Starting phenix.real_space_refine on Fri Jun 27 15:12:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v63_42988/06_2025/8v63_42988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v63_42988/06_2025/8v63_42988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v63_42988/06_2025/8v63_42988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v63_42988/06_2025/8v63_42988.map" model { file = "/net/cci-nas-00/data/ceres_data/8v63_42988/06_2025/8v63_42988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v63_42988/06_2025/8v63_42988.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.024 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 K 9 8.98 5 P 20 5.49 5 S 192 5.16 5 C 20812 2.51 5 N 4716 2.21 5 O 5916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31665 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 7212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7212 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 706 Unusual residues: {' K': 6, 'AJP': 10, 'CLR': 1, 'POV': 7} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 1019 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 701 Unusual residues: {' K': 1, 'AJP': 10, 'CLR': 1, 'POV': 7} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 811 Unresolved non-hydrogen dihedrals: 1019 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 738 Unusual residues: {' K': 1, 'AJP': 10, 'CLR': 1, 'POV': 8} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 829 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 664 Unusual residues: {' K': 1, 'AJP': 10, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 562 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 1006 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 17.28, per 1000 atoms: 0.55 Number of scatterers: 31665 At special positions: 0 Unit cell: (167.4, 167.4, 137.16, 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) K 9 19.00 S 192 16.00 P 20 15.00 O 5916 8.00 N 4716 7.00 C 20812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.18 Conformation dependent library (CDL) restraints added in 3.3 seconds 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6872 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 24 sheets defined 56.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.962A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 147 through 169 removed outlier: 3.937A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.564A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.631A pdb=" N ASN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.878A pdb=" N ALA A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 472 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 523 through 532 removed outlier: 4.147A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.580A pdb=" N VAL A 546 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.534A pdb=" N ASP A 617 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 759 through 767 removed outlier: 4.004A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.719A pdb=" N CYS A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 817 through 828 removed outlier: 3.556A pdb=" N ILE A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.012A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.554A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 917 through 930 removed outlier: 3.946A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 4.029A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 973 removed outlier: 3.925A pdb=" N ASP A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.581A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'B' and resid 21 through 46 removed outlier: 3.902A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 147 through 169 removed outlier: 3.913A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.580A pdb=" N VAL B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 260 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.518A pdb=" N GLU B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 327 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.884A pdb=" N ALA B 467 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 472 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.245A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.539A pdb=" N VAL B 546 " --> pdb=" O SER B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 617 removed outlier: 3.539A pdb=" N ASP B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 767 removed outlier: 3.986A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 766 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.749A pdb=" N CYS B 797 " --> pdb=" O ILE B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 828 removed outlier: 3.530A pdb=" N ILE B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.015A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.563A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 917 through 930 removed outlier: 3.946A pdb=" N ASP B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 3.999A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.915A pdb=" N ASP B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.596A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1021 No H-bonds generated for 'chain 'B' and resid 1019 through 1021' Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.954A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 37 " --> pdb=" O PHE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 147 through 169 removed outlier: 3.970A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.564A pdb=" N VAL C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 260 Processing helix chain 'C' and resid 261 through 265 removed outlier: 3.699A pdb=" N ASN C 265 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.875A pdb=" N ALA C 467 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 472 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 523 through 532 removed outlier: 4.237A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.519A pdb=" N VAL C 546 " --> pdb=" O SER C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 602 through 605 Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 612 through 617 removed outlier: 3.519A pdb=" N ASP C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 759 through 767 removed outlier: 3.992A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.717A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 816 Processing helix chain 'C' and resid 817 through 828 removed outlier: 3.567A pdb=" N ILE C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.008A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.554A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 891 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 917 through 930 removed outlier: 3.952A pdb=" N ASP C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.075A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 973 removed outlier: 3.924A pdb=" N ASP C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.598A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.946A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 37 " --> pdb=" O PHE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 147 through 169 removed outlier: 3.994A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'D' and resid 189 through 200 removed outlier: 3.511A pdb=" N VAL D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 260 Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.532A pdb=" N GLU D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 327 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 463 through 472 removed outlier: 3.874A pdb=" N ALA D 467 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 472 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 532 removed outlier: 4.254A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.577A pdb=" N VAL D 546 " --> pdb=" O SER D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 602 through 605 Processing helix chain 'D' and resid 606 through 611 Processing helix chain 'D' and resid 612 through 617 removed outlier: 3.500A pdb=" N ASP D 617 " --> pdb=" O LYS D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 759 through 767 removed outlier: 4.000A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 766 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 793 through 797 removed outlier: 3.743A pdb=" N CYS D 797 " --> pdb=" O ILE D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 816 Processing helix chain 'D' and resid 817 through 828 removed outlier: 3.552A pdb=" N LEU D 822 " --> pdb=" O LYS D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 876 removed outlier: 4.008A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 4.365A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 917 through 930 removed outlier: 3.944A pdb=" N ASP D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 929 " --> pdb=" O SER D 925 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 4.070A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 973 removed outlier: 3.920A pdb=" N ASP D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 removed outlier: 3.600A pdb=" N LEU D 999 " --> pdb=" O CYS D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 401 removed outlier: 6.743A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.250A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.488A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.518A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 975 through 981 removed outlier: 4.201A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 401 removed outlier: 6.749A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.294A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.483A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.514A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 975 through 981 removed outlier: 4.196A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 401 removed outlier: 6.735A pdb=" N LYS C 343 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL C 376 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 345 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 378 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 347 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.260A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.484A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.511A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 975 through 981 removed outlier: 4.178A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 401 removed outlier: 6.741A pdb=" N LYS D 343 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 376 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.297A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.468A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.520A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 975 through 981 removed outlier: 4.193A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3621 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: 11.23 Time building geometry restraints manager: 8.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5014 1.32 - 1.44: 8597 1.44 - 1.57: 18621 1.57 - 1.69: 40 1.69 - 1.81: 284 Bond restraints: 32556 Sorted by residual: bond pdb=" C21 POV B1106 " pdb=" O21 POV B1106 " ideal model delta sigma weight residual 1.330 1.204 0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C21 POV C1107 " pdb=" O21 POV C1107 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C21 POV D1105 " pdb=" O21 POV D1105 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C21 POV B1106 " pdb=" O22 POV B1106 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C21 POV A1111 " pdb=" O22 POV A1111 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.91e+01 ... (remaining 32551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 44122 2.89 - 5.78: 471 5.78 - 8.66: 11 8.66 - 11.55: 0 11.55 - 14.44: 8 Bond angle restraints: 44612 Sorted by residual: angle pdb=" C22 POV B1106 " pdb=" C21 POV B1106 " pdb=" O22 POV B1106 " ideal model delta sigma weight residual 125.44 111.00 14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV D1105 " pdb=" C21 POV D1105 " pdb=" O22 POV D1105 " ideal model delta sigma weight residual 125.44 111.00 14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV A1111 " pdb=" C21 POV A1111 " pdb=" O21 POV A1111 " ideal model delta sigma weight residual 111.03 125.46 -14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" C22 POV B1106 " pdb=" C21 POV B1106 " pdb=" O21 POV B1106 " ideal model delta sigma weight residual 111.03 125.45 -14.42 3.00e+00 1.11e-01 2.31e+01 angle pdb=" C22 POV D1105 " pdb=" C21 POV D1105 " pdb=" O21 POV D1105 " ideal model delta sigma weight residual 111.03 125.42 -14.39 3.00e+00 1.11e-01 2.30e+01 ... (remaining 44607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.58: 21674 25.58 - 51.15: 994 51.15 - 76.73: 420 76.73 - 102.31: 234 102.31 - 127.88: 294 Dihedral angle restraints: 23616 sinusoidal: 13008 harmonic: 10608 Sorted by residual: dihedral pdb=" O31 AJP C1112 " pdb=" C30 AJP C1112 " pdb=" C32 AJP C1112 " pdb=" O33 AJP C1112 " ideal model delta sinusoidal sigma weight residual 177.28 -54.84 -127.88 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" O31 AJP A1116 " pdb=" C30 AJP A1116 " pdb=" C32 AJP A1116 " pdb=" O33 AJP A1116 " ideal model delta sinusoidal sigma weight residual 177.28 -54.91 -127.81 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" O31 AJP D1110 " pdb=" C30 AJP D1110 " pdb=" C32 AJP D1110 " pdb=" O33 AJP D1110 " ideal model delta sinusoidal sigma weight residual 177.28 -54.94 -127.78 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 23613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4046 0.045 - 0.091: 1009 0.091 - 0.136: 284 0.136 - 0.181: 93 0.181 - 0.227: 64 Chirality restraints: 5496 Sorted by residual: chirality pdb=" C22 AJP B1110 " pdb=" C21 AJP B1110 " pdb=" C23 AJP B1110 " pdb=" O79 AJP B1110 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C22 AJP A1115 " pdb=" C21 AJP A1115 " pdb=" C23 AJP A1115 " pdb=" O79 AJP A1115 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C22 AJP D1109 " pdb=" C21 AJP D1109 " pdb=" C23 AJP D1109 " pdb=" O79 AJP D1109 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5493 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO A 192 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 191 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO C 192 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 191 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO D 192 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " -0.041 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 8427 2.80 - 3.39: 33302 3.39 - 3.97: 58243 3.97 - 4.56: 81748 4.56 - 5.14: 120436 Nonbonded interactions: 302156 Sorted by model distance: nonbonded pdb=" OD1 ASP A 898 " pdb=" OG1 THR A 901 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR B 290 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 284 " pdb=" OH TYR C 290 " model vdw 2.243 3.040 ... (remaining 302151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1057 or (resid 1106 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21 or name O22)) or (resid 1115 through 1118 and (name C01 or name C \ 02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or na \ me C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C \ 23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or na \ me C32 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 o \ r name O31 or name O33 or name O34 or name O77 or name O78 or name O79 or name O \ 82 or name O84)))) selection = (chain 'B' and (resid 19 through 1057 or (resid 1106 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21 or name O22)) or (resid 1115 through 1118 and (name C01 or name C \ 02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or na \ me C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C \ 23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or na \ me C32 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 o \ r name O31 or name O33 or name O34 or name O77 or name O78 or name O79 or name O \ 82 or name O84)))) selection = (chain 'C' and (resid 19 through 1057 or (resid 1106 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21 or name O22)) or (resid 1115 through 1118 and (name C01 or name C \ 02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or na \ me C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C \ 23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or na \ me C32 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 o \ r name O31 or name O33 or name O34 or name O77 or name O78 or name O79 or name O \ 82 or name O84)))) selection = (chain 'D' and (resid 19 through 1057 or (resid 1106 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21 or name O22)) or (resid 1115 through 1118 and (name C01 or name C \ 02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or na \ me C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C \ 23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or na \ me C32 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 o \ r name O31 or name O33 or name O34 or name O77 or name O78 or name O79 or name O \ 82 or name O84)))) } 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=0.00 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 63.840 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 0.126 32556 Z= 0.241 Angle : 0.672 14.438 44612 Z= 0.302 Chirality : 0.051 0.227 5496 Planarity : 0.004 0.073 5088 Dihedral : 24.125 127.881 16744 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3592 helix: 0.32 (0.12), residues: 1708 sheet: 0.33 (0.25), residues: 452 loop : 0.33 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 100 HIS 0.004 0.001 HIS D 379 PHE 0.021 0.001 PHE B 511 TYR 0.033 0.001 TYR C1015 ARG 0.002 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.16821 ( 1326) hydrogen bonds : angle 6.09099 ( 3621) covalent geometry : bond 0.00500 (32556) covalent geometry : angle 0.67213 (44612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 3.019 Fit side-chains REVERT: A 21 MET cc_start: 0.9216 (mtp) cc_final: 0.8885 (mmt) REVERT: A 565 MET cc_start: 0.9402 (ttp) cc_final: 0.9171 (ttp) REVERT: A 712 MET cc_start: 0.9032 (mmp) cc_final: 0.8819 (mmm) REVERT: A 1053 MET cc_start: 0.8566 (mmt) cc_final: 0.7803 (mmm) REVERT: B 21 MET cc_start: 0.9148 (mtp) cc_final: 0.8626 (tpt) REVERT: B 712 MET cc_start: 0.9021 (mmp) cc_final: 0.8804 (mmm) REVERT: B 1053 MET cc_start: 0.8585 (mmt) cc_final: 0.7822 (mmm) REVERT: C 21 MET cc_start: 0.9209 (mtp) cc_final: 0.8881 (mmt) REVERT: C 565 MET cc_start: 0.9398 (ttp) cc_final: 0.9166 (ttp) REVERT: C 712 MET cc_start: 0.9012 (mmp) cc_final: 0.8789 (mmm) REVERT: C 892 ASP cc_start: 0.7474 (t0) cc_final: 0.7267 (t0) REVERT: C 1053 MET cc_start: 0.8554 (mmt) cc_final: 0.8269 (mpp) REVERT: D 21 MET cc_start: 0.9199 (mtp) cc_final: 0.8867 (mmt) REVERT: D 565 MET cc_start: 0.9377 (ttp) cc_final: 0.9135 (ttp) REVERT: D 712 MET cc_start: 0.8985 (mmp) cc_final: 0.8764 (mmm) REVERT: D 1053 MET cc_start: 0.8582 (mmt) cc_final: 0.7823 (mmm) outliers start: 1 outliers final: 4 residues processed: 191 average time/residue: 1.2271 time to fit residues: 283.8154 Evaluate side-chains 155 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 9.9990 chunk 272 optimal weight: 30.0000 chunk 151 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 326 optimal weight: 5.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 534 ASN B 182 ASN B 216 GLN B 893 GLN C 893 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.059725 restraints weight = 68054.302| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.94 r_work: 0.2703 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 32556 Z= 0.273 Angle : 0.735 8.792 44612 Z= 0.330 Chirality : 0.048 0.241 5496 Planarity : 0.005 0.072 5088 Dihedral : 15.970 128.749 10080 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.85 % Allowed : 3.52 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3592 helix: 0.73 (0.12), residues: 1700 sheet: 0.54 (0.26), residues: 416 loop : 0.57 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 100 HIS 0.007 0.001 HIS A 718 PHE 0.024 0.002 PHE C 303 TYR 0.029 0.002 TYR D1015 ARG 0.003 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 1326) hydrogen bonds : angle 4.85103 ( 3621) covalent geometry : bond 0.00648 (32556) covalent geometry : angle 0.73489 (44612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 3.354 Fit side-chains REVERT: A 21 MET cc_start: 0.9225 (mtp) cc_final: 0.8881 (mmt) REVERT: A 565 MET cc_start: 0.9465 (ttp) cc_final: 0.9198 (ttp) REVERT: A 712 MET cc_start: 0.8993 (mmp) cc_final: 0.8681 (mmm) REVERT: A 1053 MET cc_start: 0.8681 (mmt) cc_final: 0.8408 (mpp) REVERT: B 321 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: B 1053 MET cc_start: 0.8688 (mmt) cc_final: 0.8420 (mpp) REVERT: C 21 MET cc_start: 0.9228 (mtp) cc_final: 0.8893 (mmt) REVERT: C 321 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: C 565 MET cc_start: 0.9488 (ttp) cc_final: 0.9219 (ttp) REVERT: C 1053 MET cc_start: 0.8707 (mmt) cc_final: 0.8432 (mpp) REVERT: D 21 MET cc_start: 0.9224 (mtp) cc_final: 0.8868 (mmt) REVERT: D 565 MET cc_start: 0.9464 (ttp) cc_final: 0.9223 (ttp) REVERT: D 1053 MET cc_start: 0.8668 (mmt) cc_final: 0.8429 (mpp) outliers start: 27 outliers final: 15 residues processed: 186 average time/residue: 1.5034 time to fit residues: 341.9918 Evaluate side-chains 169 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 349 optimal weight: 7.9990 chunk 145 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN C 216 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061831 restraints weight = 68334.156| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.99 r_work: 0.2750 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32556 Z= 0.112 Angle : 0.565 8.574 44612 Z= 0.258 Chirality : 0.041 0.310 5496 Planarity : 0.004 0.068 5088 Dihedral : 12.264 121.755 10080 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.44 % Allowed : 5.62 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3592 helix: 1.08 (0.13), residues: 1696 sheet: 0.60 (0.25), residues: 448 loop : 0.78 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 23 HIS 0.003 0.001 HIS A 254 PHE 0.016 0.001 PHE C 511 TYR 0.020 0.001 TYR A 198 ARG 0.002 0.000 ARG D 790 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1326) hydrogen bonds : angle 4.48454 ( 3621) covalent geometry : bond 0.00250 (32556) covalent geometry : angle 0.56512 (44612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 3.696 Fit side-chains REVERT: A 21 MET cc_start: 0.9218 (mtp) cc_final: 0.8887 (mmt) REVERT: A 241 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8127 (pp) REVERT: A 712 MET cc_start: 0.8984 (mmp) cc_final: 0.8637 (mmm) REVERT: A 1053 MET cc_start: 0.8621 (mmt) cc_final: 0.8269 (mpp) REVERT: B 241 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8117 (pp) REVERT: B 1053 MET cc_start: 0.8630 (mmt) cc_final: 0.8286 (mpp) REVERT: C 21 MET cc_start: 0.9217 (mtp) cc_final: 0.8932 (mmt) REVERT: C 94 MET cc_start: 0.7828 (ppp) cc_final: 0.7558 (ppp) REVERT: C 241 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8083 (pp) REVERT: C 1053 MET cc_start: 0.8656 (mmt) cc_final: 0.8375 (tpp) REVERT: D 21 MET cc_start: 0.9236 (mtp) cc_final: 0.8925 (mmt) REVERT: D 94 MET cc_start: 0.7758 (ppp) cc_final: 0.7493 (ppp) REVERT: D 241 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8118 (pp) REVERT: D 1053 MET cc_start: 0.8650 (mmt) cc_final: 0.8325 (mpp) outliers start: 14 outliers final: 4 residues processed: 175 average time/residue: 1.2234 time to fit residues: 263.8052 Evaluate side-chains 164 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 20 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 335 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059801 restraints weight = 68526.843| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.96 r_work: 0.2703 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32556 Z= 0.205 Angle : 0.599 9.748 44612 Z= 0.281 Chirality : 0.043 0.313 5496 Planarity : 0.004 0.069 5088 Dihedral : 10.954 121.075 10080 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.66 % Allowed : 6.69 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3592 helix: 0.92 (0.12), residues: 1736 sheet: 0.78 (0.26), residues: 416 loop : 0.59 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 100 HIS 0.004 0.001 HIS D 718 PHE 0.021 0.001 PHE A 159 TYR 0.018 0.001 TYR B 198 ARG 0.002 0.000 ARG D 514 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 1326) hydrogen bonds : angle 4.59399 ( 3621) covalent geometry : bond 0.00492 (32556) covalent geometry : angle 0.59864 (44612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 3.133 Fit side-chains REVERT: A 21 MET cc_start: 0.9211 (mtp) cc_final: 0.8928 (mmt) REVERT: A 565 MET cc_start: 0.9414 (ttp) cc_final: 0.8991 (ttp) REVERT: A 712 MET cc_start: 0.9028 (mmp) cc_final: 0.8666 (mmm) REVERT: A 1053 MET cc_start: 0.8666 (mmt) cc_final: 0.8359 (tpp) REVERT: B 21 MET cc_start: 0.8627 (mmm) cc_final: 0.7971 (tpt) REVERT: B 94 MET cc_start: 0.7683 (ppp) cc_final: 0.7413 (ppp) REVERT: B 1053 MET cc_start: 0.8706 (mmt) cc_final: 0.8408 (tpp) REVERT: C 21 MET cc_start: 0.9217 (mtp) cc_final: 0.8949 (mmt) REVERT: C 565 MET cc_start: 0.9441 (ttp) cc_final: 0.9229 (ttm) REVERT: C 1053 MET cc_start: 0.8707 (mmt) cc_final: 0.8374 (tpp) REVERT: D 21 MET cc_start: 0.9237 (mtp) cc_final: 0.8938 (mmt) REVERT: D 1053 MET cc_start: 0.8701 (mmt) cc_final: 0.8411 (tpp) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 1.2168 time to fit residues: 259.5159 Evaluate side-chains 167 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 73 optimal weight: 0.9980 chunk 352 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 287 optimal weight: 0.0370 chunk 116 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062144 restraints weight = 68257.601| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.97 r_work: 0.2757 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32556 Z= 0.102 Angle : 0.513 9.411 44612 Z= 0.241 Chirality : 0.039 0.274 5496 Planarity : 0.004 0.067 5088 Dihedral : 9.940 119.880 10080 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.63 % Allowed : 6.97 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3592 helix: 1.29 (0.13), residues: 1696 sheet: 0.72 (0.26), residues: 448 loop : 0.81 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 23 HIS 0.002 0.000 HIS A 254 PHE 0.016 0.001 PHE B 511 TYR 0.020 0.001 TYR A 198 ARG 0.001 0.000 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1326) hydrogen bonds : angle 4.32034 ( 3621) covalent geometry : bond 0.00218 (32556) covalent geometry : angle 0.51293 (44612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 3.611 Fit side-chains REVERT: A 21 MET cc_start: 0.9217 (mtp) cc_final: 0.8926 (mmt) REVERT: A 94 MET cc_start: 0.7572 (ppp) cc_final: 0.7188 (ppp) REVERT: A 241 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 565 MET cc_start: 0.9466 (ttp) cc_final: 0.9127 (ttp) REVERT: A 712 MET cc_start: 0.8991 (mmp) cc_final: 0.8615 (mmm) REVERT: A 1053 MET cc_start: 0.8617 (mmt) cc_final: 0.8294 (tpp) REVERT: B 1053 MET cc_start: 0.8633 (mmt) cc_final: 0.8324 (tpp) REVERT: C 21 MET cc_start: 0.9221 (mtp) cc_final: 0.8950 (mmt) REVERT: C 241 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8090 (pp) REVERT: C 1053 MET cc_start: 0.8633 (mmt) cc_final: 0.8308 (tpp) REVERT: D 21 MET cc_start: 0.9231 (mtp) cc_final: 0.8947 (mmt) REVERT: D 94 MET cc_start: 0.7579 (ppp) cc_final: 0.7286 (ppp) REVERT: D 241 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8082 (pp) REVERT: D 1053 MET cc_start: 0.8643 (mmt) cc_final: 0.8375 (tpp) outliers start: 20 outliers final: 6 residues processed: 177 average time/residue: 1.5820 time to fit residues: 342.3656 Evaluate side-chains 163 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.093518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.058940 restraints weight = 68869.237| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.97 r_work: 0.2724 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 32556 Z= 0.278 Angle : 0.612 8.393 44612 Z= 0.293 Chirality : 0.043 0.262 5496 Planarity : 0.004 0.067 5088 Dihedral : 9.809 119.635 10080 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.97 % Allowed : 7.51 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3592 helix: 0.90 (0.12), residues: 1736 sheet: 0.71 (0.26), residues: 416 loop : 0.57 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 100 HIS 0.004 0.001 HIS B 771 PHE 0.023 0.002 PHE D 159 TYR 0.021 0.002 TYR B 198 ARG 0.003 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 1326) hydrogen bonds : angle 4.68132 ( 3621) covalent geometry : bond 0.00667 (32556) covalent geometry : angle 0.61196 (44612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 3.574 Fit side-chains REVERT: A 21 MET cc_start: 0.9220 (mtp) cc_final: 0.8965 (mmt) REVERT: A 281 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 712 MET cc_start: 0.9058 (mmp) cc_final: 0.8727 (mmm) REVERT: A 1053 MET cc_start: 0.8707 (mmt) cc_final: 0.8450 (tpp) REVERT: B 281 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8406 (mm) REVERT: B 1053 MET cc_start: 0.8733 (mmt) cc_final: 0.8455 (tpp) REVERT: C 21 MET cc_start: 0.9213 (mtp) cc_final: 0.8955 (mmt) REVERT: C 94 MET cc_start: 0.7530 (ppp) cc_final: 0.7155 (ppp) REVERT: C 281 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8389 (mm) REVERT: C 1053 MET cc_start: 0.8746 (mmt) cc_final: 0.8457 (tpp) REVERT: D 21 MET cc_start: 0.9233 (mtp) cc_final: 0.8967 (mmt) REVERT: D 94 MET cc_start: 0.7621 (ppp) cc_final: 0.7316 (ppp) REVERT: D 281 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8380 (mm) REVERT: D 1053 MET cc_start: 0.8752 (mmt) cc_final: 0.8511 (tpp) outliers start: 31 outliers final: 15 residues processed: 184 average time/residue: 1.1450 time to fit residues: 260.5369 Evaluate side-chains 173 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 184 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 296 optimal weight: 0.0060 chunk 187 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 277 optimal weight: 0.0170 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062207 restraints weight = 68460.846| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.99 r_work: 0.2756 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32556 Z= 0.092 Angle : 0.495 10.131 44612 Z= 0.240 Chirality : 0.039 0.214 5496 Planarity : 0.004 0.066 5088 Dihedral : 9.046 116.233 10080 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.47 % Allowed : 8.45 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3592 helix: 1.34 (0.13), residues: 1700 sheet: 0.73 (0.26), residues: 448 loop : 0.77 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 178 HIS 0.002 0.001 HIS A 254 PHE 0.016 0.001 PHE B 511 TYR 0.019 0.001 TYR A 198 ARG 0.002 0.000 ARG D 974 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1326) hydrogen bonds : angle 4.30383 ( 3621) covalent geometry : bond 0.00191 (32556) covalent geometry : angle 0.49531 (44612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 3.357 Fit side-chains REVERT: A 21 MET cc_start: 0.9204 (mtp) cc_final: 0.8922 (mmt) REVERT: A 712 MET cc_start: 0.9003 (mmp) cc_final: 0.8669 (mmm) REVERT: A 957 ASN cc_start: 0.8306 (t0) cc_final: 0.8035 (p0) REVERT: A 1053 MET cc_start: 0.8618 (mmt) cc_final: 0.8299 (tpp) REVERT: B 94 MET cc_start: 0.7657 (ppp) cc_final: 0.7308 (ppp) REVERT: B 281 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 957 ASN cc_start: 0.8291 (t0) cc_final: 0.8035 (p0) REVERT: B 1053 MET cc_start: 0.8639 (mmt) cc_final: 0.8330 (tpp) REVERT: C 21 MET cc_start: 0.9239 (mtp) cc_final: 0.9029 (mmt) REVERT: C 94 MET cc_start: 0.7500 (ppp) cc_final: 0.7112 (ppp) REVERT: C 281 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8134 (mm) REVERT: C 957 ASN cc_start: 0.8308 (t0) cc_final: 0.8037 (p0) REVERT: C 1053 MET cc_start: 0.8636 (mmt) cc_final: 0.8311 (tpp) REVERT: D 21 MET cc_start: 0.9248 (mtp) cc_final: 0.9021 (mmt) REVERT: D 957 ASN cc_start: 0.8296 (t0) cc_final: 0.7998 (p0) REVERT: D 1053 MET cc_start: 0.8647 (mmt) cc_final: 0.8326 (tpp) outliers start: 15 outliers final: 9 residues processed: 169 average time/residue: 1.2627 time to fit residues: 264.1670 Evaluate side-chains 164 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 97 optimal weight: 0.0040 chunk 207 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 216 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061497 restraints weight = 69003.549| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.99 r_work: 0.2740 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32556 Z= 0.121 Angle : 0.502 11.130 44612 Z= 0.243 Chirality : 0.039 0.182 5496 Planarity : 0.004 0.065 5088 Dihedral : 8.750 109.591 10080 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.41 % Allowed : 8.61 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.14), residues: 3592 helix: 1.43 (0.13), residues: 1704 sheet: 0.70 (0.26), residues: 452 loop : 0.81 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 23 HIS 0.003 0.001 HIS B 771 PHE 0.022 0.001 PHE A 159 TYR 0.022 0.001 TYR C 198 ARG 0.002 0.000 ARG D 167 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1326) hydrogen bonds : angle 4.28326 ( 3621) covalent geometry : bond 0.00282 (32556) covalent geometry : angle 0.50158 (44612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 3.077 Fit side-chains REVERT: A 21 MET cc_start: 0.9238 (mtp) cc_final: 0.8975 (mmt) REVERT: A 712 MET cc_start: 0.9007 (mmp) cc_final: 0.8648 (mmm) REVERT: A 957 ASN cc_start: 0.8278 (t0) cc_final: 0.8054 (p0) REVERT: A 1053 MET cc_start: 0.8647 (mmt) cc_final: 0.8323 (tpp) REVERT: B 94 MET cc_start: 0.7636 (ppp) cc_final: 0.7258 (ppp) REVERT: B 957 ASN cc_start: 0.8268 (t0) cc_final: 0.8048 (p0) REVERT: B 1053 MET cc_start: 0.8691 (mmt) cc_final: 0.8330 (tpp) REVERT: C 21 MET cc_start: 0.9225 (mtp) cc_final: 0.9017 (mmt) REVERT: C 94 MET cc_start: 0.7505 (ppp) cc_final: 0.7230 (ppp) REVERT: C 957 ASN cc_start: 0.8281 (t0) cc_final: 0.8054 (p0) REVERT: C 1053 MET cc_start: 0.8690 (mmt) cc_final: 0.8362 (tpp) REVERT: D 21 MET cc_start: 0.9243 (mtp) cc_final: 0.9012 (mmt) REVERT: D 957 ASN cc_start: 0.8285 (t0) cc_final: 0.8048 (p0) REVERT: D 1053 MET cc_start: 0.8687 (mmt) cc_final: 0.8330 (tpp) outliers start: 13 outliers final: 11 residues processed: 167 average time/residue: 1.2933 time to fit residues: 263.2599 Evaluate side-chains 158 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 96 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 214 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.061384 restraints weight = 68597.522| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.98 r_work: 0.2741 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32556 Z= 0.128 Angle : 0.518 11.788 44612 Z= 0.248 Chirality : 0.039 0.181 5496 Planarity : 0.004 0.066 5088 Dihedral : 8.620 108.334 10078 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.38 % Allowed : 8.89 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3592 helix: 1.33 (0.13), residues: 1736 sheet: 0.72 (0.26), residues: 452 loop : 0.73 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 100 HIS 0.003 0.001 HIS A 771 PHE 0.017 0.001 PHE C 511 TYR 0.022 0.001 TYR D 198 ARG 0.002 0.000 ARG D 167 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1326) hydrogen bonds : angle 4.28148 ( 3621) covalent geometry : bond 0.00301 (32556) covalent geometry : angle 0.51822 (44612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 3.240 Fit side-chains REVERT: A 21 MET cc_start: 0.9232 (mtp) cc_final: 0.8976 (mmt) REVERT: A 104 MET cc_start: 0.7494 (mmm) cc_final: 0.7260 (mmt) REVERT: A 712 MET cc_start: 0.9003 (mmp) cc_final: 0.8643 (mmm) REVERT: A 1053 MET cc_start: 0.8657 (mmt) cc_final: 0.8325 (tpp) REVERT: B 94 MET cc_start: 0.7649 (ppp) cc_final: 0.7251 (ppp) REVERT: B 104 MET cc_start: 0.7425 (mmm) cc_final: 0.7211 (mmt) REVERT: B 1053 MET cc_start: 0.8700 (mmt) cc_final: 0.8321 (tpp) REVERT: C 21 MET cc_start: 0.9226 (mtp) cc_final: 0.9020 (mmt) REVERT: C 94 MET cc_start: 0.7516 (ppp) cc_final: 0.7246 (ppp) REVERT: C 957 ASN cc_start: 0.8283 (t0) cc_final: 0.8031 (p0) REVERT: C 1053 MET cc_start: 0.8698 (mmt) cc_final: 0.8401 (tpp) REVERT: D 21 MET cc_start: 0.9258 (mtp) cc_final: 0.9031 (mmt) REVERT: D 104 MET cc_start: 0.7672 (mmm) cc_final: 0.7445 (mpm) REVERT: D 957 ASN cc_start: 0.8270 (t0) cc_final: 0.8019 (p0) REVERT: D 1053 MET cc_start: 0.8688 (mmt) cc_final: 0.8342 (tpp) outliers start: 12 outliers final: 9 residues processed: 162 average time/residue: 1.2520 time to fit residues: 248.8959 Evaluate side-chains 152 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 359 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061912 restraints weight = 68656.084| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.99 r_work: 0.2751 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32556 Z= 0.110 Angle : 0.506 12.356 44612 Z= 0.243 Chirality : 0.039 0.190 5496 Planarity : 0.004 0.066 5088 Dihedral : 8.485 108.433 10074 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.41 % Allowed : 8.95 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3592 helix: 1.48 (0.13), residues: 1704 sheet: 0.77 (0.26), residues: 452 loop : 0.80 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 23 HIS 0.002 0.001 HIS A 254 PHE 0.025 0.001 PHE A 159 TYR 0.023 0.001 TYR D 198 ARG 0.001 0.000 ARG D 342 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 1326) hydrogen bonds : angle 4.21743 ( 3621) covalent geometry : bond 0.00254 (32556) covalent geometry : angle 0.50610 (44612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 3.191 Fit side-chains REVERT: A 21 MET cc_start: 0.9231 (mtp) cc_final: 0.8971 (mmt) REVERT: A 104 MET cc_start: 0.7610 (mmm) cc_final: 0.7280 (mmm) REVERT: A 712 MET cc_start: 0.8999 (mmp) cc_final: 0.8651 (mmm) REVERT: A 1053 MET cc_start: 0.8661 (mmt) cc_final: 0.8366 (tpp) REVERT: B 94 MET cc_start: 0.7645 (ppp) cc_final: 0.7235 (ppp) REVERT: B 104 MET cc_start: 0.7540 (mmm) cc_final: 0.7288 (mmm) REVERT: B 1053 MET cc_start: 0.8703 (mmt) cc_final: 0.8360 (tpp) REVERT: C 21 MET cc_start: 0.9217 (mtp) cc_final: 0.9013 (mmt) REVERT: C 94 MET cc_start: 0.7503 (ppp) cc_final: 0.7220 (ppp) REVERT: C 957 ASN cc_start: 0.8224 (t0) cc_final: 0.7984 (p0) REVERT: C 1053 MET cc_start: 0.8698 (mmt) cc_final: 0.8346 (tpp) REVERT: D 21 MET cc_start: 0.9269 (mtp) cc_final: 0.9042 (mmt) REVERT: D 1053 MET cc_start: 0.8715 (mmt) cc_final: 0.8405 (tpp) outliers start: 13 outliers final: 9 residues processed: 161 average time/residue: 1.2972 time to fit residues: 255.4439 Evaluate side-chains 151 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 230 optimal weight: 0.9980 chunk 210 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.062583 restraints weight = 68375.228| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.98 r_work: 0.2766 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32556 Z= 0.098 Angle : 0.486 12.113 44612 Z= 0.236 Chirality : 0.038 0.177 5496 Planarity : 0.003 0.066 5088 Dihedral : 8.295 109.151 10074 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.35 % Allowed : 9.05 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3592 helix: 1.53 (0.13), residues: 1712 sheet: 0.88 (0.26), residues: 448 loop : 0.83 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 23 HIS 0.003 0.000 HIS B 254 PHE 0.016 0.001 PHE B 511 TYR 0.024 0.001 TYR D 198 ARG 0.002 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1326) hydrogen bonds : angle 4.12942 ( 3621) covalent geometry : bond 0.00220 (32556) covalent geometry : angle 0.48610 (44612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20465.42 seconds wall clock time: 356 minutes 28.25 seconds (21388.25 seconds total)