Starting phenix.real_space_refine on Tue Aug 26 00:25:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v63_42988/08_2025/8v63_42988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v63_42988/08_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_42988/08_2025/8v63_42988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v63_42988/08_2025/8v63_42988.map" model { file = "/net/cci-nas-00/data/ceres_data/8v63_42988/08_2025/8v63_42988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v63_42988/08_2025/8v63_42988.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 2} 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-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 2} 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-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 2} 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-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 2} 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: 6.72, per 1000 atoms: 0.21 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.11 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: 5.47 Time building geometry restraints manager: 3.38 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: 1.440 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.440 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- 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 : 4.12 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (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 ARG 0.002 0.000 ARG B 514 TYR 0.033 0.001 TYR C1015 PHE 0.021 0.001 PHE B 511 TRP 0.030 0.001 TRP B 100 HIS 0.004 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00500 (32556) covalent geometry : angle 0.67213 (44612) hydrogen bonds : bond 0.16821 ( 1326) hydrogen bonds : angle 6.09099 ( 3621) *********************** 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 : 1.011 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: 0.5429 time to fit residues: 124.6293 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 : 0.997 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 216 GLN C 893 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.062384 restraints weight = 68355.929| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.97 r_work: 0.2781 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 32556 Z= 0.160 Angle : 0.678 8.827 44612 Z= 0.296 Chirality : 0.046 0.299 5496 Planarity : 0.004 0.071 5088 Dihedral : 15.163 128.471 10080 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.79 % Allowed : 3.52 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.14), residues: 3592 helix: 0.93 (0.13), residues: 1696 sheet: 0.54 (0.25), residues: 448 loop : 0.75 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 514 TYR 0.025 0.001 TYR B1015 PHE 0.022 0.001 PHE B 159 TRP 0.018 0.001 TRP B 100 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00363 (32556) covalent geometry : angle 0.67781 (44612) hydrogen bonds : bond 0.04238 ( 1326) hydrogen bonds : angle 4.58489 ( 3621) *********************** 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 188 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.109 Fit side-chains REVERT: A 21 MET cc_start: 0.9227 (mtp) cc_final: 0.8899 (mmt) REVERT: A 565 MET cc_start: 0.9468 (ttp) cc_final: 0.9207 (ttp) REVERT: A 712 MET cc_start: 0.8924 (mmp) cc_final: 0.8616 (mmm) REVERT: A 1053 MET cc_start: 0.8632 (mmt) cc_final: 0.8303 (mpp) REVERT: B 1053 MET cc_start: 0.8655 (mmt) cc_final: 0.8336 (mpp) REVERT: C 21 MET cc_start: 0.9238 (mtp) cc_final: 0.8894 (mmt) REVERT: C 241 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8126 (pp) REVERT: C 565 MET cc_start: 0.9489 (ttp) cc_final: 0.9254 (ttp) REVERT: C 1053 MET cc_start: 0.8651 (mmt) cc_final: 0.8299 (mpp) REVERT: D 21 MET cc_start: 0.9225 (mtp) cc_final: 0.8885 (mmt) REVERT: D 241 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8112 (pp) REVERT: D 565 MET cc_start: 0.9464 (ttp) cc_final: 0.9203 (ttp) REVERT: D 1053 MET cc_start: 0.8610 (mmt) cc_final: 0.8307 (mpp) outliers start: 25 outliers final: 10 residues processed: 175 average time/residue: 0.5113 time to fit residues: 109.7439 Evaluate side-chains 160 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 68 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 260 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.094751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.060261 restraints weight = 68512.770| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.97 r_work: 0.2714 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32556 Z= 0.216 Angle : 0.624 8.615 44612 Z= 0.289 Chirality : 0.044 0.328 5496 Planarity : 0.004 0.069 5088 Dihedral : 12.435 121.599 10080 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.66 % Allowed : 5.37 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.14), residues: 3592 helix: 0.81 (0.12), residues: 1732 sheet: 0.46 (0.25), residues: 452 loop : 0.73 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.018 0.001 TYR A 198 PHE 0.018 0.001 PHE C 303 TRP 0.026 0.002 TRP B 100 HIS 0.004 0.001 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00518 (32556) covalent geometry : angle 0.62417 (44612) hydrogen bonds : bond 0.04884 ( 1326) hydrogen bonds : angle 4.65743 ( 3621) *********************** 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 184 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.931 Fit side-chains REVERT: A 21 MET cc_start: 0.9217 (mtp) cc_final: 0.8883 (mmt) REVERT: A 565 MET cc_start: 0.9465 (ttp) cc_final: 0.9238 (ttp) REVERT: A 712 MET cc_start: 0.8998 (mmp) cc_final: 0.8644 (mmm) REVERT: A 1053 MET cc_start: 0.8676 (mmt) cc_final: 0.8353 (mpp) REVERT: B 1053 MET cc_start: 0.8693 (mmt) cc_final: 0.8379 (mpp) REVERT: C 21 MET cc_start: 0.9227 (mtp) cc_final: 0.8909 (mmt) REVERT: C 94 MET cc_start: 0.7596 (ppp) cc_final: 0.7232 (ppp) REVERT: C 565 MET cc_start: 0.9474 (ttp) cc_final: 0.9241 (ttp) REVERT: C 1053 MET cc_start: 0.8696 (mmt) cc_final: 0.8351 (mpp) REVERT: D 21 MET cc_start: 0.9251 (mtp) cc_final: 0.8919 (mmt) REVERT: D 94 MET cc_start: 0.7641 (ppp) cc_final: 0.7413 (ppp) REVERT: D 1053 MET cc_start: 0.8702 (mmt) cc_final: 0.8400 (mpp) outliers start: 21 outliers final: 9 residues processed: 173 average time/residue: 0.5296 time to fit residues: 111.8979 Evaluate side-chains 162 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 941 VAL 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 241 ILE Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 342 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 272 optimal weight: 30.0000 chunk 335 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.093940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059408 restraints weight = 67970.920| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.96 r_work: 0.2694 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 32556 Z= 0.240 Angle : 0.621 9.907 44612 Z= 0.292 Chirality : 0.044 0.314 5496 Planarity : 0.004 0.069 5088 Dihedral : 10.877 122.539 10072 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.75 % Allowed : 6.34 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3592 helix: 0.87 (0.12), residues: 1708 sheet: 0.63 (0.26), residues: 416 loop : 0.55 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 514 TYR 0.022 0.002 TYR D 198 PHE 0.025 0.002 PHE A 159 TRP 0.028 0.002 TRP C 100 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00574 (32556) covalent geometry : angle 0.62051 (44612) hydrogen bonds : bond 0.04947 ( 1326) hydrogen bonds : angle 4.71152 ( 3621) *********************** 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 186 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.119 Fit side-chains REVERT: A 21 MET cc_start: 0.9225 (mtp) cc_final: 0.8933 (mmt) REVERT: A 104 MET cc_start: 0.7963 (mmm) cc_final: 0.7616 (mmm) REVERT: A 712 MET cc_start: 0.9039 (mmp) cc_final: 0.8663 (mmm) REVERT: A 1053 MET cc_start: 0.8669 (mmt) cc_final: 0.8342 (tpp) REVERT: B 94 MET cc_start: 0.7530 (ppp) cc_final: 0.7268 (ppp) REVERT: B 321 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: B 1053 MET cc_start: 0.8688 (mmt) cc_final: 0.8377 (tpp) REVERT: C 21 MET cc_start: 0.9223 (mtp) cc_final: 0.8942 (mmt) REVERT: C 321 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: C 1053 MET cc_start: 0.8690 (mmt) cc_final: 0.8354 (tpp) REVERT: D 21 MET cc_start: 0.9240 (mtp) cc_final: 0.8951 (mmt) REVERT: D 104 MET cc_start: 0.7697 (mmt) cc_final: 0.7442 (mmm) REVERT: D 565 MET cc_start: 0.9469 (ttp) cc_final: 0.9262 (ttm) REVERT: D 1053 MET cc_start: 0.8701 (mmt) cc_final: 0.8418 (tpp) outliers start: 24 outliers final: 12 residues processed: 176 average time/residue: 0.6013 time to fit residues: 129.1243 Evaluate side-chains 166 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 941 VAL 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 37 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 37 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 115 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 256 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.096129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061891 restraints weight = 68330.309| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.97 r_work: 0.2750 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32556 Z= 0.104 Angle : 0.518 8.390 44612 Z= 0.244 Chirality : 0.040 0.292 5496 Planarity : 0.004 0.067 5088 Dihedral : 9.871 120.970 10072 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.85 % Allowed : 7.07 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.14), residues: 3592 helix: 1.11 (0.13), residues: 1740 sheet: 0.59 (0.25), residues: 452 loop : 0.75 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 113 TYR 0.020 0.001 TYR A 198 PHE 0.016 0.001 PHE B 511 TRP 0.019 0.001 TRP B 100 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00230 (32556) covalent geometry : angle 0.51797 (44612) hydrogen bonds : bond 0.03737 ( 1326) hydrogen bonds : angle 4.37132 ( 3621) *********************** 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 187 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.9217 (mtp) cc_final: 0.8936 (mmt) REVERT: A 94 MET cc_start: 0.7558 (ppp) cc_final: 0.7166 (ppp) REVERT: A 281 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 565 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9023 (ttp) REVERT: A 712 MET cc_start: 0.9001 (mmp) cc_final: 0.8675 (mmm) REVERT: A 1053 MET cc_start: 0.8666 (mmt) cc_final: 0.8379 (tpp) REVERT: B 94 MET cc_start: 0.7712 (ppp) cc_final: 0.7427 (ppp) REVERT: B 321 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 1053 MET cc_start: 0.8635 (mmt) cc_final: 0.8327 (tpp) REVERT: C 21 MET cc_start: 0.9216 (mtp) cc_final: 0.8956 (mmt) REVERT: C 94 MET cc_start: 0.7553 (ppp) cc_final: 0.7250 (ppp) REVERT: C 281 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8139 (mm) REVERT: C 321 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: C 565 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9031 (ttp) REVERT: C 1053 MET cc_start: 0.8654 (mmt) cc_final: 0.8334 (tpp) REVERT: D 21 MET cc_start: 0.9225 (mtp) cc_final: 0.8942 (mmt) REVERT: D 94 MET cc_start: 0.7566 (ppp) cc_final: 0.7238 (ppp) REVERT: D 281 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8140 (mm) REVERT: D 1053 MET cc_start: 0.8686 (mmt) cc_final: 0.8415 (tpp) outliers start: 27 outliers final: 3 residues processed: 178 average time/residue: 0.5474 time to fit residues: 119.0129 Evaluate side-chains 162 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 350 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 355 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 338 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 302 optimal weight: 0.0060 chunk 259 optimal weight: 0.7980 overall best weight: 1.7000 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.095992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061805 restraints weight = 68540.811| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.97 r_work: 0.2746 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32556 Z= 0.117 Angle : 0.502 8.356 44612 Z= 0.240 Chirality : 0.039 0.252 5496 Planarity : 0.004 0.066 5088 Dihedral : 9.210 117.478 10072 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.57 % Allowed : 7.73 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.14), residues: 3592 helix: 1.26 (0.13), residues: 1744 sheet: 0.64 (0.25), residues: 452 loop : 0.78 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 514 TYR 0.021 0.001 TYR D 198 PHE 0.025 0.001 PHE B 159 TRP 0.016 0.001 TRP D 100 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00271 (32556) covalent geometry : angle 0.50170 (44612) hydrogen bonds : bond 0.03797 ( 1326) hydrogen bonds : angle 4.30145 ( 3621) *********************** 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 177 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.9206 (mtp) cc_final: 0.8931 (mmt) REVERT: A 94 MET cc_start: 0.7457 (ppp) cc_final: 0.7184 (ppp) REVERT: A 104 MET cc_start: 0.7853 (mmm) cc_final: 0.7444 (mmm) REVERT: A 565 MET cc_start: 0.9457 (ttp) cc_final: 0.9141 (ttp) REVERT: A 712 MET cc_start: 0.8998 (mmp) cc_final: 0.8654 (mmm) REVERT: A 957 ASN cc_start: 0.8317 (t0) cc_final: 0.8022 (p0) REVERT: A 1053 MET cc_start: 0.8640 (mmt) cc_final: 0.8285 (tpp) REVERT: B 21 MET cc_start: 0.8548 (mmm) cc_final: 0.7794 (tpt) REVERT: B 321 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: B 1053 MET cc_start: 0.8677 (mmt) cc_final: 0.8340 (tpp) REVERT: C 21 MET cc_start: 0.9224 (mtp) cc_final: 0.8998 (mmt) REVERT: C 94 MET cc_start: 0.7735 (ppp) cc_final: 0.7414 (ppp) REVERT: C 321 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: C 565 MET cc_start: 0.9463 (ttp) cc_final: 0.9154 (ttp) REVERT: C 957 ASN cc_start: 0.8320 (t0) cc_final: 0.8041 (p0) REVERT: C 1053 MET cc_start: 0.8677 (mmt) cc_final: 0.8316 (tpp) REVERT: D 21 MET cc_start: 0.9235 (mtp) cc_final: 0.8969 (mmt) REVERT: D 94 MET cc_start: 0.7801 (ppp) cc_final: 0.7459 (ppp) REVERT: D 957 ASN cc_start: 0.8309 (t0) cc_final: 0.8020 (p0) REVERT: D 1053 MET cc_start: 0.8684 (mmt) cc_final: 0.8344 (tpp) outliers start: 18 outliers final: 4 residues processed: 173 average time/residue: 0.5446 time to fit residues: 115.8402 Evaluate side-chains 157 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 924 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 161 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 329 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.096082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061825 restraints weight = 68663.247| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.99 r_work: 0.2747 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32556 Z= 0.115 Angle : 0.496 10.898 44612 Z= 0.238 Chirality : 0.039 0.210 5496 Planarity : 0.004 0.066 5088 Dihedral : 8.756 111.942 10072 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.66 % Allowed : 7.98 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.14), residues: 3592 helix: 1.30 (0.13), residues: 1744 sheet: 0.70 (0.26), residues: 452 loop : 0.80 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.021 0.001 TYR B 198 PHE 0.017 0.001 PHE C 511 TRP 0.011 0.001 TRP B 23 HIS 0.002 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00267 (32556) covalent geometry : angle 0.49616 (44612) hydrogen bonds : bond 0.03691 ( 1326) hydrogen bonds : angle 4.24364 ( 3621) *********************** 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 175 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.9198 (mtp) cc_final: 0.8942 (mmt) REVERT: A 565 MET cc_start: 0.9468 (ttp) cc_final: 0.9196 (ttp) REVERT: A 712 MET cc_start: 0.9010 (mmp) cc_final: 0.8665 (mmm) REVERT: A 957 ASN cc_start: 0.8281 (t0) cc_final: 0.8058 (p0) REVERT: A 1053 MET cc_start: 0.8672 (mmt) cc_final: 0.8304 (tpp) REVERT: B 321 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: B 957 ASN cc_start: 0.8273 (t0) cc_final: 0.8052 (p0) REVERT: B 1053 MET cc_start: 0.8680 (mmt) cc_final: 0.8327 (tpp) REVERT: C 21 MET cc_start: 0.9246 (mtp) cc_final: 0.9027 (mmt) REVERT: C 94 MET cc_start: 0.7717 (ppp) cc_final: 0.7494 (ppp) REVERT: C 321 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: C 565 MET cc_start: 0.9477 (ttp) cc_final: 0.9217 (ttp) REVERT: C 957 ASN cc_start: 0.8279 (t0) cc_final: 0.8063 (p0) REVERT: C 1053 MET cc_start: 0.8686 (mmt) cc_final: 0.8357 (tpp) REVERT: D 21 MET cc_start: 0.9261 (mtp) cc_final: 0.9020 (mmt) REVERT: D 94 MET cc_start: 0.7723 (ppp) cc_final: 0.7490 (ppp) REVERT: D 957 ASN cc_start: 0.8283 (t0) cc_final: 0.8064 (p0) REVERT: D 1053 MET cc_start: 0.8690 (mmt) cc_final: 0.8342 (tpp) outliers start: 21 outliers final: 7 residues processed: 172 average time/residue: 0.5440 time to fit residues: 113.4534 Evaluate side-chains 159 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 924 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL 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 182 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 342 optimal weight: 0.1980 chunk 5 optimal weight: 30.0000 chunk 256 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 355 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.097010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.062953 restraints weight = 68677.708| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.99 r_work: 0.2773 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32556 Z= 0.094 Angle : 0.484 11.788 44612 Z= 0.231 Chirality : 0.038 0.203 5496 Planarity : 0.003 0.065 5088 Dihedral : 8.417 108.549 10072 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.44 % Allowed : 8.45 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.14), residues: 3592 helix: 1.45 (0.13), residues: 1736 sheet: 0.85 (0.26), residues: 448 loop : 0.78 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 167 TYR 0.026 0.001 TYR C 198 PHE 0.023 0.001 PHE C 159 TRP 0.011 0.001 TRP B 23 HIS 0.003 0.000 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00212 (32556) covalent geometry : angle 0.48412 (44612) hydrogen bonds : bond 0.03372 ( 1326) hydrogen bonds : angle 4.12811 ( 3621) *********************** 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 174 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.865 Fit side-chains REVERT: A 21 MET cc_start: 0.9203 (mtp) cc_final: 0.8947 (mmt) REVERT: A 565 MET cc_start: 0.9489 (ttp) cc_final: 0.9212 (ttp) REVERT: A 712 MET cc_start: 0.8987 (mmp) cc_final: 0.8636 (mmm) REVERT: A 957 ASN cc_start: 0.8183 (t0) cc_final: 0.7981 (p0) REVERT: A 1053 MET cc_start: 0.8663 (mmt) cc_final: 0.8337 (tpp) REVERT: B 321 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 957 ASN cc_start: 0.8229 (t0) cc_final: 0.8014 (p0) REVERT: B 1053 MET cc_start: 0.8672 (mmt) cc_final: 0.8355 (tpp) REVERT: C 21 MET cc_start: 0.9228 (mtp) cc_final: 0.9023 (mmt) REVERT: C 94 MET cc_start: 0.7729 (ppp) cc_final: 0.7478 (ppp) REVERT: C 104 MET cc_start: 0.7278 (mmm) cc_final: 0.7025 (mmm) REVERT: C 321 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: C 565 MET cc_start: 0.9497 (ttp) cc_final: 0.9193 (ttp) REVERT: C 957 ASN cc_start: 0.8182 (t0) cc_final: 0.7921 (p0) REVERT: C 1053 MET cc_start: 0.8686 (mmt) cc_final: 0.8362 (tpp) REVERT: D 21 MET cc_start: 0.9283 (mtp) cc_final: 0.9039 (mmt) REVERT: D 94 MET cc_start: 0.7700 (ppp) cc_final: 0.7437 (ppp) REVERT: D 104 MET cc_start: 0.7488 (mmm) cc_final: 0.7274 (mmt) REVERT: D 1053 MET cc_start: 0.8694 (mmt) cc_final: 0.8396 (tpp) outliers start: 14 outliers final: 6 residues processed: 171 average time/residue: 0.5140 time to fit residues: 107.1469 Evaluate side-chains 154 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 941 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 115 optimal weight: 0.0870 chunk 268 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 267 optimal weight: 0.0570 chunk 60 optimal weight: 6.9990 chunk 193 optimal weight: 0.0670 chunk 178 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 overall best weight: 1.0418 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.097037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062977 restraints weight = 68596.224| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.99 r_work: 0.2777 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1932 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= 0.093 Angle : 0.484 11.749 44612 Z= 0.232 Chirality : 0.038 0.189 5496 Planarity : 0.003 0.064 5088 Dihedral : 8.317 110.289 10072 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.35 % Allowed : 8.70 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.14), residues: 3592 helix: 1.46 (0.13), residues: 1744 sheet: 0.89 (0.26), residues: 448 loop : 0.82 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 368 TYR 0.024 0.001 TYR B 198 PHE 0.016 0.001 PHE B 511 TRP 0.012 0.001 TRP B 23 HIS 0.003 0.000 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00207 (32556) covalent geometry : angle 0.48376 (44612) hydrogen bonds : bond 0.03314 ( 1326) hydrogen bonds : angle 4.08079 ( 3621) *********************** 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: 11 poor density : 152 time to evaluate : 1.281 Fit side-chains REVERT: A 21 MET cc_start: 0.9235 (mtp) cc_final: 0.8999 (mmt) REVERT: A 565 MET cc_start: 0.9497 (ttp) cc_final: 0.9208 (ttp) REVERT: A 1053 MET cc_start: 0.8668 (mmt) cc_final: 0.8339 (tpp) REVERT: B 321 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: B 1053 MET cc_start: 0.8674 (mmt) cc_final: 0.8341 (tpp) REVERT: C 21 MET cc_start: 0.9238 (mtp) cc_final: 0.9019 (mmt) REVERT: C 321 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: C 565 MET cc_start: 0.9504 (ttp) cc_final: 0.9220 (ttp) REVERT: C 1053 MET cc_start: 0.8693 (mmt) cc_final: 0.8371 (tpp) REVERT: D 21 MET cc_start: 0.9277 (mtp) cc_final: 0.9039 (mmt) REVERT: D 1053 MET cc_start: 0.8691 (mmt) cc_final: 0.8338 (mpp) outliers start: 11 outliers final: 7 residues processed: 161 average time/residue: 0.5895 time to fit residues: 116.1036 Evaluate side-chains 156 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 321 GLU 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 239 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 355 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.095457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.061275 restraints weight = 68901.071| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.99 r_work: 0.2735 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32556 Z= 0.147 Angle : 0.522 12.267 44612 Z= 0.250 Chirality : 0.039 0.175 5496 Planarity : 0.004 0.065 5088 Dihedral : 8.353 109.847 10072 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.35 % Allowed : 8.76 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.14), residues: 3592 helix: 1.35 (0.13), residues: 1744 sheet: 0.77 (0.26), residues: 452 loop : 0.79 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 514 TYR 0.025 0.001 TYR C 198 PHE 0.022 0.001 PHE A 159 TRP 0.012 0.001 TRP B 23 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00350 (32556) covalent geometry : angle 0.52207 (44612) hydrogen bonds : bond 0.03935 ( 1326) hydrogen bonds : angle 4.23093 ( 3621) ********************** 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 158 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.9257 (mtp) cc_final: 0.9017 (mmt) REVERT: A 104 MET cc_start: 0.7349 (mmm) cc_final: 0.7019 (mmm) REVERT: A 565 MET cc_start: 0.9495 (ttp) cc_final: 0.9179 (ttp) REVERT: A 1053 MET cc_start: 0.8713 (mmt) cc_final: 0.8385 (tpp) REVERT: B 104 MET cc_start: 0.7204 (mmm) cc_final: 0.6983 (mmm) REVERT: B 321 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: B 1053 MET cc_start: 0.8720 (mmt) cc_final: 0.8399 (tpp) REVERT: C 21 MET cc_start: 0.9250 (mtp) cc_final: 0.9031 (mmt) REVERT: C 104 MET cc_start: 0.7248 (mmm) cc_final: 0.7004 (mmm) REVERT: C 321 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: C 565 MET cc_start: 0.9500 (ttp) cc_final: 0.9191 (ttp) REVERT: C 1053 MET cc_start: 0.8741 (mmt) cc_final: 0.8404 (tpp) REVERT: D 21 MET cc_start: 0.9254 (mtp) cc_final: 0.9009 (mmt) REVERT: D 1053 MET cc_start: 0.8714 (mmt) cc_final: 0.8399 (tpp) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 0.5913 time to fit residues: 112.7466 Evaluate side-chains 153 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 321 GLU 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 0 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 297 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 274 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.097087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063173 restraints weight = 68935.855| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.00 r_work: 0.2779 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32556 Z= 0.090 Angle : 0.483 12.068 44612 Z= 0.233 Chirality : 0.038 0.188 5496 Planarity : 0.003 0.064 5088 Dihedral : 8.149 110.951 10072 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.25 % Allowed : 8.86 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.14), residues: 3592 helix: 1.58 (0.13), residues: 1712 sheet: 0.96 (0.26), residues: 448 loop : 0.86 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 790 TYR 0.025 0.001 TYR C 198 PHE 0.017 0.001 PHE B 511 TRP 0.013 0.001 TRP B 23 HIS 0.002 0.000 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00195 (32556) covalent geometry : angle 0.48317 (44612) hydrogen bonds : bond 0.03251 ( 1326) hydrogen bonds : angle 4.05789 ( 3621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8235.72 seconds wall clock time: 141 minutes 44.77 seconds (8504.77 seconds total)