delta sigma weight residual 1.506 1.007 0.499 2.00e-02 2.50e+03 6.24e+02 bond pdb=" C4 CLR C1107 " pdb=" C5 CLR C1107 " ideal model delta sigma weight residual 1.506 1.007 0.499 2.00e-02 2.50e+03 6.23e+02 bond pdb=" C4 CLR B1108 " pdb=" C5 CLR B1108 " ideal model delta sigma weight residual 1.506 1.007 0.499 2.00e-02 2.50e+03 6.22e+02 ... (remaining 19862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.66: 26209 5.66 - 11.32: 415 11.32 - 16.99: 60 16.99 - 22.65: 4 22.65 - 28.31: 2 Bond angle restraints: 26690 Sorted by residual: angle pdb=" C12 CLR D1108 " pdb=" C13 CLR D1108 " pdb=" C18 CLR D1108 " ideal model delta sigma weight residual 111.01 82.70 28.31 3.00e+00 1.11e-01 8.90e+01 angle pdb=" C12 CLR B1107 " pdb=" C13 CLR B1107 " pdb=" C18 CLR B1107 " ideal model delta sigma weight residual 111.01 82.82 28.19 3.00e+00 1.11e-01 8.83e+01 angle pdb=" C17 CLR D1108 " pdb=" C20 CLR D1108 " pdb=" C22 CLR D1108 " ideal model delta sigma weight residual 109.45 129.76 -20.31 3.00e+00 1.11e-01 4.58e+01 angle pdb=" C17 CLR B1107 " pdb=" C20 CLR B1107 " pdb=" C22 CLR B1107 " ideal model delta sigma weight residual 109.45 129.37 -19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" C VAL F 115 " pdb=" N MET F 116 " pdb=" CA MET F 116 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.34e+01 ... (remaining 26685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 11173 35.85 - 71.71: 345 71.71 - 107.56: 23 107.56 - 143.41: 19 143.41 - 179.26: 7 Dihedral angle restraints: 11567 sinusoidal: 5027 harmonic: 6540 Sorted by residual: dihedral pdb=" CA MET E 123 " pdb=" C MET E 123 " pdb=" N ASN E 124 " pdb=" CA ASN E 124 " ideal model delta harmonic sigma weight residual -180.00 -123.95 -56.05 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA MET F 123 " pdb=" C MET F 123 " pdb=" N ASN F 124 " pdb=" CA ASN F 124 " ideal model delta harmonic sigma weight residual 180.00 -123.97 -56.03 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ALA F 110 " pdb=" C ALA F 110 " pdb=" N ASP F 111 " pdb=" CA ASP F 111 " ideal model delta harmonic sigma weight residual -180.00 -128.80 -51.20 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 11564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.130: 2850 1.130 - 2.259: 0 2.259 - 3.389: 2 3.389 - 4.519: 7 4.519 - 5.649: 7 Chirality restraints: 2866 Sorted by residual: chirality pdb=" C13 CLR B1108 " pdb=" C12 CLR B1108 " pdb=" C14 CLR B1108 " pdb=" C17 CLR B1108 " both_signs ideal model delta sigma weight residual False -2.93 2.72 -5.65 2.00e-01 2.50e+01 7.98e+02 chirality pdb=" C13 CLR D1109 " pdb=" C12 CLR D1109 " pdb=" C14 CLR D1109 " pdb=" C17 CLR D1109 " both_signs ideal model delta sigma weight residual False -2.93 2.71 -5.64 2.00e-01 2.50e+01 7.96e+02 chirality pdb=" C13 CLR A1107 " pdb=" C12 CLR A1107 " pdb=" C14 CLR A1107 " pdb=" C17 CLR A1107 " both_signs ideal model delta sigma weight residual False -2.93 2.68 -5.61 2.00e-01 2.50e+01 7.88e+02 ... (remaining 2863 not shown) Planarity restraints: 3132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 123 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C MET E 123 " 0.068 2.00e-02 2.50e+03 pdb=" O MET E 123 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN E 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 123 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C MET F 123 " 0.068 2.00e-02 2.50e+03 pdb=" O MET F 123 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN F 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 6ZP C1101 " 0.032 2.00e-02 2.50e+03 2.48e-02 1.38e+01 pdb=" C03 6ZP C1101 " 0.025 2.00e-02 2.50e+03 pdb=" C04 6ZP C1101 " 0.019 2.00e-02 2.50e+03 pdb=" C05 6ZP C1101 " 0.000 2.00e-02 2.50e+03 pdb=" C06 6ZP C1101 " -0.020 2.00e-02 2.50e+03 pdb=" C07 6ZP C1101 " -0.019 2.00e-02 2.50e+03 pdb=" C08 6ZP C1101 " -0.003 2.00e-02 2.50e+03 pdb=" C09 6ZP C1101 " 0.016 2.00e-02 2.50e+03 pdb=" N01 6ZP C1101 " -0.050 2.00e-02 2.50e+03 ... (remaining 3129 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4618 2.78 - 3.31: 16179 3.31 - 3.84: 31710 3.84 - 4.37: 40177 4.37 - 4.90: 66839 Nonbonded interactions: 159523 Sorted by model distance: nonbonded pdb=" OH TYR C1026 " pdb=" O2P PCW C1105 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A1026 " pdb=" O2P PCW A1105 " model vdw 2.260 3.040 nonbonded pdb=" O PHE A 517 " pdb=" OH TYR A 616 " model vdw 2.275 3.040 nonbonded pdb=" O PHE C 517 " pdb=" OH TYR C 616 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.280 3.040 ... (remaining 159518 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 1110) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 392 through 817 or resid 1104 through 1106 or resid 1108)) \ selection = (chain 'D' and (resid 392 through 817 or resid 1104 through 1105 or (resid 1106 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23)) or resid 1108)) } ncs_group { reference = (chain 'E' and (resid 2 through 202 or (resid 203 and (name C13 or name C14 or n \ ame 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 'F' and (resid 2 through 159 or (resid 201 through 203 and (name C13 or n \ ame 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)))) } 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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.780 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.022 0.501 19875 Z= 1.088 Angle : 1.638 28.308 26706 Z= 0.737 Chirality : 0.362 5.649 2866 Planarity : 0.007 0.065 3132 Dihedral : 17.401 179.265 7363 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.66 % Favored : 93.80 % Rotamer: Outliers : 1.45 % Allowed : 4.15 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.13), residues: 2226 helix: -3.89 (0.08), residues: 1276 sheet: -2.24 (0.30), residues: 220 loop : -2.78 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 692 TYR 0.037 0.003 TYR B 702 PHE 0.032 0.003 PHE B 667 TRP 0.023 0.003 TRP C 861 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.02216 / 1.09 (19867) covalent geometry : angle 1.63792 / 0.74 (26690) SS BOND : bond 0.01197 / 0.63 ( 8) SS BOND : angle 2.02994 / 1.15 ( 16) hydrogen bonds : bond 0.28082 / 18.79 ( 972) hydrogen bonds : angle 10.16249 / 7.02 ( 2844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 355 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 860 TYR cc_start: 0.6636 (m-80) cc_final: 0.6153 (m-80) REVERT: A 907 MET cc_start: 0.3329 (mmt) cc_final: 0.2763 (mmt) REVERT: A 924 MET cc_start: 0.5201 (mmp) cc_final: 0.4970 (ttt) REVERT: A 926 ARG cc_start: 0.6932 (ttt-90) cc_final: 0.5915 (tpt170) REVERT: A 1002 LYS cc_start: 0.6979 (mtpm) cc_final: 0.6732 (tttp) REVERT: A 1005 TRP cc_start: 0.7451 (p-90) cc_final: 0.7222 (p-90) REVERT: B 435 HIS cc_start: 0.7919 (m-70) cc_final: 0.7682 (m-70) REVERT: B 635 SER cc_start: 0.8156 (t) cc_final: 0.7641 (p) REVERT: B 638 ASP cc_start: 0.7010 (m-30) cc_final: 0.6691 (m-30) REVERT: B 657 GLU cc_start: 0.7158 (tp30) cc_final: 0.6931 (tt0) REVERT: B 697 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7598 (ptmm) REVERT: C 860 TYR cc_start: 0.6576 (m-80) cc_final: 0.6355 (m-80) REVERT: C 864 LEU cc_start: 0.7030 (tt) cc_final: 0.6769 (tt) REVERT: C 880 MET cc_start: 0.5136 (tpt) cc_final: 0.4357 (tmt) REVERT: C 907 MET cc_start: 0.3259 (mmt) cc_final: 0.2413 (mmt) REVERT: C 924 MET cc_start: 0.5730 (mmp) cc_final: 0.5229 (ttt) REVERT: C 926 ARG cc_start: 0.6578 (ttt-90) cc_final: 0.5832 (tpt170) REVERT: C 988 MET cc_start: 0.7183 (mmm) cc_final: 0.6767 (mmm) REVERT: C 1002 LYS cc_start: 0.7184 (mtpm) cc_final: 0.6813 (tttp) REVERT: C 1005 TRP cc_start: 0.7559 (p-90) cc_final: 0.7334 (p-90) REVERT: C 1012 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7192 (mp) REVERT: D 435 HIS cc_start: 0.8001 (m-70) cc_final: 0.7723 (m-70) REVERT: D 635 SER cc_start: 0.8083 (t) cc_final: 0.7531 (p) REVERT: D 638 ASP cc_start: 0.6939 (m-30) cc_final: 0.6618 (m-30) REVERT: D 657 GLU cc_start: 0.7117 (tp30) cc_final: 0.6842 (tt0) REVERT: D 697 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7436 (ptmm) REVERT: D 764 ASN cc_start: 0.8089 (m110) cc_final: 0.7835 (m-40) outliers start: 28 outliers final: 11 residues processed: 380 average time/residue: 0.5209 time to fit residues: 226.7643 Evaluate side-chains 272 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 1012 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain E residue 25 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN A 747 ASN A 947 ASN A 950 HIS A 990 ASN B 747 ASN C 726 ASN C 747 ASN C 947 ASN C 950 HIS C 990 ASN D 747 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135213 restraints weight = 22384.938| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.20 r_work: 0.3257 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19875 Z= 0.148 Angle : 1.053 32.742 26706 Z= 0.436 Chirality : 0.093 1.875 2866 Planarity : 0.006 0.050 3132 Dihedral : 19.032 167.513 3295 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.99 % Favored : 94.83 % Rotamer: Outliers : 4.04 % Allowed : 9.02 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.16), residues: 2226 helix: -0.94 (0.13), residues: 1276 sheet: -1.90 (0.30), residues: 230 loop : -2.37 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 104 TYR 0.023 0.002 TYR E 117 PHE 0.016 0.002 PHE C 546 TRP 0.013 0.001 TRP A 766 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (19867) covalent geometry : angle 1.05263 / 0.44 (26690) SS BOND : bond 0.00067 / 0.03 ( 8) SS BOND : angle 0.89898 / 0.54 ( 16) hydrogen bonds : bond 0.04994 / 3.39 ( 972) hydrogen bonds : angle 4.54292 / 3.11 ( 2844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 283 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8138 (tttp) cc_final: 0.7854 (mtpp) REVERT: A 496 MET cc_start: 0.9380 (ttm) cc_final: 0.9151 (ttm) REVERT: A 585 MET cc_start: 0.9205 (mmt) cc_final: 0.8914 (mmt) REVERT: A 634 GLU cc_start: 0.7542 (pt0) cc_final: 0.7330 (mt-10) REVERT: A 860 TYR cc_start: 0.6905 (m-80) cc_final: 0.6299 (m-80) REVERT: A 907 MET cc_start: 0.3229 (mmt) cc_final: 0.2714 (mmt) REVERT: A 924 MET cc_start: 0.5287 (mmp) cc_final: 0.5075 (ttt) REVERT: A 926 ARG cc_start: 0.6971 (ttt-90) cc_final: 0.6103 (tpt170) REVERT: A 947 ASN cc_start: 0.7015 (m-40) cc_final: 0.6768 (m-40) REVERT: A 958 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5389 (mt) REVERT: A 980 TYR cc_start: 0.8175 (t80) cc_final: 0.7284 (t80) REVERT: A 988 MET cc_start: 0.7698 (mmm) cc_final: 0.7241 (mmm) REVERT: A 1002 LYS cc_start: 0.7474 (mtpm) cc_final: 0.6920 (tttp) REVERT: B 657 GLU cc_start: 0.7875 (tp30) cc_final: 0.7593 (mt-10) REVERT: B 697 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7684 (ptmm) REVERT: C 496 MET cc_start: 0.9375 (ttm) cc_final: 0.9174 (ttm) REVERT: C 524 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: C 585 MET cc_start: 0.9176 (mmt) cc_final: 0.8762 (mmt) REVERT: C 736 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7590 (p) REVERT: C 860 TYR cc_start: 0.6956 (m-80) cc_final: 0.6680 (m-80) REVERT: C 864 LEU cc_start: 0.7487 (tt) cc_final: 0.7265 (tt) REVERT: C 868 ILE cc_start: 0.4802 (OUTLIER) cc_final: 0.4470 (mm) REVERT: C 880 MET cc_start: 0.5167 (tpt) cc_final: 0.4065 (tmt) REVERT: C 924 MET cc_start: 0.5795 (mmp) cc_final: 0.5517 (mtt) REVERT: C 926 ARG cc_start: 0.6699 (ttt-90) cc_final: 0.6096 (tpt170) REVERT: C 980 TYR cc_start: 0.8214 (t80) cc_final: 0.7866 (t80) REVERT: C 988 MET cc_start: 0.7598 (mmm) cc_final: 0.7211 (mmm) REVERT: C 1002 LYS cc_start: 0.7450 (mtpm) cc_final: 0.6900 (tttp) REVERT: C 1012 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7467 (mp) REVERT: D 697 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7615 (ptmm) REVERT: D 756 GLN cc_start: 0.8674 (mt0) cc_final: 0.8432 (mt0) outliers start: 78 outliers final: 27 residues processed: 333 average time/residue: 0.5231 time to fit residues: 200.3311 Evaluate side-chains 270 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1012 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 HIS C 411 ASN C 709 ASN C 947 ASN C 950 HIS D 435 HIS D 764 ASN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130538 restraints weight = 22597.036| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.37 r_work: 0.3198 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19875 Z= 0.169 Angle : 1.023 31.446 26706 Z= 0.420 Chirality : 0.097 1.925 2866 Planarity : 0.005 0.063 3132 Dihedral : 18.082 161.332 3287 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 4.25 % Allowed : 11.09 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2226 helix: 0.36 (0.14), residues: 1282 sheet: -1.81 (0.30), residues: 246 loop : -2.19 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 485 TYR 0.022 0.002 TYR F 117 PHE 0.017 0.002 PHE D 531 TRP 0.011 0.001 TRP F 88 HIS 0.007 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (19867) covalent geometry : angle 1.02287 / 0.42 (26690) SS BOND : bond 0.00168 / 0.09 ( 8) SS BOND : angle 0.63679 / 0.36 ( 16) hydrogen bonds : bond 0.04448 / 3.01 ( 972) hydrogen bonds : angle 4.04870 / 2.78 ( 2844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 236 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.4696 (mmm) REVERT: A 439 LYS cc_start: 0.8261 (tttp) cc_final: 0.7875 (mtpp) REVERT: A 736 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7732 (p) REVERT: A 860 TYR cc_start: 0.7021 (m-80) cc_final: 0.6401 (m-80) REVERT: A 864 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6782 (tt) REVERT: A 907 MET cc_start: 0.3174 (mmt) cc_final: 0.2613 (mmt) REVERT: A 924 MET cc_start: 0.5299 (mmp) cc_final: 0.5047 (ttt) REVERT: A 926 ARG cc_start: 0.7023 (ttt-90) cc_final: 0.6123 (tpt170) REVERT: A 958 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5479 (mt) REVERT: A 980 TYR cc_start: 0.8274 (t80) cc_final: 0.7411 (t80) REVERT: A 988 MET cc_start: 0.7414 (mmm) cc_final: 0.7158 (mmm) REVERT: A 1002 LYS cc_start: 0.7461 (mtpm) cc_final: 0.6749 (tttt) REVERT: A 1023 MET cc_start: 0.8075 (mtt) cc_final: 0.7077 (mtt) REVERT: B 657 GLU cc_start: 0.7950 (tp30) cc_final: 0.7635 (mt-10) REVERT: B 697 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7651 (ptmm) REVERT: C 416 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7656 (pp20) REVERT: C 868 ILE cc_start: 0.4909 (OUTLIER) cc_final: 0.4614 (mm) REVERT: C 924 MET cc_start: 0.5841 (mmp) cc_final: 0.5524 (mtt) REVERT: C 926 ARG cc_start: 0.6730 (ttt-90) cc_final: 0.6035 (tpt170) REVERT: C 939 MET cc_start: 0.7670 (mtm) cc_final: 0.7444 (mtm) REVERT: C 980 TYR cc_start: 0.8214 (t80) cc_final: 0.7780 (t80) REVERT: C 988 MET cc_start: 0.7515 (mmm) cc_final: 0.7237 (mmm) REVERT: C 1002 LYS cc_start: 0.7438 (mtpm) cc_final: 0.6809 (tttt) REVERT: D 509 LYS cc_start: 0.7658 (mmtp) cc_final: 0.7219 (tptm) REVERT: D 657 GLU cc_start: 0.7980 (tp30) cc_final: 0.7369 (mm-30) REVERT: D 697 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7568 (ptmm) REVERT: E 105 TYR cc_start: 0.6049 (t80) cc_final: 0.5452 (t80) outliers start: 82 outliers final: 40 residues processed: 291 average time/residue: 0.5052 time to fit residues: 169.0660 Evaluate side-chains 270 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 11 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 947 ASN B 435 HIS B 587 GLN C 411 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133352 restraints weight = 22559.133| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.19 r_work: 0.3215 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19875 Z= 0.139 Angle : 0.993 31.519 26706 Z= 0.402 Chirality : 0.095 1.888 2866 Planarity : 0.004 0.053 3132 Dihedral : 17.091 159.339 3283 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 4.30 % Allowed : 12.18 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2226 helix: 1.16 (0.14), residues: 1282 sheet: -1.50 (0.30), residues: 242 loop : -2.06 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 684 TYR 0.021 0.001 TYR B 816 PHE 0.016 0.001 PHE A 901 TRP 0.010 0.001 TRP A1005 HIS 0.009 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (19867) covalent geometry : angle 0.99329 / 0.40 (26690) SS BOND : bond 0.00121 / 0.05 ( 8) SS BOND : angle 0.63919 / 0.36 ( 16) hydrogen bonds : bond 0.03837 / 2.59 ( 972) hydrogen bonds : angle 3.76759 / 2.59 ( 2844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 248 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.4801 (mmm) REVERT: A 860 TYR cc_start: 0.7073 (m-80) cc_final: 0.6790 (m-80) REVERT: A 864 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6507 (tt) REVERT: A 907 MET cc_start: 0.3148 (mmt) cc_final: 0.2595 (mmt) REVERT: A 924 MET cc_start: 0.5274 (mmp) cc_final: 0.5043 (ttt) REVERT: A 926 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.6002 (tpt170) REVERT: A 958 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5607 (mt) REVERT: A 980 TYR cc_start: 0.8271 (t80) cc_final: 0.7378 (t80) REVERT: A 988 MET cc_start: 0.7467 (mmm) cc_final: 0.7172 (mmm) REVERT: A 1002 LYS cc_start: 0.7519 (mtpm) cc_final: 0.6859 (tttt) REVERT: A 1023 MET cc_start: 0.8101 (mtt) cc_final: 0.7064 (mtt) REVERT: B 697 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7621 (ptmm) REVERT: C 416 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7631 (pp20) REVERT: C 496 MET cc_start: 0.9359 (ttm) cc_final: 0.9122 (ttm) REVERT: C 736 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7459 (p) REVERT: C 864 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6738 (tt) REVERT: C 868 ILE cc_start: 0.5065 (OUTLIER) cc_final: 0.4769 (mm) REVERT: C 924 MET cc_start: 0.5926 (mmp) cc_final: 0.5561 (mtt) REVERT: C 926 ARG cc_start: 0.6763 (ttt-90) cc_final: 0.5997 (tpt170) REVERT: C 980 TYR cc_start: 0.8257 (t80) cc_final: 0.7696 (t80) REVERT: C 988 MET cc_start: 0.7497 (mmm) cc_final: 0.7168 (mmm) REVERT: C 1002 LYS cc_start: 0.7501 (mtpm) cc_final: 0.6829 (tttt) REVERT: D 509 LYS cc_start: 0.7649 (mmtp) cc_final: 0.7281 (tptm) REVERT: D 697 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7575 (ptmm) REVERT: D 808 LEU cc_start: 0.8543 (mt) cc_final: 0.8312 (tt) REVERT: F 67 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7149 (tp) outliers start: 83 outliers final: 35 residues processed: 299 average time/residue: 0.5201 time to fit residues: 179.1725 Evaluate side-chains 276 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 67 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 HIS C 411 ASN C 709 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128641 restraints weight = 22607.047| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.17 r_work: 0.3158 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 19875 Z= 0.254 Angle : 1.062 33.043 26706 Z= 0.437 Chirality : 0.097 1.893 2866 Planarity : 0.005 0.056 3132 Dihedral : 17.260 159.272 3279 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 4.25 % Allowed : 12.59 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2226 helix: 1.02 (0.14), residues: 1286 sheet: -1.67 (0.30), residues: 246 loop : -2.13 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 684 TYR 0.023 0.002 TYR B 816 PHE 0.025 0.002 PHE D 531 TRP 0.011 0.002 TRP B 578 HIS 0.009 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 (19867) covalent geometry : angle 1.06255 / 0.44 (26690) SS BOND : bond 0.00263 / 0.13 ( 8) SS BOND : angle 0.50817 / 0.28 ( 16) hydrogen bonds : bond 0.04600 / 3.09 ( 972) hydrogen bonds : angle 3.98588 / 2.75 ( 2844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 232 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 GLU cc_start: 0.7729 (pt0) cc_final: 0.7493 (mt-10) REVERT: A 860 TYR cc_start: 0.7085 (m-80) cc_final: 0.6752 (m-80) REVERT: A 864 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6823 (tt) REVERT: A 907 MET cc_start: 0.3236 (mmt) cc_final: 0.2682 (mmt) REVERT: A 924 MET cc_start: 0.5506 (mmp) cc_final: 0.5164 (ttt) REVERT: A 926 ARG cc_start: 0.7075 (ttt-90) cc_final: 0.6004 (tpt170) REVERT: A 958 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5676 (mt) REVERT: A 980 TYR cc_start: 0.8360 (t80) cc_final: 0.7471 (t80) REVERT: A 988 MET cc_start: 0.7500 (mmm) cc_final: 0.7252 (mmm) REVERT: A 1002 LYS cc_start: 0.7520 (mtpm) cc_final: 0.6861 (tttp) REVERT: A 1023 MET cc_start: 0.8112 (mtt) cc_final: 0.7079 (mtt) REVERT: B 697 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7821 (ptmm) REVERT: C 411 ASN cc_start: 0.6209 (p0) cc_final: 0.5981 (p0) REVERT: C 416 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7723 (pp20) REVERT: C 715 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6810 (mmp80) REVERT: C 864 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6757 (tt) REVERT: C 868 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4786 (mm) REVERT: C 906 VAL cc_start: 0.5072 (OUTLIER) cc_final: 0.4635 (t) REVERT: C 924 MET cc_start: 0.5910 (mmp) cc_final: 0.5513 (mtt) REVERT: C 926 ARG cc_start: 0.6925 (ttt-90) cc_final: 0.6039 (tpt170) REVERT: C 939 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7285 (mtm) REVERT: C 980 TYR cc_start: 0.8302 (t80) cc_final: 0.7589 (t80) REVERT: C 988 MET cc_start: 0.7611 (mmm) cc_final: 0.7307 (mmm) REVERT: C 1002 LYS cc_start: 0.7542 (mtpm) cc_final: 0.6844 (tttp) REVERT: C 1005 TRP cc_start: 0.7223 (p-90) cc_final: 0.7011 (p-90) REVERT: C 1023 MET cc_start: 0.8104 (mtt) cc_final: 0.6966 (mtt) REVERT: D 509 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7236 (tptm) REVERT: D 657 GLU cc_start: 0.7954 (tp30) cc_final: 0.7402 (mm-30) REVERT: D 697 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7675 (ptmm) outliers start: 82 outliers final: 40 residues processed: 284 average time/residue: 0.5718 time to fit residues: 185.2383 Evaluate side-chains 274 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 715 ARG Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 902 THR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 223 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 947 ASN B 435 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 587 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132541 restraints weight = 22441.540| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.19 r_work: 0.3214 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19875 Z= 0.130 Angle : 0.986 31.654 26706 Z= 0.396 Chirality : 0.095 1.913 2866 Planarity : 0.004 0.050 3132 Dihedral : 16.390 160.074 3279 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 3.32 % Allowed : 14.15 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2226 helix: 1.61 (0.15), residues: 1286 sheet: -1.41 (0.31), residues: 242 loop : -1.96 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 684 TYR 0.021 0.001 TYR B 816 PHE 0.013 0.001 PHE B 546 TRP 0.012 0.001 TRP C1005 HIS 0.008 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (19867) covalent geometry : angle 0.98604 / 0.40 (26690) SS BOND : bond 0.00099 / 0.05 ( 8) SS BOND : angle 0.55616 / 0.38 ( 16) hydrogen bonds : bond 0.03638 / 2.46 ( 972) hydrogen bonds : angle 3.67677 / 2.53 ( 2844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 227 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7028 (m-80) cc_final: 0.6756 (m-80) REVERT: A 907 MET cc_start: 0.3134 (mmt) cc_final: 0.2540 (mmt) REVERT: A 924 MET cc_start: 0.5302 (mmp) cc_final: 0.5024 (ttt) REVERT: A 926 ARG cc_start: 0.6992 (ttt-90) cc_final: 0.5963 (tpt170) REVERT: A 958 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5715 (mt) REVERT: A 980 TYR cc_start: 0.8218 (t80) cc_final: 0.7368 (t80) REVERT: A 988 MET cc_start: 0.7472 (mmm) cc_final: 0.7183 (mmm) REVERT: A 1002 LYS cc_start: 0.7479 (mtpm) cc_final: 0.6812 (tttp) REVERT: A 1012 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 1023 MET cc_start: 0.8029 (mtt) cc_final: 0.6909 (mtt) REVERT: B 697 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7726 (ptmm) REVERT: C 496 MET cc_start: 0.9357 (ttm) cc_final: 0.9151 (ttm) REVERT: C 736 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7468 (p) REVERT: C 839 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6037 (tt) REVERT: C 864 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6447 (tt) REVERT: C 868 ILE cc_start: 0.5011 (OUTLIER) cc_final: 0.4752 (mm) REVERT: C 906 VAL cc_start: 0.5049 (OUTLIER) cc_final: 0.4639 (t) REVERT: C 924 MET cc_start: 0.5615 (mmp) cc_final: 0.5309 (mtt) REVERT: C 980 TYR cc_start: 0.8215 (t80) cc_final: 0.7512 (t80) REVERT: C 988 MET cc_start: 0.7495 (mmm) cc_final: 0.7219 (mmm) REVERT: C 1002 LYS cc_start: 0.7418 (mtpm) cc_final: 0.6788 (tttp) REVERT: C 1005 TRP cc_start: 0.7027 (p-90) cc_final: 0.6774 (p-90) REVERT: C 1023 MET cc_start: 0.8070 (mtt) cc_final: 0.6869 (mtt) REVERT: D 509 LYS cc_start: 0.7472 (mmtp) cc_final: 0.7249 (tptm) REVERT: D 657 GLU cc_start: 0.7897 (tp30) cc_final: 0.7366 (mm-30) REVERT: D 697 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7648 (ptmm) REVERT: D 808 LEU cc_start: 0.8505 (mt) cc_final: 0.8289 (tt) outliers start: 64 outliers final: 37 residues processed: 267 average time/residue: 0.5239 time to fit residues: 161.0783 Evaluate side-chains 270 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 67 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 0.0040 chunk 223 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 37 optimal weight: 0.0270 chunk 175 optimal weight: 0.1980 chunk 205 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129710 restraints weight = 22636.845| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.21 r_work: 0.3161 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19875 Z= 0.204 Angle : 1.034 32.749 26706 Z= 0.420 Chirality : 0.096 1.915 2866 Planarity : 0.004 0.053 3132 Dihedral : 16.403 159.328 3279 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 3.58 % Allowed : 14.66 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2226 helix: 1.50 (0.14), residues: 1286 sheet: -1.46 (0.31), residues: 242 loop : -1.98 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.022 0.002 TYR B 816 PHE 0.022 0.002 PHE D 531 TRP 0.009 0.002 TRP B 578 HIS 0.010 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (19867) covalent geometry : angle 1.03446 / 0.42 (26690) SS BOND : bond 0.00193 / 0.09 ( 8) SS BOND : angle 0.41858 / 0.23 ( 16) hydrogen bonds : bond 0.04212 / 2.83 ( 972) hydrogen bonds : angle 3.82570 / 2.64 ( 2844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 233 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7184 (m-80) cc_final: 0.6880 (m-80) REVERT: A 907 MET cc_start: 0.3180 (mmt) cc_final: 0.2617 (mmt) REVERT: A 924 MET cc_start: 0.5447 (mmp) cc_final: 0.5127 (ttt) REVERT: A 926 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.5922 (tpt170) REVERT: A 958 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5663 (mt) REVERT: A 980 TYR cc_start: 0.8263 (t80) cc_final: 0.7340 (t80) REVERT: A 1002 LYS cc_start: 0.7466 (mtpm) cc_final: 0.6805 (tttp) REVERT: A 1023 MET cc_start: 0.8062 (mtt) cc_final: 0.6955 (mtt) REVERT: B 697 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7949 (ptmt) REVERT: C 416 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7154 (mm-30) REVERT: C 839 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6112 (tt) REVERT: C 864 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6528 (tt) REVERT: C 868 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4776 (mm) REVERT: C 888 ARG cc_start: 0.5990 (mpt180) cc_final: 0.5752 (mpt-90) REVERT: C 906 VAL cc_start: 0.5019 (OUTLIER) cc_final: 0.4605 (t) REVERT: C 924 MET cc_start: 0.5702 (mmp) cc_final: 0.5359 (mtt) REVERT: C 926 ARG cc_start: 0.6912 (ttt-90) cc_final: 0.5949 (tpt170) REVERT: C 980 TYR cc_start: 0.8276 (t80) cc_final: 0.7499 (t80) REVERT: C 988 MET cc_start: 0.7548 (mmm) cc_final: 0.7271 (mmm) REVERT: C 1002 LYS cc_start: 0.7485 (mtpm) cc_final: 0.6814 (tttp) REVERT: C 1005 TRP cc_start: 0.7205 (p-90) cc_final: 0.6966 (p-90) REVERT: C 1023 MET cc_start: 0.8083 (mtt) cc_final: 0.6867 (mtt) REVERT: D 509 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7238 (tptm) REVERT: D 657 GLU cc_start: 0.7906 (tp30) cc_final: 0.7432 (mm-30) REVERT: D 697 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7842 (ptmm) REVERT: D 808 LEU cc_start: 0.8509 (mt) cc_final: 0.8281 (tt) outliers start: 69 outliers final: 43 residues processed: 278 average time/residue: 0.5259 time to fit residues: 168.7235 Evaluate side-chains 275 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 115 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 142 optimal weight: 0.0070 chunk 19 optimal weight: 0.6980 chunk 201 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 947 ASN B 435 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN F 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131245 restraints weight = 22643.638| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.29 r_work: 0.3208 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19875 Z= 0.127 Angle : 0.987 31.676 26706 Z= 0.396 Chirality : 0.096 1.930 2866 Planarity : 0.004 0.049 3132 Dihedral : 15.585 159.906 3279 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.01 % Allowed : 15.60 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 2226 helix: 1.89 (0.15), residues: 1286 sheet: -1.30 (0.31), residues: 242 loop : -1.87 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 684 TYR 0.019 0.001 TYR B 673 PHE 0.014 0.001 PHE B 546 TRP 0.011 0.001 TRP C1005 HIS 0.009 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (19867) covalent geometry : angle 0.98694 / 0.40 (26690) SS BOND : bond 0.00071 / 0.03 ( 8) SS BOND : angle 0.44426 / 0.27 ( 16) hydrogen bonds : bond 0.03545 / 2.39 ( 972) hydrogen bonds : angle 3.63696 / 2.50 ( 2844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7011 (m-80) cc_final: 0.6721 (m-80) REVERT: A 907 MET cc_start: 0.3133 (mmt) cc_final: 0.2607 (mmt) REVERT: A 924 MET cc_start: 0.5270 (mmp) cc_final: 0.5004 (ttt) REVERT: A 926 ARG cc_start: 0.6887 (ttt-90) cc_final: 0.5848 (tpt170) REVERT: A 958 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5653 (mt) REVERT: A 980 TYR cc_start: 0.8149 (t80) cc_final: 0.7285 (t80) REVERT: A 1002 LYS cc_start: 0.7403 (mtpm) cc_final: 0.6723 (tttp) REVERT: A 1012 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 1023 MET cc_start: 0.8009 (mtt) cc_final: 0.6868 (mtt) REVERT: B 697 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7610 (ptmm) REVERT: C 416 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7098 (mm-30) REVERT: C 509 LYS cc_start: 0.6485 (mmmm) cc_final: 0.5886 (ptmm) REVERT: C 864 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6472 (tt) REVERT: C 868 ILE cc_start: 0.5274 (OUTLIER) cc_final: 0.4946 (mm) REVERT: C 906 VAL cc_start: 0.5007 (OUTLIER) cc_final: 0.4596 (t) REVERT: C 924 MET cc_start: 0.5508 (mmp) cc_final: 0.5168 (ttt) REVERT: C 980 TYR cc_start: 0.8170 (t80) cc_final: 0.7397 (t80) REVERT: C 988 MET cc_start: 0.7486 (mmm) cc_final: 0.7244 (mmm) REVERT: C 1002 LYS cc_start: 0.7364 (mtpm) cc_final: 0.6731 (tttp) REVERT: C 1005 TRP cc_start: 0.6969 (p-90) cc_final: 0.6717 (p-90) REVERT: D 654 SER cc_start: 0.8723 (m) cc_final: 0.8462 (p) REVERT: D 697 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7580 (ptmm) REVERT: D 808 LEU cc_start: 0.8468 (mt) cc_final: 0.8239 (tt) REVERT: F 56 ASN cc_start: 0.5425 (OUTLIER) cc_final: 0.5208 (t160) REVERT: F 132 GLN cc_start: 0.4722 (tm-30) cc_final: 0.4395 (tm130) outliers start: 58 outliers final: 38 residues processed: 267 average time/residue: 0.5159 time to fit residues: 158.9204 Evaluate side-chains 268 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 86 optimal weight: 0.0060 chunk 125 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 170 optimal weight: 0.0010 chunk 164 optimal weight: 2.9990 overall best weight: 1.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 HIS B 508 GLN C 709 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129550 restraints weight = 22560.857| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.23 r_work: 0.3157 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19875 Z= 0.218 Angle : 1.039 32.967 26706 Z= 0.423 Chirality : 0.097 1.925 2866 Planarity : 0.004 0.053 3132 Dihedral : 15.786 159.148 3279 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.52 % Rotamer: Outliers : 3.11 % Allowed : 15.96 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2226 helix: 1.61 (0.14), residues: 1286 sheet: -1.40 (0.31), residues: 242 loop : -1.91 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 684 TYR 0.022 0.002 TYR B 816 PHE 0.023 0.002 PHE D 531 TRP 0.009 0.002 TRP B 578 HIS 0.012 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (19867) covalent geometry : angle 1.03905 / 0.42 (26690) SS BOND : bond 0.00196 / 0.10 ( 8) SS BOND : angle 0.37758 / 0.21 ( 16) hydrogen bonds : bond 0.04247 / 2.85 ( 972) hydrogen bonds : angle 3.82707 / 2.63 ( 2844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7062 (m-80) cc_final: 0.6785 (m-80) REVERT: A 907 MET cc_start: 0.2995 (mmt) cc_final: 0.2509 (mmt) REVERT: A 924 MET cc_start: 0.5434 (mmp) cc_final: 0.5130 (ttt) REVERT: A 958 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5724 (mt) REVERT: A 980 TYR cc_start: 0.8229 (t80) cc_final: 0.7367 (t80) REVERT: A 1002 LYS cc_start: 0.7425 (mtpm) cc_final: 0.6782 (tttp) REVERT: A 1023 MET cc_start: 0.8066 (mtt) cc_final: 0.6970 (mtt) REVERT: B 461 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8044 (p0) REVERT: B 697 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7799 (ptmt) REVERT: C 416 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7125 (mm-30) REVERT: C 509 LYS cc_start: 0.6450 (mmmm) cc_final: 0.5899 (ptmm) REVERT: C 864 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6539 (tt) REVERT: C 868 ILE cc_start: 0.5110 (OUTLIER) cc_final: 0.4810 (mm) REVERT: C 906 VAL cc_start: 0.4964 (OUTLIER) cc_final: 0.4564 (t) REVERT: C 924 MET cc_start: 0.5614 (mmp) cc_final: 0.5317 (ttt) REVERT: C 926 ARG cc_start: 0.6878 (ttt-90) cc_final: 0.5854 (tpt170) REVERT: C 980 TYR cc_start: 0.8270 (t80) cc_final: 0.7493 (t80) REVERT: C 988 MET cc_start: 0.7544 (mmm) cc_final: 0.7285 (mmm) REVERT: C 1002 LYS cc_start: 0.7484 (mtpm) cc_final: 0.6818 (tttp) REVERT: C 1005 TRP cc_start: 0.7193 (p-90) cc_final: 0.6938 (p-90) REVERT: C 1023 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7236 (mtt) REVERT: D 697 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7784 (ptmt) outliers start: 60 outliers final: 42 residues processed: 265 average time/residue: 0.5299 time to fit residues: 162.3246 Evaluate side-chains 272 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 66 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 947 ASN B 435 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131758 restraints weight = 22563.772| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.26 r_work: 0.3196 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19875 Z= 0.141 Angle : 0.996 31.941 26706 Z= 0.400 Chirality : 0.096 1.932 2866 Planarity : 0.004 0.049 3132 Dihedral : 15.302 159.420 3279 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 2.54 % Allowed : 16.68 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 2226 helix: 1.87 (0.15), residues: 1286 sheet: -1.31 (0.31), residues: 242 loop : -1.83 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 684 TYR 0.019 0.001 TYR B 816 PHE 0.014 0.001 PHE C 574 TRP 0.010 0.001 TRP C1005 HIS 0.012 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (19867) covalent geometry : angle 0.99624 / 0.40 (26690) SS BOND : bond 0.00089 / 0.04 ( 8) SS BOND : angle 0.40450 / 0.22 ( 16) hydrogen bonds : bond 0.03679 / 2.48 ( 972) hydrogen bonds : angle 3.68585 / 2.53 ( 2844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 509 LYS cc_start: 0.6382 (mmmm) cc_final: 0.6006 (ptmm) REVERT: A 736 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7609 (p) REVERT: A 860 TYR cc_start: 0.7047 (m-80) cc_final: 0.6771 (m-80) REVERT: A 907 MET cc_start: 0.2939 (mmt) cc_final: 0.2612 (mmt) REVERT: A 924 MET cc_start: 0.5332 (mmp) cc_final: 0.5029 (ttt) REVERT: A 958 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5641 (mt) REVERT: A 980 TYR cc_start: 0.8166 (t80) cc_final: 0.7336 (t80) REVERT: A 1002 LYS cc_start: 0.7407 (mtpm) cc_final: 0.6773 (tttp) REVERT: A 1023 MET cc_start: 0.8009 (mtt) cc_final: 0.6860 (mtt) REVERT: B 697 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7747 (ptmt) REVERT: C 416 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7037 (mm-30) REVERT: C 509 LYS cc_start: 0.6176 (mmmm) cc_final: 0.5838 (ptmm) REVERT: C 736 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7660 (p) REVERT: C 864 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6382 (tt) REVERT: C 868 ILE cc_start: 0.5157 (OUTLIER) cc_final: 0.4920 (mm) REVERT: C 906 VAL cc_start: 0.5068 (OUTLIER) cc_final: 0.4642 (t) REVERT: C 924 MET cc_start: 0.5496 (mmp) cc_final: 0.5157 (ttt) REVERT: C 980 TYR cc_start: 0.8226 (t80) cc_final: 0.7432 (t80) REVERT: C 988 MET cc_start: 0.7421 (mmm) cc_final: 0.7196 (mmm) REVERT: C 1002 LYS cc_start: 0.7433 (mtpm) cc_final: 0.6782 (tttp) REVERT: C 1005 TRP cc_start: 0.6987 (p-90) cc_final: 0.6751 (p-90) REVERT: D 697 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7581 (ptmm) REVERT: D 808 LEU cc_start: 0.8482 (mt) cc_final: 0.8256 (tt) REVERT: F 155 TYR cc_start: 0.7783 (t80) cc_final: 0.7512 (t80) outliers start: 49 outliers final: 38 residues processed: 265 average time/residue: 0.5025 time to fit residues: 153.5932 Evaluate side-chains 269 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 165 optimal weight: 0.0980 chunk 113 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 HIS B 508 GLN C 709 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.178423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132270 restraints weight = 22660.481| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.33 r_work: 0.3217 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19875 Z= 0.121 Angle : 0.976 31.539 26706 Z= 0.391 Chirality : 0.096 1.948 2866 Planarity : 0.004 0.049 3132 Dihedral : 14.632 159.318 3279 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.38 % Allowed : 17.10 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 2226 helix: 2.10 (0.15), residues: 1286 sheet: -1.15 (0.31), residues: 242 loop : -1.78 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 684 TYR 0.027 0.001 TYR C1001 PHE 0.012 0.001 PHE A 574 TRP 0.011 0.001 TRP C1005 HIS 0.013 0.001 HIS C 950 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19867) covalent geometry : angle 0.97673 / 0.39 (26690) SS BOND : bond 0.00075 / 0.04 ( 8) SS BOND : angle 0.38264 / 0.23 ( 16) hydrogen bonds : bond 0.03435 / 2.32 ( 972) hydrogen bonds : angle 3.61420 / 2.47 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6077.89 seconds wall clock time: 104 minutes 35.70 seconds (6275.70 seconds total)