Starting phenix.real_space_refine on Sat Aug 8 13:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjr_65120/08_2026/9vjr_65120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjr_65120/08_2026/9vjr_65120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vjr_65120/08_2026/9vjr_65120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjr_65120/08_2026/9vjr_65120.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjr_65120/08_2026/9vjr_65120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjr_65120/08_2026/9vjr_65120.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 S 120 5.16 5 C 18060 2.51 5 N 4500 2.21 5 O 4948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27644 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6812 Classifications: {'peptide': 839} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 818} Chain breaks: 16 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6812 Classifications: {'peptide': 839} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 818} Chain breaks: 16 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6812 Classifications: {'peptide': 839} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 818} Chain breaks: 16 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6812 Classifications: {'peptide': 839} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 818} Chain breaks: 16 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {' CA': 1, 'CLR': 1, 'KX7': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.94, per 1000 atoms: 0.21 Number of scatterers: 27644 At special positions: 0 Unit cell: (133.35, 133.35, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 120 16.00 P 12 15.00 O 4948 8.00 N 4500 7.00 C 18060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 8 sheets defined 75.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.586A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 276 through 288 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 363 through 366 removed outlier: 3.551A pdb=" N VAL A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.649A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 425 through 437 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 454 through 468 removed outlier: 5.188A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 588 through 602 Processing helix chain 'A' and resid 609 through 636 removed outlier: 3.723A pdb=" N GLU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.668A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.530A pdb=" N TRP A 651 " --> pdb=" O CYS A 648 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 652' Processing helix chain 'A' and resid 655 through 663 removed outlier: 3.701A pdb=" N ALA A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 788 removed outlier: 3.897A pdb=" N MET A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 797 through 818 Processing helix chain 'A' and resid 821 through 842 removed outlier: 3.747A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 837 " --> pdb=" O CYS A 833 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 850 removed outlier: 3.762A pdb=" N VAL A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 890 removed outlier: 4.770A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 876 " --> pdb=" O PHE A 872 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 904 through 912 removed outlier: 3.980A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 912 " --> pdb=" O TYR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 929 removed outlier: 3.973A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 955 through 969 removed outlier: 4.010A pdb=" N LEU A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 989 Processing helix chain 'A' and resid 989 through 1008 removed outlier: 4.028A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1023 removed outlier: 3.652A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1072 Processing helix chain 'A' and resid 1075 through 1104 removed outlier: 4.025A pdb=" N ARG A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.588A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 187 through 200 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 363 through 366 removed outlier: 3.531A pdb=" N VAL C 366 " --> pdb=" O PRO C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 366' Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.675A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 Processing helix chain 'C' and resid 425 through 437 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 454 through 468 removed outlier: 5.183A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 588 through 602 Processing helix chain 'C' and resid 609 through 636 removed outlier: 3.706A pdb=" N GLU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 627 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 628 " --> pdb=" O ARG C 624 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE C 629 " --> pdb=" O ALA C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 645 removed outlier: 3.668A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.529A pdb=" N TRP C 651 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.686A pdb=" N ALA C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 727 through 732 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 788 removed outlier: 3.909A pdb=" N MET C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 796 Processing helix chain 'C' and resid 797 through 818 Processing helix chain 'C' and resid 821 through 842 removed outlier: 3.743A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 837 " --> pdb=" O CYS C 833 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 850 removed outlier: 3.758A pdb=" N VAL C 849 " --> pdb=" O ILE C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 890 removed outlier: 4.806A pdb=" N ILE C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP C 866 " --> pdb=" O ARG C 862 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 867 " --> pdb=" O MET C 863 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 904 through 912 removed outlier: 4.007A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 929 removed outlier: 3.960A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 955 through 969 removed outlier: 4.018A pdb=" N LEU C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 989 Processing helix chain 'C' and resid 989 through 1008 removed outlier: 3.998A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C1002 " --> pdb=" O ARG C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1023 removed outlier: 3.654A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1072 Processing helix chain 'C' and resid 1075 through 1104 removed outlier: 4.027A pdb=" N ARG C1079 " --> pdb=" O SER C1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.588A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 363 through 366 removed outlier: 3.533A pdb=" N VAL B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 366' Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.679A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 425 through 437 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 454 through 468 removed outlier: 5.178A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 588 through 602 Processing helix chain 'B' and resid 609 through 636 removed outlier: 3.725A pdb=" N GLU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.668A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.529A pdb=" N TRP B 651 " --> pdb=" O CYS B 648 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 652 " --> pdb=" O GLU B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 652' Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.685A pdb=" N ALA B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 727 through 732 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 788 removed outlier: 3.896A pdb=" N MET B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 797 through 818 Processing helix chain 'B' and resid 821 through 842 removed outlier: 3.745A pdb=" N LEU B 825 " --> pdb=" O ASN B 821 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 837 " --> pdb=" O CYS B 833 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 850 removed outlier: 3.787A pdb=" N VAL B 849 " --> pdb=" O ILE B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 890 removed outlier: 4.789A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP B 866 " --> pdb=" O ARG B 862 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 867 " --> pdb=" O MET B 863 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B 876 " --> pdb=" O PHE B 872 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 904 through 912 removed outlier: 4.004A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.974A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 955 through 969 removed outlier: 4.019A pdb=" N LEU B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 989 Processing helix chain 'B' and resid 989 through 1008 removed outlier: 4.001A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1023 removed outlier: 3.637A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1072 Processing helix chain 'B' and resid 1075 through 1104 removed outlier: 4.031A pdb=" N ARG B1079 " --> pdb=" O SER B1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.581A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 276 through 288 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 363 through 366 removed outlier: 3.531A pdb=" N VAL D 366 " --> pdb=" O PRO D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 366' Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.708A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 Processing helix chain 'D' and resid 425 through 437 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 454 through 468 removed outlier: 5.183A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 588 through 602 Processing helix chain 'D' and resid 609 through 636 removed outlier: 3.722A pdb=" N GLU D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 627 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 628 " --> pdb=" O ARG D 624 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE D 629 " --> pdb=" O ALA D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 removed outlier: 3.668A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 removed outlier: 3.529A pdb=" N TRP D 651 " --> pdb=" O CYS D 648 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 652 " --> pdb=" O GLU D 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 652' Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.690A pdb=" N ALA D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 727 through 732 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 788 removed outlier: 3.905A pdb=" N MET D 788 " --> pdb=" O ARG D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 796 Processing helix chain 'D' and resid 797 through 818 Processing helix chain 'D' and resid 821 through 842 removed outlier: 3.747A pdb=" N LEU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 837 " --> pdb=" O CYS D 833 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 850 removed outlier: 3.760A pdb=" N VAL D 849 " --> pdb=" O ILE D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 890 removed outlier: 4.780A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP D 866 " --> pdb=" O ARG D 862 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 867 " --> pdb=" O MET D 863 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL D 876 " --> pdb=" O PHE D 872 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 912 removed outlier: 4.030A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE D 912 " --> pdb=" O TYR D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 929 removed outlier: 3.971A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 955 through 969 removed outlier: 4.011A pdb=" N LEU D 959 " --> pdb=" O ILE D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 989 Processing helix chain 'D' and resid 989 through 1008 removed outlier: 3.999A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D1002 " --> pdb=" O ARG D 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1023 removed outlier: 3.636A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1072 Processing helix chain 'D' and resid 1075 through 1104 removed outlier: 4.031A pdb=" N ARG D1079 " --> pdb=" O SER D1075 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 removed outlier: 6.664A pdb=" N LYS A 116 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 6.414A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117 removed outlier: 6.634A pdb=" N LYS C 116 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.420A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.626A pdb=" N LYS B 116 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 146 removed outlier: 6.410A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.619A pdb=" N LYS D 116 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146 removed outlier: 6.420A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) 1712 hydrogen bonds defined for protein. 5088 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: 4.70 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4344 1.30 - 1.43: 7807 1.43 - 1.56: 15925 1.56 - 1.68: 20 1.68 - 1.81: 184 Bond restraints: 28280 Sorted by residual: bond pdb=" N21 KX7 C1203 " pdb=" O22 KX7 C1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" N21 KX7 A1203 " pdb=" O22 KX7 A1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" N21 KX7 D1203 " pdb=" O22 KX7 D1203 " ideal model delta sigma weight residual 1.208 1.401 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" N21 KX7 B1203 " pdb=" O22 KX7 B1203 " ideal model delta sigma weight residual 1.208 1.400 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" C02 KX7 D1203 " pdb=" C03 KX7 D1203 " ideal model delta sigma weight residual 1.331 1.477 -0.146 2.00e-02 2.50e+03 5.30e+01 ... (remaining 28275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 37673 2.30 - 4.60: 558 4.60 - 6.91: 125 6.91 - 9.21: 16 9.21 - 11.51: 8 Bond angle restraints: 38380 Sorted by residual: angle pdb=" N VAL C 986 " pdb=" CA VAL C 986 " pdb=" CB VAL C 986 " ideal model delta sigma weight residual 110.58 116.39 -5.81 1.50e+00 4.44e-01 1.50e+01 angle pdb=" N VAL D 986 " pdb=" CA VAL D 986 " pdb=" CB VAL D 986 " ideal model delta sigma weight residual 110.58 116.36 -5.78 1.50e+00 4.44e-01 1.48e+01 angle pdb=" O11 PIO A1201 " pdb=" P1 PIO A1201 " pdb=" O12 PIO A1201 " ideal model delta sigma weight residual 121.09 109.58 11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O11 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O12 PIO D1201 " ideal model delta sigma weight residual 121.09 109.59 11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O11 PIO C1201 " pdb=" P1 PIO C1201 " pdb=" O12 PIO C1201 " ideal model delta sigma weight residual 121.09 109.62 11.47 3.00e+00 1.11e-01 1.46e+01 ... (remaining 38375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14377 17.92 - 35.84: 1753 35.84 - 53.76: 427 53.76 - 71.68: 104 71.68 - 89.60: 15 Dihedral angle restraints: 16676 sinusoidal: 6764 harmonic: 9912 Sorted by residual: dihedral pdb=" CA TRP A 137 " pdb=" C TRP A 137 " pdb=" N HIS A 138 " pdb=" CA HIS A 138 " ideal model delta harmonic sigma weight residual 180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP C 137 " pdb=" C TRP C 137 " pdb=" N HIS C 138 " pdb=" CA HIS C 138 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP B 137 " pdb=" C TRP B 137 " pdb=" N HIS B 138 " pdb=" CA HIS B 138 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 16673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3771 0.060 - 0.119: 520 0.119 - 0.179: 45 0.179 - 0.239: 17 0.239 - 0.298: 3 Chirality restraints: 4356 Sorted by residual: chirality pdb=" CG LEU B 974 " pdb=" CB LEU B 974 " pdb=" CD1 LEU B 974 " pdb=" CD2 LEU B 974 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CG LEU A 974 " pdb=" CB LEU A 974 " pdb=" CD1 LEU A 974 " pdb=" CD2 LEU A 974 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA VAL C 915 " pdb=" N VAL C 915 " pdb=" C VAL C 915 " pdb=" CB VAL C 915 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 4353 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 854 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 855 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 855 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 855 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 854 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 855 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 855 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 855 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 854 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO C 855 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 855 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 855 " -0.028 5.00e-02 4.00e+02 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2253 2.74 - 3.28: 27191 3.28 - 3.82: 46014 3.82 - 4.36: 49439 4.36 - 4.90: 89978 Nonbonded interactions: 214875 Sorted by model distance: nonbonded pdb=" O VAL C 986 " pdb=" N ASN C 990 " model vdw 2.204 3.120 nonbonded pdb=" O VAL D 986 " pdb=" N ASN D 990 " model vdw 2.329 3.120 nonbonded pdb=" O VAL B 986 " pdb=" N ASN B 990 " model vdw 2.377 3.120 nonbonded pdb=" O VAL A 986 " pdb=" N ASN A 990 " model vdw 2.383 3.120 nonbonded pdb=" O ASN C 989 " pdb=" N GLN C 992 " model vdw 2.392 3.120 ... (remaining 214870 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.005 0.193 28284 Z= 0.297 Angle : 0.683 11.509 38388 Z= 0.376 Chirality : 0.041 0.298 4356 Planarity : 0.004 0.050 4692 Dihedral : 16.745 89.600 10184 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.78 % Allowed : 24.76 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.15), residues: 3220 helix: 1.99 (0.11), residues: 2388 sheet: 0.89 (0.78), residues: 52 loop : -0.68 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 278 TYR 0.017 0.001 TYR C 170 PHE 0.030 0.001 PHE B 868 TRP 0.016 0.001 TRP C 786 HIS 0.006 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.30 (28280) covalent geometry : angle 0.68353 / 0.38 (38380) SS BOND : bond 0.00066 / 0.04 ( 4) SS BOND : angle 0.32298 / 0.16 ( 8) hydrogen bonds : bond 0.08776 / 5.85 ( 1712) hydrogen bonds : angle 4.49571 / 3.25 ( 5088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 444 time to evaluate : 1.021 Fit side-chains REVERT: A 117 TYR cc_start: 0.7428 (p90) cc_final: 0.6777 (p90) REVERT: A 144 LEU cc_start: 0.8627 (tp) cc_final: 0.8383 (tp) REVERT: A 258 THR cc_start: 0.8992 (m) cc_final: 0.8688 (p) REVERT: A 694 LYS cc_start: 0.8327 (mttt) cc_final: 0.7619 (tttm) REVERT: A 697 LEU cc_start: 0.7453 (mp) cc_final: 0.6987 (tt) REVERT: A 919 VAL cc_start: 0.6872 (m) cc_final: 0.6633 (m) REVERT: A 1056 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: C 117 TYR cc_start: 0.7495 (p90) cc_final: 0.6698 (p90) REVERT: C 144 LEU cc_start: 0.8634 (tp) cc_final: 0.8386 (tp) REVERT: C 258 THR cc_start: 0.8994 (m) cc_final: 0.8694 (p) REVERT: C 694 LYS cc_start: 0.8333 (mttt) cc_final: 0.7624 (tttm) REVERT: C 697 LEU cc_start: 0.7454 (mp) cc_final: 0.7005 (tt) REVERT: C 919 VAL cc_start: 0.6907 (m) cc_final: 0.6639 (m) REVERT: C 1056 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: B 117 TYR cc_start: 0.7487 (p90) cc_final: 0.6686 (p90) REVERT: B 144 LEU cc_start: 0.8608 (tp) cc_final: 0.8364 (tp) REVERT: B 258 THR cc_start: 0.8952 (m) cc_final: 0.8656 (p) REVERT: B 495 GLU cc_start: 0.8340 (tp30) cc_final: 0.7938 (tp30) REVERT: B 694 LYS cc_start: 0.8299 (mttt) cc_final: 0.7591 (tttm) REVERT: B 697 LEU cc_start: 0.7426 (mp) cc_final: 0.6967 (tt) REVERT: B 919 VAL cc_start: 0.6930 (m) cc_final: 0.6673 (m) REVERT: B 1056 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8306 (tp30) REVERT: D 117 TYR cc_start: 0.7482 (p90) cc_final: 0.6664 (p90) REVERT: D 144 LEU cc_start: 0.8630 (tp) cc_final: 0.8382 (tp) REVERT: D 258 THR cc_start: 0.8963 (m) cc_final: 0.8662 (p) REVERT: D 495 GLU cc_start: 0.8269 (tp30) cc_final: 0.7934 (tp30) REVERT: D 694 LYS cc_start: 0.8321 (mttt) cc_final: 0.7615 (tttm) REVERT: D 697 LEU cc_start: 0.7438 (mp) cc_final: 0.6991 (tt) REVERT: D 919 VAL cc_start: 0.6927 (m) cc_final: 0.6681 (m) REVERT: D 1056 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8312 (tp30) outliers start: 52 outliers final: 39 residues processed: 482 average time/residue: 0.1546 time to fit residues: 123.6805 Evaluate side-chains 464 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 421 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1056 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 934 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1056 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 934 ASN Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1056 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 789 ASN B 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116844 restraints weight = 37785.024| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.65 r_work: 0.3292 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28284 Z= 0.122 Angle : 0.451 7.887 38388 Z= 0.233 Chirality : 0.036 0.152 4356 Planarity : 0.004 0.049 4692 Dihedral : 6.899 55.217 4009 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.51 % Allowed : 21.41 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.15), residues: 3220 helix: 2.07 (0.11), residues: 2376 sheet: 1.03 (0.66), residues: 72 loop : -0.78 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 998 TYR 0.013 0.001 TYR A 981 PHE 0.023 0.001 PHE B 752 TRP 0.016 0.001 TRP C 786 HIS 0.004 0.001 HIS D 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (28280) covalent geometry : angle 0.45100 / 0.23 (38380) SS BOND : bond 0.00029 / 0.02 ( 4) SS BOND : angle 0.31618 / 0.16 ( 8) hydrogen bonds : bond 0.03759 / 2.52 ( 1712) hydrogen bonds : angle 3.82780 / 2.73 ( 5088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 420 time to evaluate : 0.930 Fit side-chains REVERT: A 117 TYR cc_start: 0.7382 (p90) cc_final: 0.6727 (p90) REVERT: A 144 LEU cc_start: 0.8400 (tp) cc_final: 0.8169 (tp) REVERT: A 258 THR cc_start: 0.9054 (m) cc_final: 0.8663 (p) REVERT: A 694 LYS cc_start: 0.8337 (mttt) cc_final: 0.7660 (tttm) REVERT: C 117 TYR cc_start: 0.7458 (p90) cc_final: 0.6640 (p90) REVERT: C 144 LEU cc_start: 0.8405 (tp) cc_final: 0.8165 (tp) REVERT: C 258 THR cc_start: 0.9067 (m) cc_final: 0.8682 (p) REVERT: C 694 LYS cc_start: 0.8310 (mttt) cc_final: 0.7636 (tttm) REVERT: B 117 TYR cc_start: 0.7454 (p90) cc_final: 0.6633 (p90) REVERT: B 144 LEU cc_start: 0.8390 (tp) cc_final: 0.8154 (tp) REVERT: B 258 THR cc_start: 0.9080 (m) cc_final: 0.8687 (p) REVERT: B 694 LYS cc_start: 0.8313 (mttt) cc_final: 0.7640 (tttm) REVERT: D 117 TYR cc_start: 0.7448 (p90) cc_final: 0.6624 (p90) REVERT: D 144 LEU cc_start: 0.8403 (tp) cc_final: 0.8160 (tp) REVERT: D 258 THR cc_start: 0.9070 (m) cc_final: 0.8665 (p) REVERT: D 694 LYS cc_start: 0.8328 (mttt) cc_final: 0.7652 (tttm) outliers start: 132 outliers final: 77 residues processed: 534 average time/residue: 0.1417 time to fit residues: 125.6594 Evaluate side-chains 481 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 404 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 191 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 821 ASN A 861 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117712 restraints weight = 37812.664| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.66 r_work: 0.3307 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 28284 Z= 0.100 Angle : 0.429 6.613 38388 Z= 0.221 Chirality : 0.035 0.125 4356 Planarity : 0.003 0.049 4692 Dihedral : 6.039 54.693 3960 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.97 % Allowed : 22.37 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.15), residues: 3220 helix: 2.19 (0.11), residues: 2376 sheet: 1.18 (0.67), residues: 72 loop : -0.73 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 223 TYR 0.012 0.001 TYR B 191 PHE 0.018 0.001 PHE D 868 TRP 0.014 0.001 TRP C 786 HIS 0.002 0.001 HIS C 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (28280) covalent geometry : angle 0.42861 / 0.22 (38380) SS BOND : bond 0.00017 / 0.01 ( 4) SS BOND : angle 0.28434 / 0.14 ( 8) hydrogen bonds : bond 0.03442 / 2.30 ( 1712) hydrogen bonds : angle 3.70928 / 2.64 ( 5088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 427 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7393 (p90) cc_final: 0.6745 (p90) REVERT: A 144 LEU cc_start: 0.8364 (tp) cc_final: 0.8121 (tp) REVERT: A 258 THR cc_start: 0.9009 (m) cc_final: 0.8621 (p) REVERT: A 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: A 495 GLU cc_start: 0.8198 (tp30) cc_final: 0.7808 (tp30) REVERT: A 694 LYS cc_start: 0.8307 (mttt) cc_final: 0.7642 (tttm) REVERT: C 117 TYR cc_start: 0.7440 (p90) cc_final: 0.6625 (p90) REVERT: C 144 LEU cc_start: 0.8367 (tp) cc_final: 0.8117 (tp) REVERT: C 258 THR cc_start: 0.9023 (m) cc_final: 0.8638 (p) REVERT: C 356 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: C 495 GLU cc_start: 0.8192 (tp30) cc_final: 0.7802 (tp30) REVERT: C 694 LYS cc_start: 0.8286 (mttt) cc_final: 0.7622 (tttm) REVERT: C 796 ASP cc_start: 0.8188 (t0) cc_final: 0.7773 (t70) REVERT: B 117 TYR cc_start: 0.7442 (p90) cc_final: 0.6622 (p90) REVERT: B 144 LEU cc_start: 0.8358 (tp) cc_final: 0.8109 (tp) REVERT: B 258 THR cc_start: 0.9028 (m) cc_final: 0.8639 (p) REVERT: B 356 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8507 (pt0) REVERT: B 694 LYS cc_start: 0.8292 (mttt) cc_final: 0.7629 (tttm) REVERT: B 796 ASP cc_start: 0.8261 (t0) cc_final: 0.7852 (t70) REVERT: B 1008 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7109 (ptp-170) REVERT: D 117 TYR cc_start: 0.7416 (p90) cc_final: 0.6613 (p90) REVERT: D 144 LEU cc_start: 0.8363 (tp) cc_final: 0.8112 (tp) REVERT: D 258 THR cc_start: 0.9026 (m) cc_final: 0.8634 (p) REVERT: D 356 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8511 (pt0) REVERT: D 694 LYS cc_start: 0.8312 (mttt) cc_final: 0.7646 (tttm) REVERT: D 796 ASP cc_start: 0.8280 (t0) cc_final: 0.7871 (t70) REVERT: D 1008 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7134 (ptp-170) outliers start: 116 outliers final: 67 residues processed: 526 average time/residue: 0.1542 time to fit residues: 132.9750 Evaluate side-chains 483 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 410 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 222 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 112 optimal weight: 0.0670 chunk 94 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN C 427 ASN D 427 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.171514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118632 restraints weight = 36855.250| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.54 r_work: 0.3300 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28284 Z= 0.122 Angle : 0.443 6.840 38388 Z= 0.227 Chirality : 0.035 0.129 4356 Planarity : 0.003 0.048 4692 Dihedral : 6.042 54.257 3960 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.79 % Allowed : 21.82 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.15), residues: 3220 helix: 2.19 (0.11), residues: 2376 sheet: 1.19 (0.66), residues: 72 loop : -0.75 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 842 TYR 0.018 0.001 TYR D 981 PHE 0.019 0.001 PHE C 868 TRP 0.014 0.001 TRP C 786 HIS 0.007 0.001 HIS C 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (28280) covalent geometry : angle 0.44283 / 0.23 (38380) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.32889 / 0.16 ( 8) hydrogen bonds : bond 0.03609 / 2.41 ( 1712) hydrogen bonds : angle 3.72206 / 2.65 ( 5088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 429 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7396 (p90) cc_final: 0.6762 (p90) REVERT: A 144 LEU cc_start: 0.8414 (tp) cc_final: 0.8155 (tp) REVERT: A 258 THR cc_start: 0.9016 (m) cc_final: 0.8629 (p) REVERT: A 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: A 694 LYS cc_start: 0.8382 (mttt) cc_final: 0.7677 (tttm) REVERT: A 697 LEU cc_start: 0.7511 (mp) cc_final: 0.7046 (tt) REVERT: A 1008 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7030 (ptp-170) REVERT: C 117 TYR cc_start: 0.7452 (p90) cc_final: 0.6634 (p90) REVERT: C 144 LEU cc_start: 0.8414 (tp) cc_final: 0.8148 (tp) REVERT: C 258 THR cc_start: 0.9027 (m) cc_final: 0.8644 (p) REVERT: C 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (pt0) REVERT: C 694 LYS cc_start: 0.8373 (mttt) cc_final: 0.7679 (tttm) REVERT: C 796 ASP cc_start: 0.8276 (t0) cc_final: 0.7888 (t70) REVERT: C 970 LEU cc_start: 0.7831 (tp) cc_final: 0.7628 (tp) REVERT: C 1008 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7029 (ptp-170) REVERT: B 117 TYR cc_start: 0.7450 (p90) cc_final: 0.6622 (p90) REVERT: B 144 LEU cc_start: 0.8410 (tp) cc_final: 0.8148 (tp) REVERT: B 258 THR cc_start: 0.9029 (m) cc_final: 0.8644 (p) REVERT: B 356 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: B 495 GLU cc_start: 0.8201 (tp30) cc_final: 0.7682 (tp30) REVERT: B 694 LYS cc_start: 0.8377 (mttt) cc_final: 0.7684 (tttm) REVERT: B 795 THR cc_start: 0.8505 (t) cc_final: 0.8280 (p) REVERT: B 1008 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7013 (ptp-170) REVERT: D 117 TYR cc_start: 0.7427 (p90) cc_final: 0.6623 (p90) REVERT: D 144 LEU cc_start: 0.8417 (tp) cc_final: 0.8151 (tp) REVERT: D 258 THR cc_start: 0.9033 (m) cc_final: 0.8645 (p) REVERT: D 356 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8511 (pt0) REVERT: D 495 GLU cc_start: 0.8209 (tp30) cc_final: 0.7709 (tp30) REVERT: D 694 LYS cc_start: 0.8384 (mttt) cc_final: 0.7688 (tttm) REVERT: D 795 THR cc_start: 0.8345 (t) cc_final: 0.8134 (p) REVERT: D 796 ASP cc_start: 0.8310 (t0) cc_final: 0.7882 (t70) REVERT: D 1008 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7015 (ptp-170) outliers start: 140 outliers final: 96 residues processed: 556 average time/residue: 0.1536 time to fit residues: 141.5915 Evaluate side-chains 517 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 413 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 240 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 175 optimal weight: 0.0060 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 821 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116370 restraints weight = 37007.286| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.54 r_work: 0.3271 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28284 Z= 0.165 Angle : 0.485 8.774 38388 Z= 0.249 Chirality : 0.037 0.151 4356 Planarity : 0.004 0.047 4692 Dihedral : 6.160 53.607 3960 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.10 % Allowed : 21.79 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.15), residues: 3220 helix: 2.07 (0.11), residues: 2376 sheet: 1.04 (0.66), residues: 72 loop : -0.82 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 842 TYR 0.014 0.001 TYR D 191 PHE 0.024 0.001 PHE B 868 TRP 0.016 0.001 TRP C 786 HIS 0.005 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (28280) covalent geometry : angle 0.48461 / 0.25 (38380) SS BOND : bond 0.00072 / 0.04 ( 4) SS BOND : angle 0.40638 / 0.20 ( 8) hydrogen bonds : bond 0.04111 / 2.74 ( 1712) hydrogen bonds : angle 3.84541 / 2.74 ( 5088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 429 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7416 (p90) cc_final: 0.6729 (p90) REVERT: A 144 LEU cc_start: 0.8515 (tp) cc_final: 0.8228 (tp) REVERT: A 258 THR cc_start: 0.9037 (m) cc_final: 0.8658 (p) REVERT: A 356 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: A 451 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5614 (ptt-90) REVERT: A 495 GLU cc_start: 0.8224 (tp30) cc_final: 0.7690 (tp30) REVERT: A 694 LYS cc_start: 0.8375 (mttt) cc_final: 0.7677 (tttm) REVERT: A 697 LEU cc_start: 0.7534 (mp) cc_final: 0.7076 (tt) REVERT: A 1008 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6949 (ptp-170) REVERT: C 117 TYR cc_start: 0.7504 (p90) cc_final: 0.6656 (p90) REVERT: C 144 LEU cc_start: 0.8525 (tp) cc_final: 0.8227 (tp) REVERT: C 258 THR cc_start: 0.9051 (m) cc_final: 0.8677 (p) REVERT: C 356 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: C 495 GLU cc_start: 0.8215 (tp30) cc_final: 0.7680 (tp30) REVERT: C 694 LYS cc_start: 0.8359 (mttt) cc_final: 0.7663 (tttm) REVERT: C 697 LEU cc_start: 0.7517 (mp) cc_final: 0.7061 (tt) REVERT: C 796 ASP cc_start: 0.8263 (t0) cc_final: 0.7886 (t70) REVERT: C 1008 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6958 (ptp-170) REVERT: B 117 TYR cc_start: 0.7508 (p90) cc_final: 0.6655 (p90) REVERT: B 144 LEU cc_start: 0.8522 (tp) cc_final: 0.8228 (tp) REVERT: B 258 THR cc_start: 0.9048 (m) cc_final: 0.8673 (p) REVERT: B 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: B 694 LYS cc_start: 0.8371 (mttt) cc_final: 0.7675 (tttm) REVERT: B 697 LEU cc_start: 0.7530 (mp) cc_final: 0.7071 (tt) REVERT: B 1008 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6874 (ptp-170) REVERT: D 117 TYR cc_start: 0.7507 (p90) cc_final: 0.6662 (p90) REVERT: D 144 LEU cc_start: 0.8515 (tp) cc_final: 0.8226 (tp) REVERT: D 258 THR cc_start: 0.9054 (m) cc_final: 0.8677 (p) REVERT: D 356 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: D 694 LYS cc_start: 0.8369 (mttt) cc_final: 0.7671 (tttm) REVERT: D 697 LEU cc_start: 0.7525 (mp) cc_final: 0.7073 (tt) REVERT: D 1008 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6866 (ptp-170) outliers start: 149 outliers final: 95 residues processed: 556 average time/residue: 0.1559 time to fit residues: 141.7967 Evaluate side-chains 515 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 411 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 ARG Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 102 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 821 ASN D 821 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118129 restraints weight = 37612.766| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.65 r_work: 0.3305 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28284 Z= 0.102 Angle : 0.448 7.960 38388 Z= 0.229 Chirality : 0.035 0.145 4356 Planarity : 0.003 0.049 4692 Dihedral : 5.973 53.831 3960 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.07 % Allowed : 23.22 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.15), residues: 3220 helix: 2.21 (0.11), residues: 2376 sheet: 0.83 (0.80), residues: 52 loop : -0.68 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 842 TYR 0.021 0.001 TYR C 981 PHE 0.028 0.001 PHE C 868 TRP 0.019 0.001 TRP C 786 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (28280) covalent geometry : angle 0.44798 / 0.23 (38380) SS BOND : bond 0.00028 / 0.02 ( 4) SS BOND : angle 0.31088 / 0.15 ( 8) hydrogen bonds : bond 0.03441 / 2.30 ( 1712) hydrogen bonds : angle 3.70181 / 2.64 ( 5088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 424 time to evaluate : 1.047 Fit side-chains REVERT: A 117 TYR cc_start: 0.7442 (p90) cc_final: 0.6753 (p90) REVERT: A 144 LEU cc_start: 0.8402 (tp) cc_final: 0.8137 (tp) REVERT: A 258 THR cc_start: 0.8969 (m) cc_final: 0.8584 (p) REVERT: A 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8519 (pt0) REVERT: A 694 LYS cc_start: 0.8342 (mttt) cc_final: 0.7637 (tttm) REVERT: A 697 LEU cc_start: 0.7432 (mp) cc_final: 0.7007 (tt) REVERT: A 796 ASP cc_start: 0.8238 (t0) cc_final: 0.7823 (t70) REVERT: A 1008 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7017 (ptp-170) REVERT: C 117 TYR cc_start: 0.7445 (p90) cc_final: 0.6627 (p90) REVERT: C 144 LEU cc_start: 0.8414 (tp) cc_final: 0.8138 (tp) REVERT: C 258 THR cc_start: 0.8993 (m) cc_final: 0.8613 (p) REVERT: C 356 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: C 694 LYS cc_start: 0.8324 (mttt) cc_final: 0.7615 (tttm) REVERT: C 697 LEU cc_start: 0.7409 (mp) cc_final: 0.6962 (tt) REVERT: C 796 ASP cc_start: 0.8205 (t0) cc_final: 0.7791 (t70) REVERT: C 1008 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7070 (ptp-170) REVERT: B 117 TYR cc_start: 0.7447 (p90) cc_final: 0.6621 (p90) REVERT: B 144 LEU cc_start: 0.8394 (tp) cc_final: 0.8132 (tp) REVERT: B 258 THR cc_start: 0.8979 (m) cc_final: 0.8595 (p) REVERT: B 356 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: B 694 LYS cc_start: 0.8337 (mttt) cc_final: 0.7627 (tttm) REVERT: B 697 LEU cc_start: 0.7424 (mp) cc_final: 0.6974 (tt) REVERT: B 796 ASP cc_start: 0.8292 (t0) cc_final: 0.7910 (t70) REVERT: B 970 LEU cc_start: 0.7797 (tp) cc_final: 0.7584 (tp) REVERT: B 1008 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7065 (ptp-170) REVERT: D 117 TYR cc_start: 0.7459 (p90) cc_final: 0.6649 (p90) REVERT: D 144 LEU cc_start: 0.8404 (tp) cc_final: 0.8135 (tp) REVERT: D 258 THR cc_start: 0.8990 (m) cc_final: 0.8612 (p) REVERT: D 356 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8519 (pt0) REVERT: D 694 LYS cc_start: 0.8344 (mttt) cc_final: 0.7637 (tttm) REVERT: D 697 LEU cc_start: 0.7433 (mp) cc_final: 0.6983 (tt) REVERT: D 796 ASP cc_start: 0.8258 (t0) cc_final: 0.7844 (t70) REVERT: D 1008 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7065 (ptp-170) outliers start: 119 outliers final: 78 residues processed: 527 average time/residue: 0.1695 time to fit residues: 146.0190 Evaluate side-chains 489 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 403 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 92 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115883 restraints weight = 37025.973| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.54 r_work: 0.3272 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28284 Z= 0.179 Angle : 0.508 8.034 38388 Z= 0.262 Chirality : 0.037 0.163 4356 Planarity : 0.004 0.047 4692 Dihedral : 6.167 53.533 3960 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.92 % Allowed : 22.40 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.15), residues: 3220 helix: 2.04 (0.11), residues: 2376 sheet: 1.10 (0.66), residues: 72 loop : -0.81 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 842 TYR 0.013 0.001 TYR A 191 PHE 0.029 0.002 PHE A 868 TRP 0.021 0.001 TRP C 786 HIS 0.008 0.001 HIS D 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (28280) covalent geometry : angle 0.50814 / 0.26 (38380) SS BOND : bond 0.00074 / 0.04 ( 4) SS BOND : angle 0.41202 / 0.20 ( 8) hydrogen bonds : bond 0.04194 / 2.80 ( 1712) hydrogen bonds : angle 3.86246 / 2.75 ( 5088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 420 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7414 (p90) cc_final: 0.6710 (p90) REVERT: A 144 LEU cc_start: 0.8537 (tp) cc_final: 0.8238 (tp) REVERT: A 258 THR cc_start: 0.9030 (m) cc_final: 0.8653 (p) REVERT: A 356 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: A 694 LYS cc_start: 0.8370 (mttt) cc_final: 0.7668 (tttm) REVERT: A 697 LEU cc_start: 0.7547 (mp) cc_final: 0.7090 (tt) REVERT: A 1008 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6850 (ptp-170) REVERT: A 1056 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8273 (tp30) REVERT: C 117 TYR cc_start: 0.7502 (p90) cc_final: 0.6655 (p90) REVERT: C 144 LEU cc_start: 0.8536 (tp) cc_final: 0.8232 (tp) REVERT: C 258 THR cc_start: 0.9041 (m) cc_final: 0.8668 (p) REVERT: C 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: C 694 LYS cc_start: 0.8359 (mttt) cc_final: 0.7657 (tttm) REVERT: C 697 LEU cc_start: 0.7518 (mp) cc_final: 0.7065 (tt) REVERT: C 796 ASP cc_start: 0.8245 (t0) cc_final: 0.7869 (t70) REVERT: C 1008 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6854 (ptp-170) REVERT: C 1056 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: B 117 TYR cc_start: 0.7499 (p90) cc_final: 0.6767 (p90) REVERT: B 119 ARG cc_start: 0.4071 (OUTLIER) cc_final: 0.2166 (ptp90) REVERT: B 144 LEU cc_start: 0.8535 (tp) cc_final: 0.8240 (tp) REVERT: B 258 THR cc_start: 0.9036 (m) cc_final: 0.8660 (p) REVERT: B 356 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: B 694 LYS cc_start: 0.8363 (mttt) cc_final: 0.7664 (tttm) REVERT: B 697 LEU cc_start: 0.7523 (mp) cc_final: 0.7066 (tt) REVERT: B 1008 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6853 (ptp-170) REVERT: B 1056 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: D 117 TYR cc_start: 0.7510 (p90) cc_final: 0.6770 (p90) REVERT: D 119 ARG cc_start: 0.3741 (OUTLIER) cc_final: 0.1992 (ptp90) REVERT: D 144 LEU cc_start: 0.8537 (tp) cc_final: 0.8236 (tp) REVERT: D 258 THR cc_start: 0.9040 (m) cc_final: 0.8664 (p) REVERT: D 356 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: D 694 LYS cc_start: 0.8376 (mttt) cc_final: 0.7675 (tttm) REVERT: D 697 LEU cc_start: 0.7536 (mp) cc_final: 0.7081 (tt) REVERT: D 796 ASP cc_start: 0.8301 (t0) cc_final: 0.7914 (t70) REVERT: D 1008 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6851 (ptp-170) REVERT: D 1056 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8226 (tp30) outliers start: 144 outliers final: 99 residues processed: 542 average time/residue: 0.1695 time to fit residues: 150.2181 Evaluate side-chains 514 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 401 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1056 GLU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1056 GLU Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1056 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.172754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120016 restraints weight = 36778.756| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.55 r_work: 0.3310 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28284 Z= 0.105 Angle : 0.466 8.062 38388 Z= 0.238 Chirality : 0.035 0.156 4356 Planarity : 0.003 0.048 4692 Dihedral : 5.987 53.666 3960 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.49 % Allowed : 23.67 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.15), residues: 3220 helix: 2.19 (0.11), residues: 2376 sheet: 0.85 (0.80), residues: 52 loop : -0.64 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 842 TYR 0.023 0.001 TYR C 981 PHE 0.029 0.001 PHE A 868 TRP 0.018 0.001 TRP C 786 HIS 0.004 0.001 HIS D 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (28280) covalent geometry : angle 0.46612 / 0.24 (38380) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.30980 / 0.15 ( 8) hydrogen bonds : bond 0.03468 / 2.32 ( 1712) hydrogen bonds : angle 3.71515 / 2.64 ( 5088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 420 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7614 (p90) cc_final: 0.6870 (p90) REVERT: A 144 LEU cc_start: 0.8444 (tp) cc_final: 0.8169 (tp) REVERT: A 258 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 356 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: A 694 LYS cc_start: 0.8371 (mttt) cc_final: 0.7670 (tttm) REVERT: A 796 ASP cc_start: 0.8244 (t0) cc_final: 0.7824 (t70) REVERT: A 1008 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7057 (ptp-170) REVERT: C 117 TYR cc_start: 0.7458 (p90) cc_final: 0.6762 (p90) REVERT: C 119 ARG cc_start: 0.3960 (OUTLIER) cc_final: 0.2090 (ptp90) REVERT: C 144 LEU cc_start: 0.8453 (tp) cc_final: 0.8176 (tp) REVERT: C 258 THR cc_start: 0.8999 (m) cc_final: 0.8622 (p) REVERT: C 356 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: C 694 LYS cc_start: 0.8356 (mttt) cc_final: 0.7646 (tttm) REVERT: C 697 LEU cc_start: 0.7455 (mp) cc_final: 0.6991 (tt) REVERT: C 796 ASP cc_start: 0.8198 (t0) cc_final: 0.7794 (t70) REVERT: C 1008 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7114 (ptp-170) REVERT: B 117 TYR cc_start: 0.7459 (p90) cc_final: 0.6754 (p90) REVERT: B 119 ARG cc_start: 0.3931 (OUTLIER) cc_final: 0.2009 (ptp90) REVERT: B 144 LEU cc_start: 0.8429 (tp) cc_final: 0.8163 (tp) REVERT: B 258 THR cc_start: 0.8986 (m) cc_final: 0.8613 (p) REVERT: B 356 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: B 621 TYR cc_start: 0.8620 (m-80) cc_final: 0.8408 (m-80) REVERT: B 694 LYS cc_start: 0.8361 (mttt) cc_final: 0.7651 (tttm) REVERT: B 697 LEU cc_start: 0.7457 (mp) cc_final: 0.6995 (tt) REVERT: B 796 ASP cc_start: 0.8285 (t0) cc_final: 0.7900 (t70) REVERT: B 1008 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7050 (ptp-170) REVERT: D 117 TYR cc_start: 0.7459 (p90) cc_final: 0.6753 (p90) REVERT: D 119 ARG cc_start: 0.3607 (OUTLIER) cc_final: 0.1839 (ptp90) REVERT: D 144 LEU cc_start: 0.8439 (tp) cc_final: 0.8163 (tp) REVERT: D 258 THR cc_start: 0.8989 (m) cc_final: 0.8614 (p) REVERT: D 356 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: D 694 LYS cc_start: 0.8374 (mttt) cc_final: 0.7662 (tttm) REVERT: D 697 LEU cc_start: 0.7478 (mp) cc_final: 0.7013 (tt) REVERT: D 796 ASP cc_start: 0.8256 (t0) cc_final: 0.7851 (t70) REVERT: D 1008 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7083 (ptp-170) REVERT: D 1056 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8226 (tp30) outliers start: 102 outliers final: 75 residues processed: 512 average time/residue: 0.1654 time to fit residues: 137.5489 Evaluate side-chains 493 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 405 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1056 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 54 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115976 restraints weight = 36893.043| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.53 r_work: 0.3267 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28284 Z= 0.191 Angle : 0.531 7.432 38388 Z= 0.273 Chirality : 0.038 0.175 4356 Planarity : 0.004 0.047 4692 Dihedral : 6.224 53.920 3960 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.80 % Allowed : 23.08 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.15), residues: 3220 helix: 1.99 (0.11), residues: 2380 sheet: 1.10 (0.66), residues: 72 loop : -0.79 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 842 TYR 0.024 0.001 TYR B 981 PHE 0.030 0.002 PHE A 868 TRP 0.027 0.001 TRP C 786 HIS 0.011 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (28280) covalent geometry : angle 0.53086 / 0.27 (38380) SS BOND : bond 0.00087 / 0.05 ( 4) SS BOND : angle 0.40293 / 0.20 ( 8) hydrogen bonds : bond 0.04302 / 2.87 ( 1712) hydrogen bonds : angle 3.89158 / 2.77 ( 5088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 404 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7423 (p90) cc_final: 0.6733 (p90) REVERT: A 144 LEU cc_start: 0.8538 (tp) cc_final: 0.8232 (tp) REVERT: A 258 THR cc_start: 0.9034 (m) cc_final: 0.8660 (p) REVERT: A 356 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: A 694 LYS cc_start: 0.8394 (mttt) cc_final: 0.7688 (tttm) REVERT: A 697 LEU cc_start: 0.7611 (mp) cc_final: 0.7161 (tt) REVERT: A 1008 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6718 (ptp-170) REVERT: A 1056 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: C 117 TYR cc_start: 0.7481 (p90) cc_final: 0.6761 (p90) REVERT: C 119 ARG cc_start: 0.4037 (OUTLIER) cc_final: 0.2169 (ptp90) REVERT: C 144 LEU cc_start: 0.8537 (tp) cc_final: 0.8238 (tp) REVERT: C 258 THR cc_start: 0.9044 (m) cc_final: 0.8672 (p) REVERT: C 356 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: C 694 LYS cc_start: 0.8378 (mttt) cc_final: 0.7671 (tttm) REVERT: C 697 LEU cc_start: 0.7535 (mp) cc_final: 0.7108 (tt) REVERT: C 796 ASP cc_start: 0.8236 (t0) cc_final: 0.7856 (t70) REVERT: C 1008 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6745 (ptp-170) REVERT: C 1056 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: B 117 TYR cc_start: 0.7480 (p90) cc_final: 0.6837 (p90) REVERT: B 119 ARG cc_start: 0.4087 (OUTLIER) cc_final: 0.2159 (ptp90) REVERT: B 144 LEU cc_start: 0.8540 (tp) cc_final: 0.8240 (tp) REVERT: B 258 THR cc_start: 0.9043 (m) cc_final: 0.8670 (p) REVERT: B 356 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: B 694 LYS cc_start: 0.8383 (mttt) cc_final: 0.7678 (tttm) REVERT: B 697 LEU cc_start: 0.7539 (mp) cc_final: 0.7108 (tt) REVERT: B 796 ASP cc_start: 0.8270 (t0) cc_final: 0.7886 (t70) REVERT: B 1008 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6777 (ptp-170) REVERT: B 1056 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: D 117 TYR cc_start: 0.7516 (p90) cc_final: 0.6768 (p90) REVERT: D 119 ARG cc_start: 0.3782 (OUTLIER) cc_final: 0.2092 (ptp90) REVERT: D 144 LEU cc_start: 0.8538 (tp) cc_final: 0.8230 (tp) REVERT: D 258 THR cc_start: 0.9041 (m) cc_final: 0.8664 (p) REVERT: D 356 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: D 694 LYS cc_start: 0.8399 (mttt) cc_final: 0.7692 (tttm) REVERT: D 697 LEU cc_start: 0.7559 (mp) cc_final: 0.7130 (tt) REVERT: D 1008 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6770 (ptp-170) REVERT: D 1056 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8118 (tp30) outliers start: 111 outliers final: 85 residues processed: 498 average time/residue: 0.1730 time to fit residues: 139.6430 Evaluate side-chains 489 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 389 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1056 GLU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1056 GLU Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1056 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 91 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 295 optimal weight: 0.0060 chunk 7 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 861 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.172694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119802 restraints weight = 36759.772| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.54 r_work: 0.3308 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28284 Z= 0.109 Angle : 0.481 7.575 38388 Z= 0.246 Chirality : 0.035 0.155 4356 Planarity : 0.003 0.048 4692 Dihedral : 6.025 53.518 3960 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.18 % Allowed : 23.63 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.15), residues: 3220 helix: 2.15 (0.11), residues: 2376 sheet: 1.32 (0.67), residues: 72 loop : -0.73 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.022 0.001 TYR C 981 PHE 0.030 0.001 PHE A 868 TRP 0.026 0.001 TRP C 786 HIS 0.006 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28280) covalent geometry : angle 0.48076 / 0.25 (38380) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.34156 / 0.17 ( 8) hydrogen bonds : bond 0.03505 / 2.35 ( 1712) hydrogen bonds : angle 3.73563 / 2.66 ( 5088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 399 time to evaluate : 1.079 Fit side-chains REVERT: A 117 TYR cc_start: 0.7693 (p90) cc_final: 0.6976 (p90) REVERT: A 144 LEU cc_start: 0.8462 (tp) cc_final: 0.8184 (tp) REVERT: A 258 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 356 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: A 694 LYS cc_start: 0.8377 (mttt) cc_final: 0.7666 (tttm) REVERT: A 697 LEU cc_start: 0.7548 (mp) cc_final: 0.7089 (tt) REVERT: A 796 ASP cc_start: 0.8244 (t0) cc_final: 0.7824 (t70) REVERT: A 1008 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7067 (ptp-170) REVERT: A 1056 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8246 (tp30) REVERT: C 117 TYR cc_start: 0.7445 (p90) cc_final: 0.6752 (p90) REVERT: C 119 ARG cc_start: 0.3955 (OUTLIER) cc_final: 0.2088 (ptp90) REVERT: C 144 LEU cc_start: 0.8500 (tp) cc_final: 0.8224 (tp) REVERT: C 258 THR cc_start: 0.8996 (m) cc_final: 0.8621 (p) REVERT: C 356 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8483 (pt0) REVERT: C 621 TYR cc_start: 0.8632 (m-80) cc_final: 0.8379 (m-80) REVERT: C 694 LYS cc_start: 0.8359 (mttt) cc_final: 0.7646 (tttm) REVERT: C 697 LEU cc_start: 0.7482 (mp) cc_final: 0.7020 (tt) REVERT: C 796 ASP cc_start: 0.8239 (t0) cc_final: 0.7848 (t70) REVERT: C 1008 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7073 (ptp-170) REVERT: B 117 TYR cc_start: 0.7441 (p90) cc_final: 0.6747 (p90) REVERT: B 119 ARG cc_start: 0.4011 (OUTLIER) cc_final: 0.2096 (ptp90) REVERT: B 144 LEU cc_start: 0.8445 (tp) cc_final: 0.8178 (tp) REVERT: B 258 THR cc_start: 0.8993 (m) cc_final: 0.8620 (p) REVERT: B 356 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8477 (pt0) REVERT: B 621 TYR cc_start: 0.8627 (m-80) cc_final: 0.8376 (m-80) REVERT: B 694 LYS cc_start: 0.8361 (mttt) cc_final: 0.7649 (tttm) REVERT: B 697 LEU cc_start: 0.7483 (mp) cc_final: 0.7020 (tt) REVERT: B 796 ASP cc_start: 0.8294 (t0) cc_final: 0.7912 (t70) REVERT: B 1008 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7032 (ptp-170) REVERT: D 117 TYR cc_start: 0.7458 (p90) cc_final: 0.6751 (p90) REVERT: D 119 ARG cc_start: 0.3628 (OUTLIER) cc_final: 0.1853 (ptp90) REVERT: D 144 LEU cc_start: 0.8462 (tp) cc_final: 0.8181 (tp) REVERT: D 258 THR cc_start: 0.8989 (m) cc_final: 0.8615 (p) REVERT: D 356 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (pt0) REVERT: D 621 TYR cc_start: 0.8639 (m-80) cc_final: 0.8385 (m-80) REVERT: D 694 LYS cc_start: 0.8372 (mttt) cc_final: 0.7661 (tttm) REVERT: D 697 LEU cc_start: 0.7498 (mp) cc_final: 0.7038 (tt) REVERT: D 796 ASP cc_start: 0.8276 (t0) cc_final: 0.7886 (t70) REVERT: D 1008 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7069 (ptp-170) REVERT: D 1056 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8226 (tp30) outliers start: 93 outliers final: 74 residues processed: 481 average time/residue: 0.1708 time to fit residues: 132.9508 Evaluate side-chains 483 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 395 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 872 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 890 ARG Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 872 PHE Chi-restraints excluded: chain D residue 890 ARG Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1056 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 40 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117892 restraints weight = 36792.062| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.53 r_work: 0.3281 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28284 Z= 0.154 Angle : 0.512 7.282 38388 Z= 0.263 Chirality : 0.037 0.194 4356 Planarity : 0.004 0.047 4692 Dihedral : 6.148 54.062 3960 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.69 % Allowed : 23.19 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.15), residues: 3220 helix: 2.07 (0.11), residues: 2376 sheet: 1.27 (0.66), residues: 72 loop : -0.78 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 890 TYR 0.023 0.001 TYR D 981 PHE 0.030 0.001 PHE D 868 TRP 0.023 0.001 TRP C 786 HIS 0.007 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (28280) covalent geometry : angle 0.51252 / 0.26 (38380) SS BOND : bond 0.00068 / 0.04 ( 4) SS BOND : angle 0.36305 / 0.18 ( 8) hydrogen bonds : bond 0.03945 / 2.64 ( 1712) hydrogen bonds : angle 3.80930 / 2.71 ( 5088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6582.69 seconds wall clock time: 113 minutes 10.13 seconds (6790.13 seconds total)