Starting phenix.real_space_refine on Tue May 20 16:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss7_40746/05_2025/8ss7_40746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss7_40746/05_2025/8ss7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss7_40746/05_2025/8ss7_40746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss7_40746/05_2025/8ss7_40746.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss7_40746/05_2025/8ss7_40746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss7_40746/05_2025/8ss7_40746.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 54 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: 51 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: 54 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: 51 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: 81 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: 81 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: 11.98, per 1000 atoms: 0.62 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: 5.04 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.84 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: 6.06 Time building geometry restraints manager: 5.75 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: 11634 35.85 - 71.71: 540 71.71 - 107.56: 71 107.56 - 143.41: 55 143.41 - 179.26: 19 Dihedral angle restraints: 12319 sinusoidal: 5779 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 12316 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 1034 or resid 1101 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 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)))) 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: 5.120 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: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.070 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 22.549 179.265 8115 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.003 TRP C 861 HIS 0.006 0.001 HIS F 75 PHE 0.032 0.003 PHE B 667 TYR 0.037 0.003 TYR B 702 ARG 0.010 0.001 ARG C 692 Details of bonding type rmsd hydrogen bonds : bond 0.28082 ( 972) hydrogen bonds : angle 10.16249 ( 2844) SS BOND : bond 0.01197 ( 8) SS BOND : angle 2.02994 ( 16) covalent geometry : bond 0.02216 (19867) covalent geometry : angle 1.63792 (26690) *********************** 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 : 2.141 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: 1.1305 time to fit residues: 490.2720 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 : 1.870 ------------------------------------------------------------------------------- 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 190 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 205 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 F 132 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134601 restraints weight = 22452.292| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.15 r_work: 0.3247 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2004 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= 0.152 Angle : 1.069 33.995 26706 Z= 0.442 Chirality : 0.088 1.711 2866 Planarity : 0.006 0.050 3132 Dihedral : 24.178 179.948 4047 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.94 % Favored : 94.83 % Rotamer: Outliers : 3.99 % Allowed : 8.96 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.16), residues: 2226 helix: -1.01 (0.13), residues: 1264 sheet: -1.91 (0.31), residues: 216 loop : -2.20 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 766 HIS 0.002 0.001 HIS F 75 PHE 0.015 0.002 PHE C 546 TYR 0.024 0.002 TYR E 117 ARG 0.004 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 972) hydrogen bonds : angle 4.59773 ( 2844) SS BOND : bond 0.00105 ( 8) SS BOND : angle 0.87067 ( 16) covalent geometry : bond 0.00330 (19867) covalent geometry : angle 1.06942 (26690) *********************** 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 359 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 282 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8161 (tttp) cc_final: 0.7861 (mtpp) REVERT: A 496 MET cc_start: 0.9379 (ttm) cc_final: 0.9157 (ttm) REVERT: A 585 MET cc_start: 0.9215 (mmt) cc_final: 0.8944 (mmt) REVERT: A 634 GLU cc_start: 0.7563 (pt0) cc_final: 0.7351 (mt-10) REVERT: A 860 TYR cc_start: 0.6926 (m-80) cc_final: 0.6319 (m-80) REVERT: A 907 MET cc_start: 0.3217 (mmt) cc_final: 0.2698 (mmt) REVERT: A 924 MET cc_start: 0.5297 (mmp) cc_final: 0.5078 (ttt) REVERT: A 926 ARG cc_start: 0.6970 (ttt-90) cc_final: 0.6103 (tpt170) REVERT: A 939 MET cc_start: 0.7513 (mtm) cc_final: 0.7241 (mtm) REVERT: A 947 ASN cc_start: 0.7025 (m-40) cc_final: 0.6780 (m-40) REVERT: A 958 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5400 (mt) REVERT: A 980 TYR cc_start: 0.8207 (t80) cc_final: 0.7358 (t80) REVERT: A 988 MET cc_start: 0.7609 (mmm) cc_final: 0.7183 (mmm) REVERT: A 1002 LYS cc_start: 0.7475 (mtpm) cc_final: 0.6923 (tttp) REVERT: B 697 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7691 (ptmm) REVERT: B 760 ASP cc_start: 0.8044 (m-30) cc_final: 0.7831 (m-30) REVERT: C 524 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: C 585 MET cc_start: 0.9192 (mmt) cc_final: 0.8782 (mmt) REVERT: C 736 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7713 (p) REVERT: C 860 TYR cc_start: 0.6972 (m-80) cc_final: 0.6699 (m-80) REVERT: C 864 LEU cc_start: 0.7494 (tt) cc_final: 0.7272 (tt) REVERT: C 868 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4452 (mm) REVERT: C 880 MET cc_start: 0.5164 (tpt) cc_final: 0.4071 (tmt) REVERT: C 888 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5395 (mpt-90) REVERT: C 924 MET cc_start: 0.5818 (mmp) cc_final: 0.5525 (mtt) REVERT: C 926 ARG cc_start: 0.6707 (ttt-90) cc_final: 0.6104 (tpt170) REVERT: C 980 TYR cc_start: 0.8225 (t80) cc_final: 0.7881 (t80) REVERT: C 988 MET cc_start: 0.7592 (mmm) cc_final: 0.7194 (mmm) REVERT: C 1002 LYS cc_start: 0.7491 (mtpm) cc_final: 0.6874 (tttp) REVERT: D 435 HIS cc_start: 0.7690 (m-70) cc_final: 0.7481 (m-70) REVERT: D 697 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7561 (ptmm) REVERT: D 756 GLN cc_start: 0.8680 (mt0) cc_final: 0.8436 (mt0) REVERT: F 123 MET cc_start: 0.4428 (mtp) cc_final: 0.4136 (mtp) outliers start: 77 outliers final: 26 residues processed: 331 average time/residue: 1.0710 time to fit residues: 409.6053 Evaluate side-chains 265 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 888 ARG 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 697 LYS Chi-restraints excluded: chain D residue 704 LEU 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 153 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS C 411 ASN C 709 ASN C 947 ASN C 950 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132650 restraints weight = 22340.781| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.01 r_work: 0.3240 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2529 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= 0.140 Angle : 1.024 33.438 26706 Z= 0.416 Chirality : 0.089 1.724 2866 Planarity : 0.005 0.063 3132 Dihedral : 23.145 179.532 4035 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 4.40 % Allowed : 10.88 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2226 helix: 0.51 (0.14), residues: 1276 sheet: -1.63 (0.30), residues: 242 loop : -2.17 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 88 HIS 0.007 0.001 HIS C 950 PHE 0.013 0.001 PHE C 574 TYR 0.022 0.001 TYR B 816 ARG 0.004 0.000 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 972) hydrogen bonds : angle 3.92990 ( 2844) SS BOND : bond 0.00454 ( 8) SS BOND : angle 0.73312 ( 16) covalent geometry : bond 0.00313 (19867) covalent geometry : angle 1.02431 (26690) *********************** 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 326 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 241 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.4690 (mmm) REVERT: A 439 LYS cc_start: 0.8211 (tttp) cc_final: 0.7834 (mtpp) REVERT: A 860 TYR cc_start: 0.6924 (m-80) cc_final: 0.6302 (m-80) REVERT: A 864 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6692 (tt) REVERT: A 907 MET cc_start: 0.3158 (mmt) cc_final: 0.2600 (mmt) REVERT: A 924 MET cc_start: 0.5228 (mmp) cc_final: 0.4985 (ttt) REVERT: A 926 ARG cc_start: 0.6996 (ttt-90) cc_final: 0.6078 (tpt170) REVERT: A 958 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5447 (mt) REVERT: A 980 TYR cc_start: 0.8171 (t80) cc_final: 0.7271 (t80) REVERT: A 988 MET cc_start: 0.7386 (mmm) cc_final: 0.7121 (mmm) REVERT: A 1002 LYS cc_start: 0.7493 (mtpm) cc_final: 0.6870 (tttp) REVERT: A 1023 MET cc_start: 0.7996 (mtt) cc_final: 0.6982 (mtt) REVERT: B 657 GLU cc_start: 0.7790 (tp30) cc_final: 0.7165 (mm-30) REVERT: B 697 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7601 (ptmm) REVERT: C 416 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7610 (pp20) REVERT: C 524 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 736 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7462 (p) REVERT: C 868 ILE cc_start: 0.4952 (OUTLIER) cc_final: 0.4647 (mm) REVERT: C 924 MET cc_start: 0.5768 (mmp) cc_final: 0.5494 (mtt) REVERT: C 926 ARG cc_start: 0.6693 (ttt-90) cc_final: 0.6004 (tpt170) REVERT: C 980 TYR cc_start: 0.8139 (t80) cc_final: 0.7704 (t80) REVERT: C 988 MET cc_start: 0.7491 (mmm) cc_final: 0.7234 (mmm) REVERT: C 1002 LYS cc_start: 0.7355 (mtpm) cc_final: 0.6716 (tttt) REVERT: C 1012 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7464 (mp) REVERT: D 435 HIS cc_start: 0.7828 (m-70) cc_final: 0.7570 (m-70) REVERT: D 509 LYS cc_start: 0.7559 (mmtp) cc_final: 0.7172 (tptm) REVERT: D 657 GLU cc_start: 0.7909 (tp30) cc_final: 0.7263 (mm-30) REVERT: D 697 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7520 (ptmm) outliers start: 85 outliers final: 37 residues processed: 298 average time/residue: 1.0720 time to fit residues: 368.1272 Evaluate side-chains 273 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 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 524 GLU 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 69 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 129 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 435 HIS C 411 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129918 restraints weight = 22588.553| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.20 r_work: 0.3178 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2808 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= 0.203 Angle : 1.060 34.760 26706 Z= 0.432 Chirality : 0.088 1.691 2866 Planarity : 0.005 0.055 3132 Dihedral : 22.850 179.476 4031 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 4.56 % Allowed : 12.02 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2226 helix: 0.91 (0.14), residues: 1284 sheet: -1.60 (0.30), residues: 246 loop : -2.11 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 88 HIS 0.009 0.001 HIS C 950 PHE 0.021 0.002 PHE B 546 TYR 0.023 0.002 TYR B 816 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 972) hydrogen bonds : angle 3.95986 ( 2844) SS BOND : bond 0.00203 ( 8) SS BOND : angle 0.58331 ( 16) covalent geometry : bond 0.00481 (19867) covalent geometry : angle 1.06055 (26690) *********************** 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 329 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 241 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.4736 (mmm) REVERT: A 860 TYR cc_start: 0.7075 (m-80) cc_final: 0.6783 (m-80) REVERT: A 864 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6668 (tt) REVERT: A 907 MET cc_start: 0.3152 (mmt) cc_final: 0.2591 (mmt) REVERT: A 924 MET cc_start: 0.5408 (mmp) cc_final: 0.5106 (ttt) REVERT: A 926 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.5998 (tpt170) REVERT: A 958 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5573 (mt) REVERT: A 980 TYR cc_start: 0.8302 (t80) cc_final: 0.7390 (t80) REVERT: A 988 MET cc_start: 0.7468 (mmm) cc_final: 0.7187 (mmm) REVERT: A 1002 LYS cc_start: 0.7511 (mtpm) cc_final: 0.6861 (tttp) REVERT: A 1023 MET cc_start: 0.8084 (mtt) cc_final: 0.7059 (mtt) REVERT: B 697 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7680 (ptmm) REVERT: C 416 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7693 (pp20) REVERT: C 715 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6786 (mmp80) REVERT: C 864 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6705 (tt) REVERT: C 868 ILE cc_start: 0.4982 (OUTLIER) cc_final: 0.4708 (mm) REVERT: C 924 MET cc_start: 0.6064 (mmp) cc_final: 0.5593 (mtt) REVERT: C 926 ARG cc_start: 0.6829 (ttt-90) cc_final: 0.6044 (tpt170) REVERT: C 939 MET cc_start: 0.7617 (mtm) cc_final: 0.7368 (mtm) REVERT: C 980 TYR cc_start: 0.8260 (t80) cc_final: 0.7603 (t80) REVERT: C 988 MET cc_start: 0.7521 (mmm) cc_final: 0.7182 (mmm) REVERT: C 1002 LYS cc_start: 0.7527 (mtpm) cc_final: 0.6836 (tttp) REVERT: C 1005 TRP cc_start: 0.7024 (p-90) cc_final: 0.6815 (p-90) REVERT: D 435 HIS cc_start: 0.7832 (m-70) cc_final: 0.7532 (m-70) REVERT: D 509 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7331 (tptm) REVERT: D 697 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7619 (ptmm) REVERT: D 808 LEU cc_start: 0.8508 (mt) cc_final: 0.8296 (tt) REVERT: E 87 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7387 (mm-30) outliers start: 88 outliers final: 39 residues processed: 302 average time/residue: 1.1232 time to fit residues: 390.6348 Evaluate side-chains 282 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 524 GLU 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 719 ASP 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 D residue 397 VAL 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 87 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 132 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 435 HIS B 587 GLN C 411 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4091 r_free = 0.4091 target = 0.176956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131494 restraints weight = 22566.871| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.15 r_work: 0.3209 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3035 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= 0.136 Angle : 1.012 33.811 26706 Z= 0.405 Chirality : 0.088 1.708 2866 Planarity : 0.004 0.052 3132 Dihedral : 22.477 179.985 4031 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.78 % Allowed : 12.95 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2226 helix: 1.43 (0.15), residues: 1286 sheet: -1.35 (0.31), residues: 242 loop : -1.99 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 766 HIS 0.008 0.001 HIS C 950 PHE 0.016 0.001 PHE B 546 TYR 0.021 0.001 TYR B 816 ARG 0.004 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 972) hydrogen bonds : angle 3.72335 ( 2844) SS BOND : bond 0.00098 ( 8) SS BOND : angle 0.47714 ( 16) covalent geometry : bond 0.00311 (19867) covalent geometry : angle 1.01188 (26690) *********************** 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: 73 poor density : 241 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 GLU cc_start: 0.7668 (pt0) cc_final: 0.7422 (mt-10) REVERT: A 736 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7587 (p) REVERT: A 860 TYR cc_start: 0.7077 (m-80) cc_final: 0.6797 (m-80) REVERT: A 907 MET cc_start: 0.3197 (mmt) cc_final: 0.2647 (mmt) REVERT: A 924 MET cc_start: 0.5363 (mmp) cc_final: 0.5064 (ttt) REVERT: A 926 ARG cc_start: 0.6970 (ttt-90) cc_final: 0.5906 (tpt170) REVERT: A 958 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5734 (mt) REVERT: A 980 TYR cc_start: 0.8256 (t80) cc_final: 0.7401 (t80) REVERT: A 988 MET cc_start: 0.7498 (mmm) cc_final: 0.7245 (mmm) REVERT: A 1002 LYS cc_start: 0.7503 (mtpm) cc_final: 0.6848 (tttp) REVERT: A 1012 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7470 (mp) REVERT: A 1023 MET cc_start: 0.8029 (mtt) cc_final: 0.6936 (mtt) REVERT: B 697 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7662 (ptmm) REVERT: C 411 ASN cc_start: 0.6019 (p0) cc_final: 0.5797 (p0) REVERT: C 715 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6844 (mmp80) REVERT: C 736 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7669 (p) REVERT: C 839 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5986 (tt) REVERT: C 864 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6668 (tt) REVERT: C 868 ILE cc_start: 0.5057 (OUTLIER) cc_final: 0.4783 (mm) REVERT: C 906 VAL cc_start: 0.4930 (OUTLIER) cc_final: 0.4572 (t) REVERT: C 924 MET cc_start: 0.5715 (mmp) cc_final: 0.5349 (mtt) REVERT: C 926 ARG cc_start: 0.6802 (ttt-90) cc_final: 0.5981 (tpt170) REVERT: C 980 TYR cc_start: 0.8237 (t80) cc_final: 0.7594 (t80) REVERT: C 988 MET cc_start: 0.7518 (mmm) cc_final: 0.7214 (mmm) REVERT: C 1002 LYS cc_start: 0.7532 (mtpm) cc_final: 0.6869 (tttp) REVERT: C 1005 TRP cc_start: 0.6939 (p-90) cc_final: 0.6671 (p-90) REVERT: C 1012 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7437 (mp) REVERT: C 1023 MET cc_start: 0.8129 (mtt) cc_final: 0.7033 (mtt) REVERT: D 435 HIS cc_start: 0.7899 (m-70) cc_final: 0.7594 (m-70) REVERT: D 509 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7217 (tptm) REVERT: D 627 GLU cc_start: 0.8184 (tp30) cc_final: 0.7983 (tp30) REVERT: D 657 GLU cc_start: 0.7920 (tp30) cc_final: 0.7333 (mm-30) REVERT: D 678 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6492 (mm-30) REVERT: D 697 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7620 (ptmm) REVERT: D 808 LEU cc_start: 0.8496 (mt) cc_final: 0.8284 (tt) REVERT: E 87 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: F 67 LEU cc_start: 0.7634 (tp) cc_final: 0.7355 (tp) outliers start: 73 outliers final: 37 residues processed: 289 average time/residue: 1.1833 time to fit residues: 392.8685 Evaluate side-chains 282 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 958 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 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 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 1012 ILE 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 650 LEU Chi-restraints excluded: chain D residue 678 GLU 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 87 GLU 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 153 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 192 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 114 optimal weight: 0.0060 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 435 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN 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 = 0.4096 r_free = 0.4096 target = 0.177659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130836 restraints weight = 22487.599| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.04 r_work: 0.3212 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3159 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= 0.138 Angle : 1.007 33.879 26706 Z= 0.402 Chirality : 0.088 1.724 2866 Planarity : 0.004 0.051 3132 Dihedral : 22.218 179.678 4031 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 3.68 % Allowed : 14.25 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2226 helix: 1.68 (0.15), residues: 1286 sheet: -1.28 (0.31), residues: 242 loop : -1.92 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1005 HIS 0.008 0.001 HIS C 950 PHE 0.014 0.001 PHE B 546 TYR 0.019 0.001 TYR B 816 ARG 0.004 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 972) hydrogen bonds : angle 3.65384 ( 2844) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.52412 ( 16) covalent geometry : bond 0.00316 (19867) covalent geometry : angle 1.00768 (26690) *********************** 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 301 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7026 (m-80) cc_final: 0.6686 (m-80) REVERT: A 907 MET cc_start: 0.3149 (mmt) cc_final: 0.2527 (mmt) REVERT: A 924 MET cc_start: 0.5457 (mmp) cc_final: 0.5137 (ttt) REVERT: A 926 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.5891 (tpt170) REVERT: A 958 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5703 (mt) REVERT: A 980 TYR cc_start: 0.8212 (t80) cc_final: 0.7353 (t80) REVERT: A 988 MET cc_start: 0.7454 (mmm) cc_final: 0.7154 (mmm) REVERT: A 1002 LYS cc_start: 0.7470 (mtpm) cc_final: 0.6792 (tttp) REVERT: A 1012 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 1023 MET cc_start: 0.8026 (mtt) cc_final: 0.6910 (mtt) REVERT: B 466 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 627 GLU cc_start: 0.8263 (tp30) cc_final: 0.8039 (tp30) REVERT: B 697 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7691 (ptmm) REVERT: C 416 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7125 (mm-30) REVERT: C 736 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7401 (p) REVERT: C 839 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6012 (tt) REVERT: C 859 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: C 864 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6465 (tt) REVERT: C 868 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4753 (mm) REVERT: C 906 VAL cc_start: 0.5013 (OUTLIER) cc_final: 0.4607 (t) REVERT: C 924 MET cc_start: 0.5629 (mmp) cc_final: 0.5292 (mtt) REVERT: C 980 TYR cc_start: 0.8207 (t80) cc_final: 0.7498 (t80) REVERT: C 988 MET cc_start: 0.7480 (mmm) cc_final: 0.7198 (mmm) REVERT: C 1002 LYS cc_start: 0.7415 (mtpm) cc_final: 0.6779 (tttp) REVERT: C 1005 TRP cc_start: 0.6886 (p-90) cc_final: 0.6612 (p-90) REVERT: C 1012 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7423 (mp) REVERT: C 1023 MET cc_start: 0.8098 (mtt) cc_final: 0.6901 (mtt) REVERT: D 435 HIS cc_start: 0.7855 (m-70) cc_final: 0.7543 (m-70) REVERT: D 509 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7221 (tptm) REVERT: D 657 GLU cc_start: 0.7900 (tp30) cc_final: 0.7382 (mm-30) REVERT: D 678 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6432 (mm-30) REVERT: D 697 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7622 (ptmm) REVERT: D 808 LEU cc_start: 0.8481 (mt) cc_final: 0.8256 (tt) REVERT: E 87 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7412 (mm-30) outliers start: 71 outliers final: 40 residues processed: 276 average time/residue: 1.0491 time to fit residues: 334.5233 Evaluate side-chains 281 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 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 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 C residue 979 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 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 678 GLU 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 87 GLU 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 Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 95 optimal weight: 0.4980 chunk 220 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS C 411 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4071 r_free = 0.4071 target = 0.175294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129081 restraints weight = 22527.738| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.24 r_work: 0.3179 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19875 Z= 0.177 Angle : 1.034 34.538 26706 Z= 0.415 Chirality : 0.088 1.702 2866 Planarity : 0.004 0.051 3132 Dihedral : 22.082 179.467 4031 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 3.73 % Allowed : 14.61 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2226 helix: 1.62 (0.14), residues: 1286 sheet: -1.32 (0.31), residues: 242 loop : -1.90 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1005 HIS 0.009 0.001 HIS C 950 PHE 0.019 0.002 PHE D 531 TYR 0.020 0.002 TYR C1001 ARG 0.005 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 972) hydrogen bonds : angle 3.74034 ( 2844) SS BOND : bond 0.00181 ( 8) SS BOND : angle 0.42895 ( 16) covalent geometry : bond 0.00419 (19867) covalent geometry : angle 1.03430 (26690) *********************** 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 309 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7061 (m-80) cc_final: 0.6791 (m-80) REVERT: A 907 MET cc_start: 0.3139 (mmt) cc_final: 0.2591 (mmt) REVERT: A 924 MET cc_start: 0.5434 (mmp) cc_final: 0.5157 (ttt) REVERT: A 926 ARG cc_start: 0.6834 (ttt-90) cc_final: 0.5744 (tmt170) REVERT: A 958 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5712 (mt) REVERT: A 980 TYR cc_start: 0.8245 (t80) cc_final: 0.7391 (t80) REVERT: A 1002 LYS cc_start: 0.7469 (mtpm) cc_final: 0.6817 (tttp) REVERT: A 1023 MET cc_start: 0.8029 (mtt) cc_final: 0.6906 (mtt) REVERT: B 697 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7813 (ptmm) REVERT: C 416 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7148 (mm-30) REVERT: C 715 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6788 (mmp80) REVERT: C 839 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6118 (tt) REVERT: C 864 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6481 (tt) REVERT: C 868 ILE cc_start: 0.5112 (OUTLIER) cc_final: 0.4793 (mm) REVERT: C 906 VAL cc_start: 0.5000 (OUTLIER) cc_final: 0.4582 (t) REVERT: C 924 MET cc_start: 0.5671 (mmp) cc_final: 0.5324 (mtt) REVERT: C 980 TYR cc_start: 0.8249 (t80) cc_final: 0.7486 (t80) REVERT: C 988 MET cc_start: 0.7506 (mmm) cc_final: 0.7223 (mmm) REVERT: C 1002 LYS cc_start: 0.7384 (mtpm) cc_final: 0.6717 (tttp) REVERT: C 1005 TRP cc_start: 0.7058 (p-90) cc_final: 0.6799 (p-90) REVERT: C 1012 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7449 (mp) REVERT: C 1023 MET cc_start: 0.8077 (mtt) cc_final: 0.6907 (mtt) REVERT: D 435 HIS cc_start: 0.7867 (m-70) cc_final: 0.7546 (m-70) REVERT: D 509 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7266 (tptm) REVERT: D 657 GLU cc_start: 0.7891 (tp30) cc_final: 0.7430 (mm-30) REVERT: D 697 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7770 (ptmm) REVERT: D 808 LEU cc_start: 0.8494 (mt) cc_final: 0.8267 (tt) REVERT: E 87 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7409 (mm-30) outliers start: 72 outliers final: 43 residues processed: 284 average time/residue: 1.0769 time to fit residues: 352.4324 Evaluate side-chains 285 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 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 958 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1001 TYR 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 715 ARG 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 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 1001 TYR 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 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 87 GLU 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 Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 435 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4073 r_free = 0.4073 target = 0.175436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129866 restraints weight = 22669.259| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.24 r_work: 0.3187 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19875 Z= 0.176 Angle : 1.041 34.505 26706 Z= 0.417 Chirality : 0.088 1.702 2866 Planarity : 0.004 0.051 3132 Dihedral : 21.937 179.950 4031 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 3.37 % Allowed : 15.28 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2226 helix: 1.67 (0.14), residues: 1286 sheet: -1.31 (0.31), residues: 242 loop : -1.86 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1005 HIS 0.009 0.001 HIS C 950 PHE 0.019 0.002 PHE C 937 TYR 0.021 0.002 TYR C1001 ARG 0.007 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 972) hydrogen bonds : angle 3.74853 ( 2844) SS BOND : bond 0.00167 ( 8) SS BOND : angle 0.45104 ( 16) covalent geometry : bond 0.00418 (19867) covalent geometry : angle 1.04141 (26690) *********************** 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 306 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: A 860 TYR cc_start: 0.7009 (m-80) cc_final: 0.6705 (m-80) REVERT: A 907 MET cc_start: 0.2996 (mmt) cc_final: 0.2519 (mmt) REVERT: A 924 MET cc_start: 0.5296 (mmp) cc_final: 0.5032 (ttt) REVERT: A 958 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5761 (mt) REVERT: A 980 TYR cc_start: 0.8218 (t80) cc_final: 0.7381 (t80) REVERT: A 1002 LYS cc_start: 0.7458 (mtpm) cc_final: 0.6794 (tttp) REVERT: A 1012 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7568 (mp) REVERT: A 1023 MET cc_start: 0.8023 (mtt) cc_final: 0.6907 (mtt) REVERT: B 697 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7797 (ptmt) REVERT: C 416 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7050 (mm-30) REVERT: C 509 LYS cc_start: 0.6490 (mmmm) cc_final: 0.5903 (ptmm) REVERT: C 715 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6773 (mmp80) REVERT: C 839 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6143 (tt) REVERT: C 864 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6475 (tt) REVERT: C 868 ILE cc_start: 0.5159 (OUTLIER) cc_final: 0.4839 (mm) REVERT: C 906 VAL cc_start: 0.5032 (OUTLIER) cc_final: 0.4606 (t) REVERT: C 924 MET cc_start: 0.5538 (mmp) cc_final: 0.5295 (mtt) REVERT: C 980 TYR cc_start: 0.8249 (t80) cc_final: 0.7487 (t80) REVERT: C 988 MET cc_start: 0.7506 (mmm) cc_final: 0.7232 (mmm) REVERT: C 1002 LYS cc_start: 0.7456 (mtpm) cc_final: 0.6773 (tttp) REVERT: C 1005 TRP cc_start: 0.7055 (p-90) cc_final: 0.6802 (p-90) REVERT: C 1012 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7474 (mp) REVERT: D 435 HIS cc_start: 0.7858 (m-70) cc_final: 0.7534 (m-70) REVERT: D 509 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7195 (tptm) REVERT: D 657 GLU cc_start: 0.7884 (tp30) cc_final: 0.7430 (mm-30) REVERT: D 697 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7653 (ptmm) REVERT: D 808 LEU cc_start: 0.8493 (mt) cc_final: 0.8266 (tt) REVERT: E 87 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: F 132 GLN cc_start: 0.4702 (tm-30) cc_final: 0.4367 (tm130) outliers start: 65 outliers final: 42 residues processed: 283 average time/residue: 1.1476 time to fit residues: 372.5553 Evaluate side-chains 283 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 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 715 ARG 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 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 1001 TYR 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 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 87 GLU 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 Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 61 optimal weight: 0.0570 chunk 165 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 chunk 176 optimal weight: 0.0570 chunk 153 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 435 HIS B 508 GLN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133608 restraints weight = 22551.587| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.05 r_work: 0.3240 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19875 Z= 0.108 Angle : 0.991 33.261 26706 Z= 0.392 Chirality : 0.088 1.766 2866 Planarity : 0.004 0.049 3132 Dihedral : 21.495 179.968 4031 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 2.75 % Allowed : 16.37 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2226 helix: 2.14 (0.15), residues: 1286 sheet: -1.03 (0.32), residues: 240 loop : -1.78 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1005 HIS 0.010 0.001 HIS C 950 PHE 0.010 0.001 PHE A 574 TYR 0.026 0.001 TYR A1001 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 972) hydrogen bonds : angle 3.53576 ( 2844) SS BOND : bond 0.00041 ( 8) SS BOND : angle 0.50146 ( 16) covalent geometry : bond 0.00232 (19867) covalent geometry : angle 0.99167 (26690) *********************** 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 295 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 2.228 Fit side-chains REVERT: A 496 MET cc_start: 0.9394 (ttm) cc_final: 0.9143 (ttm) REVERT: A 509 LYS cc_start: 0.6175 (mmmm) cc_final: 0.5370 (mtpp) REVERT: A 591 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8174 (pp) REVERT: A 860 TYR cc_start: 0.6938 (m-80) cc_final: 0.6654 (m-80) REVERT: A 907 MET cc_start: 0.2996 (mmt) cc_final: 0.2632 (mmt) REVERT: A 924 MET cc_start: 0.5188 (mmp) cc_final: 0.4930 (ttt) REVERT: A 926 ARG cc_start: 0.6328 (ttt90) cc_final: 0.5462 (tmt170) REVERT: A 958 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5585 (mt) REVERT: A 980 TYR cc_start: 0.8044 (t80) cc_final: 0.7137 (t80) REVERT: A 1002 LYS cc_start: 0.7394 (mtpm) cc_final: 0.6728 (tttp) REVERT: A 1023 MET cc_start: 0.7928 (mtt) cc_final: 0.6774 (mtt) REVERT: B 697 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7570 (ptmm) REVERT: C 416 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7037 (mm-30) REVERT: C 509 LYS cc_start: 0.5940 (mmmm) cc_final: 0.5731 (ptmm) REVERT: C 591 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7928 (pp) REVERT: C 715 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6588 (mtp85) REVERT: C 868 ILE cc_start: 0.5257 (OUTLIER) cc_final: 0.4918 (mm) REVERT: C 906 VAL cc_start: 0.5036 (OUTLIER) cc_final: 0.4633 (t) REVERT: C 924 MET cc_start: 0.5375 (mmp) cc_final: 0.5056 (ttt) REVERT: C 980 TYR cc_start: 0.8096 (t80) cc_final: 0.7353 (t80) REVERT: C 988 MET cc_start: 0.7432 (mmm) cc_final: 0.7206 (mmm) REVERT: C 1002 LYS cc_start: 0.7341 (mtpm) cc_final: 0.6699 (tttp) REVERT: C 1005 TRP cc_start: 0.6751 (p-90) cc_final: 0.6505 (p-90) REVERT: C 1012 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7349 (mp) REVERT: D 435 HIS cc_start: 0.7816 (m-70) cc_final: 0.7479 (m-70) REVERT: D 654 SER cc_start: 0.8717 (m) cc_final: 0.8474 (p) REVERT: D 657 GLU cc_start: 0.7855 (tp30) cc_final: 0.7338 (mm-30) REVERT: D 697 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7534 (ptmm) REVERT: E 11 MET cc_start: 0.8801 (mtt) cc_final: 0.8472 (mtp) REVERT: E 87 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7419 (mm-30) outliers start: 53 outliers final: 33 residues processed: 272 average time/residue: 1.0836 time to fit residues: 340.8999 Evaluate side-chains 272 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 864 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1001 TYR 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 790 SER Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE 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 736 THR Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 1001 TYR 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 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 E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 87 GLU 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 85 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 chunk 125 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 191 optimal weight: 0.1980 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN B 435 HIS B 508 GLN C 709 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.176365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131808 restraints weight = 22585.066| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.39 r_work: 0.3182 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19875 Z= 0.161 Angle : 1.023 34.303 26706 Z= 0.409 Chirality : 0.088 1.732 2866 Planarity : 0.004 0.050 3132 Dihedral : 21.473 179.453 4029 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 2.28 % Allowed : 17.41 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 2226 helix: 1.98 (0.15), residues: 1286 sheet: -1.11 (0.32), residues: 242 loop : -1.78 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 766 HIS 0.015 0.001 HIS C 950 PHE 0.029 0.002 PHE A 937 TYR 0.024 0.002 TYR A1001 ARG 0.007 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 972) hydrogen bonds : angle 3.68673 ( 2844) SS BOND : bond 0.00162 ( 8) SS BOND : angle 0.27094 ( 16) covalent geometry : bond 0.00380 (19867) covalent geometry : angle 1.02339 (26690) ********************** 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 274 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 2.258 Fit side-chains REVERT: A 509 LYS cc_start: 0.6189 (mmmm) cc_final: 0.5408 (mtpp) REVERT: A 860 TYR cc_start: 0.7161 (m-80) cc_final: 0.6545 (m-80) REVERT: A 907 MET cc_start: 0.2958 (mmt) cc_final: 0.2616 (mmt) REVERT: A 924 MET cc_start: 0.5407 (mmp) cc_final: 0.5073 (ttt) REVERT: A 958 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5632 (mt) REVERT: A 980 TYR cc_start: 0.8185 (t80) cc_final: 0.7306 (t80) REVERT: A 1002 LYS cc_start: 0.7453 (mtpm) cc_final: 0.6774 (tttp) REVERT: A 1023 MET cc_start: 0.8020 (mtt) cc_final: 0.6897 (mtt) REVERT: B 697 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7578 (ptmm) REVERT: C 416 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7024 (mm-30) REVERT: C 591 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8099 (pp) REVERT: C 715 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6703 (mtp85) REVERT: C 868 ILE cc_start: 0.5089 (OUTLIER) cc_final: 0.4785 (mm) REVERT: C 906 VAL cc_start: 0.5026 (OUTLIER) cc_final: 0.4603 (t) REVERT: C 924 MET cc_start: 0.5466 (mmp) cc_final: 0.5231 (ttt) REVERT: C 980 TYR cc_start: 0.8212 (t80) cc_final: 0.7429 (t80) REVERT: C 988 MET cc_start: 0.7474 (mmm) cc_final: 0.7244 (mmm) REVERT: C 1002 LYS cc_start: 0.7401 (mtpm) cc_final: 0.6746 (tttp) REVERT: C 1005 TRP cc_start: 0.6922 (p-90) cc_final: 0.6637 (p-90) REVERT: C 1012 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7420 (mp) REVERT: C 1023 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.6950 (mtt) REVERT: D 435 HIS cc_start: 0.7855 (m-70) cc_final: 0.7521 (m-70) REVERT: D 657 GLU cc_start: 0.7921 (tp30) cc_final: 0.7359 (mm-30) REVERT: D 697 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7717 (ptmt) REVERT: D 816 TYR cc_start: 0.7441 (t80) cc_final: 0.7186 (t80) REVERT: E 87 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: F 132 GLN cc_start: 0.6386 (mt0) cc_final: 0.5801 (tp-100) outliers start: 44 outliers final: 33 residues processed: 258 average time/residue: 1.1132 time to fit residues: 330.1024 Evaluate side-chains 267 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 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 A residue 1001 TYR 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 790 SER Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 591 ILE 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 736 THR Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 868 ILE Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 1001 TYR Chi-restraints excluded: chain C residue 1012 ILE Chi-restraints excluded: chain C residue 1023 MET 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 E residue 64 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 87 GLU 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 129 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 222 optimal weight: 0.0770 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 183 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 435 HIS B 508 GLN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4109 r_free = 0.4109 target = 0.179292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133177 restraints weight = 22796.894| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.21 r_work: 0.3216 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19875 Z= 0.114 Angle : 0.995 33.498 26706 Z= 0.395 Chirality : 0.087 1.724 2866 Planarity : 0.004 0.049 3132 Dihedral : 21.282 179.774 4029 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 2.28 % Allowed : 17.82 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2226 helix: 2.20 (0.15), residues: 1282 sheet: -0.91 (0.32), residues: 240 loop : -1.81 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 766 HIS 0.016 0.001 HIS C 950 PHE 0.044 0.001 PHE A 937 TYR 0.026 0.001 TYR A1001 ARG 0.007 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 972) hydrogen bonds : angle 3.59844 ( 2844) SS BOND : bond 0.00056 ( 8) SS BOND : angle 0.36236 ( 16) covalent geometry : bond 0.00254 (19867) covalent geometry : angle 0.99522 (26690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12231.05 seconds wall clock time: 212 minutes 33.97 seconds (12753.97 seconds total)